Annotation of imach/src/imach.c, revision 1.328

1.328   ! brouard     1: /* $Id: imach.c,v 1.327 2022/07/27 14:47:35 brouard Exp $
1.126     brouard     2:   $State: Exp $
1.163     brouard     3:   $Log: imach.c,v $
1.328   ! brouard     4:   Revision 1.327  2022/07/27 14:47:35  brouard
        !             5:   Summary: Still a problem for one-step probabilities in case of quantitative variables
        !             6: 
1.327     brouard     7:   Revision 1.326  2022/07/26 17:33:55  brouard
                      8:   Summary: some test with nres=1
                      9: 
1.326     brouard    10:   Revision 1.325  2022/07/25 14:27:23  brouard
                     11:   Summary: r30
                     12: 
                     13:   * imach.c (Module): Error cptcovn instead of nsd in bmij (was
                     14:   coredumped, revealed by Feiuno, thank you.
                     15: 
1.325     brouard    16:   Revision 1.324  2022/07/23 17:44:26  brouard
                     17:   *** empty log message ***
                     18: 
1.324     brouard    19:   Revision 1.323  2022/07/22 12:30:08  brouard
                     20:   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
                     21: 
1.323     brouard    22:   Revision 1.322  2022/07/22 12:27:48  brouard
                     23:   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
                     24: 
1.322     brouard    25:   Revision 1.321  2022/07/22 12:04:24  brouard
                     26:   Summary: r28
                     27: 
                     28:   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
                     29: 
1.321     brouard    30:   Revision 1.320  2022/06/02 05:10:11  brouard
                     31:   *** empty log message ***
                     32: 
1.320     brouard    33:   Revision 1.319  2022/06/02 04:45:11  brouard
                     34:   * imach.c (Module): Adding the Wald tests from the log to the main
                     35:   htm for better display of the maximum likelihood estimators.
                     36: 
1.319     brouard    37:   Revision 1.318  2022/05/24 08:10:59  brouard
                     38:   * imach.c (Module): Some attempts to find a bug of wrong estimates
                     39:   of confidencce intervals with product in the equation modelC
                     40: 
1.318     brouard    41:   Revision 1.317  2022/05/15 15:06:23  brouard
                     42:   * imach.c (Module):  Some minor improvements
                     43: 
1.317     brouard    44:   Revision 1.316  2022/05/11 15:11:31  brouard
                     45:   Summary: r27
                     46: 
1.316     brouard    47:   Revision 1.315  2022/05/11 15:06:32  brouard
                     48:   *** empty log message ***
                     49: 
1.315     brouard    50:   Revision 1.314  2022/04/13 17:43:09  brouard
                     51:   * imach.c (Module): Adding link to text data files
                     52: 
1.314     brouard    53:   Revision 1.313  2022/04/11 15:57:42  brouard
                     54:   * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
                     55: 
1.313     brouard    56:   Revision 1.312  2022/04/05 21:24:39  brouard
                     57:   *** empty log message ***
                     58: 
1.312     brouard    59:   Revision 1.311  2022/04/05 21:03:51  brouard
                     60:   Summary: Fixed quantitative covariates
                     61: 
                     62:          Fixed covariates (dummy or quantitative)
                     63:        with missing values have never been allowed but are ERRORS and
                     64:        program quits. Standard deviations of fixed covariates were
                     65:        wrongly computed. Mean and standard deviations of time varying
                     66:        covariates are still not computed.
                     67: 
1.311     brouard    68:   Revision 1.310  2022/03/17 08:45:53  brouard
                     69:   Summary: 99r25
                     70: 
                     71:   Improving detection of errors: result lines should be compatible with
                     72:   the model.
                     73: 
1.310     brouard    74:   Revision 1.309  2021/05/20 12:39:14  brouard
                     75:   Summary: Version 0.99r24
                     76: 
1.309     brouard    77:   Revision 1.308  2021/03/31 13:11:57  brouard
                     78:   Summary: Version 0.99r23
                     79: 
                     80: 
                     81:   * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
                     82: 
1.308     brouard    83:   Revision 1.307  2021/03/08 18:11:32  brouard
                     84:   Summary: 0.99r22 fixed bug on result:
                     85: 
1.307     brouard    86:   Revision 1.306  2021/02/20 15:44:02  brouard
                     87:   Summary: Version 0.99r21
                     88: 
                     89:   * imach.c (Module): Fix bug on quitting after result lines!
                     90:   (Module): Version 0.99r21
                     91: 
1.306     brouard    92:   Revision 1.305  2021/02/20 15:28:30  brouard
                     93:   * imach.c (Module): Fix bug on quitting after result lines!
                     94: 
1.305     brouard    95:   Revision 1.304  2021/02/12 11:34:20  brouard
                     96:   * imach.c (Module): The use of a Windows BOM (huge) file is now an error
                     97: 
1.304     brouard    98:   Revision 1.303  2021/02/11 19:50:15  brouard
                     99:   *  (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
                    100: 
1.303     brouard   101:   Revision 1.302  2020/02/22 21:00:05  brouard
                    102:   *  (Module): imach.c Update mle=-3 (for computing Life expectancy
                    103:   and life table from the data without any state)
                    104: 
1.302     brouard   105:   Revision 1.301  2019/06/04 13:51:20  brouard
                    106:   Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
                    107: 
1.301     brouard   108:   Revision 1.300  2019/05/22 19:09:45  brouard
                    109:   Summary: version 0.99r19 of May 2019
                    110: 
1.300     brouard   111:   Revision 1.299  2019/05/22 18:37:08  brouard
                    112:   Summary: Cleaned 0.99r19
                    113: 
1.299     brouard   114:   Revision 1.298  2019/05/22 18:19:56  brouard
                    115:   *** empty log message ***
                    116: 
1.298     brouard   117:   Revision 1.297  2019/05/22 17:56:10  brouard
                    118:   Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
                    119: 
1.297     brouard   120:   Revision 1.296  2019/05/20 13:03:18  brouard
                    121:   Summary: Projection syntax simplified
                    122: 
                    123: 
                    124:   We can now start projections, forward or backward, from the mean date
                    125:   of inteviews up to or down to a number of years of projection:
                    126:   prevforecast=1 yearsfproj=15.3 mobil_average=0
                    127:   or
                    128:   prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
                    129:   or
                    130:   prevbackcast=1 yearsbproj=12.3 mobil_average=1
                    131:   or
                    132:   prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
                    133: 
1.296     brouard   134:   Revision 1.295  2019/05/18 09:52:50  brouard
                    135:   Summary: doxygen tex bug
                    136: 
1.295     brouard   137:   Revision 1.294  2019/05/16 14:54:33  brouard
                    138:   Summary: There was some wrong lines added
                    139: 
1.294     brouard   140:   Revision 1.293  2019/05/09 15:17:34  brouard
                    141:   *** empty log message ***
                    142: 
1.293     brouard   143:   Revision 1.292  2019/05/09 14:17:20  brouard
                    144:   Summary: Some updates
                    145: 
1.292     brouard   146:   Revision 1.291  2019/05/09 13:44:18  brouard
                    147:   Summary: Before ncovmax
                    148: 
1.291     brouard   149:   Revision 1.290  2019/05/09 13:39:37  brouard
                    150:   Summary: 0.99r18 unlimited number of individuals
                    151: 
                    152:   The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
                    153: 
1.290     brouard   154:   Revision 1.289  2018/12/13 09:16:26  brouard
                    155:   Summary: Bug for young ages (<-30) will be in r17
                    156: 
1.289     brouard   157:   Revision 1.288  2018/05/02 20:58:27  brouard
                    158:   Summary: Some bugs fixed
                    159: 
1.288     brouard   160:   Revision 1.287  2018/05/01 17:57:25  brouard
                    161:   Summary: Bug fixed by providing frequencies only for non missing covariates
                    162: 
1.287     brouard   163:   Revision 1.286  2018/04/27 14:27:04  brouard
                    164:   Summary: some minor bugs
                    165: 
1.286     brouard   166:   Revision 1.285  2018/04/21 21:02:16  brouard
                    167:   Summary: Some bugs fixed, valgrind tested
                    168: 
1.285     brouard   169:   Revision 1.284  2018/04/20 05:22:13  brouard
                    170:   Summary: Computing mean and stdeviation of fixed quantitative variables
                    171: 
1.284     brouard   172:   Revision 1.283  2018/04/19 14:49:16  brouard
                    173:   Summary: Some minor bugs fixed
                    174: 
1.283     brouard   175:   Revision 1.282  2018/02/27 22:50:02  brouard
                    176:   *** empty log message ***
                    177: 
1.282     brouard   178:   Revision 1.281  2018/02/27 19:25:23  brouard
                    179:   Summary: Adding second argument for quitting
                    180: 
1.281     brouard   181:   Revision 1.280  2018/02/21 07:58:13  brouard
                    182:   Summary: 0.99r15
                    183: 
                    184:   New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
                    185: 
1.280     brouard   186:   Revision 1.279  2017/07/20 13:35:01  brouard
                    187:   Summary: temporary working
                    188: 
1.279     brouard   189:   Revision 1.278  2017/07/19 14:09:02  brouard
                    190:   Summary: Bug for mobil_average=0 and prevforecast fixed(?)
                    191: 
1.278     brouard   192:   Revision 1.277  2017/07/17 08:53:49  brouard
                    193:   Summary: BOM files can be read now
                    194: 
1.277     brouard   195:   Revision 1.276  2017/06/30 15:48:31  brouard
                    196:   Summary: Graphs improvements
                    197: 
1.276     brouard   198:   Revision 1.275  2017/06/30 13:39:33  brouard
                    199:   Summary: Saito's color
                    200: 
1.275     brouard   201:   Revision 1.274  2017/06/29 09:47:08  brouard
                    202:   Summary: Version 0.99r14
                    203: 
1.274     brouard   204:   Revision 1.273  2017/06/27 11:06:02  brouard
                    205:   Summary: More documentation on projections
                    206: 
1.273     brouard   207:   Revision 1.272  2017/06/27 10:22:40  brouard
                    208:   Summary: Color of backprojection changed from 6 to 5(yellow)
                    209: 
1.272     brouard   210:   Revision 1.271  2017/06/27 10:17:50  brouard
                    211:   Summary: Some bug with rint
                    212: 
1.271     brouard   213:   Revision 1.270  2017/05/24 05:45:29  brouard
                    214:   *** empty log message ***
                    215: 
1.270     brouard   216:   Revision 1.269  2017/05/23 08:39:25  brouard
                    217:   Summary: Code into subroutine, cleanings
                    218: 
1.269     brouard   219:   Revision 1.268  2017/05/18 20:09:32  brouard
                    220:   Summary: backprojection and confidence intervals of backprevalence
                    221: 
1.268     brouard   222:   Revision 1.267  2017/05/13 10:25:05  brouard
                    223:   Summary: temporary save for backprojection
                    224: 
1.267     brouard   225:   Revision 1.266  2017/05/13 07:26:12  brouard
                    226:   Summary: Version 0.99r13 (improvements and bugs fixed)
                    227: 
1.266     brouard   228:   Revision 1.265  2017/04/26 16:22:11  brouard
                    229:   Summary: imach 0.99r13 Some bugs fixed
                    230: 
1.265     brouard   231:   Revision 1.264  2017/04/26 06:01:29  brouard
                    232:   Summary: Labels in graphs
                    233: 
1.264     brouard   234:   Revision 1.263  2017/04/24 15:23:15  brouard
                    235:   Summary: to save
                    236: 
1.263     brouard   237:   Revision 1.262  2017/04/18 16:48:12  brouard
                    238:   *** empty log message ***
                    239: 
1.262     brouard   240:   Revision 1.261  2017/04/05 10:14:09  brouard
                    241:   Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
                    242: 
1.261     brouard   243:   Revision 1.260  2017/04/04 17:46:59  brouard
                    244:   Summary: Gnuplot indexations fixed (humm)
                    245: 
1.260     brouard   246:   Revision 1.259  2017/04/04 13:01:16  brouard
                    247:   Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
                    248: 
1.259     brouard   249:   Revision 1.258  2017/04/03 10:17:47  brouard
                    250:   Summary: Version 0.99r12
                    251: 
                    252:   Some cleanings, conformed with updated documentation.
                    253: 
1.258     brouard   254:   Revision 1.257  2017/03/29 16:53:30  brouard
                    255:   Summary: Temp
                    256: 
1.257     brouard   257:   Revision 1.256  2017/03/27 05:50:23  brouard
                    258:   Summary: Temporary
                    259: 
1.256     brouard   260:   Revision 1.255  2017/03/08 16:02:28  brouard
                    261:   Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
                    262: 
1.255     brouard   263:   Revision 1.254  2017/03/08 07:13:00  brouard
                    264:   Summary: Fixing data parameter line
                    265: 
1.254     brouard   266:   Revision 1.253  2016/12/15 11:59:41  brouard
                    267:   Summary: 0.99 in progress
                    268: 
1.253     brouard   269:   Revision 1.252  2016/09/15 21:15:37  brouard
                    270:   *** empty log message ***
                    271: 
1.252     brouard   272:   Revision 1.251  2016/09/15 15:01:13  brouard
                    273:   Summary: not working
                    274: 
1.251     brouard   275:   Revision 1.250  2016/09/08 16:07:27  brouard
                    276:   Summary: continue
                    277: 
1.250     brouard   278:   Revision 1.249  2016/09/07 17:14:18  brouard
                    279:   Summary: Starting values from frequencies
                    280: 
1.249     brouard   281:   Revision 1.248  2016/09/07 14:10:18  brouard
                    282:   *** empty log message ***
                    283: 
1.248     brouard   284:   Revision 1.247  2016/09/02 11:11:21  brouard
                    285:   *** empty log message ***
                    286: 
1.247     brouard   287:   Revision 1.246  2016/09/02 08:49:22  brouard
                    288:   *** empty log message ***
                    289: 
1.246     brouard   290:   Revision 1.245  2016/09/02 07:25:01  brouard
                    291:   *** empty log message ***
                    292: 
1.245     brouard   293:   Revision 1.244  2016/09/02 07:17:34  brouard
                    294:   *** empty log message ***
                    295: 
1.244     brouard   296:   Revision 1.243  2016/09/02 06:45:35  brouard
                    297:   *** empty log message ***
                    298: 
1.243     brouard   299:   Revision 1.242  2016/08/30 15:01:20  brouard
                    300:   Summary: Fixing a lots
                    301: 
1.242     brouard   302:   Revision 1.241  2016/08/29 17:17:25  brouard
                    303:   Summary: gnuplot problem in Back projection to fix
                    304: 
1.241     brouard   305:   Revision 1.240  2016/08/29 07:53:18  brouard
                    306:   Summary: Better
                    307: 
1.240     brouard   308:   Revision 1.239  2016/08/26 15:51:03  brouard
                    309:   Summary: Improvement in Powell output in order to copy and paste
                    310: 
                    311:   Author:
                    312: 
1.239     brouard   313:   Revision 1.238  2016/08/26 14:23:35  brouard
                    314:   Summary: Starting tests of 0.99
                    315: 
1.238     brouard   316:   Revision 1.237  2016/08/26 09:20:19  brouard
                    317:   Summary: to valgrind
                    318: 
1.237     brouard   319:   Revision 1.236  2016/08/25 10:50:18  brouard
                    320:   *** empty log message ***
                    321: 
1.236     brouard   322:   Revision 1.235  2016/08/25 06:59:23  brouard
                    323:   *** empty log message ***
                    324: 
1.235     brouard   325:   Revision 1.234  2016/08/23 16:51:20  brouard
                    326:   *** empty log message ***
                    327: 
1.234     brouard   328:   Revision 1.233  2016/08/23 07:40:50  brouard
                    329:   Summary: not working
                    330: 
1.233     brouard   331:   Revision 1.232  2016/08/22 14:20:21  brouard
                    332:   Summary: not working
                    333: 
1.232     brouard   334:   Revision 1.231  2016/08/22 07:17:15  brouard
                    335:   Summary: not working
                    336: 
1.231     brouard   337:   Revision 1.230  2016/08/22 06:55:53  brouard
                    338:   Summary: Not working
                    339: 
1.230     brouard   340:   Revision 1.229  2016/07/23 09:45:53  brouard
                    341:   Summary: Completing for func too
                    342: 
1.229     brouard   343:   Revision 1.228  2016/07/22 17:45:30  brouard
                    344:   Summary: Fixing some arrays, still debugging
                    345: 
1.227     brouard   346:   Revision 1.226  2016/07/12 18:42:34  brouard
                    347:   Summary: temp
                    348: 
1.226     brouard   349:   Revision 1.225  2016/07/12 08:40:03  brouard
                    350:   Summary: saving but not running
                    351: 
1.225     brouard   352:   Revision 1.224  2016/07/01 13:16:01  brouard
                    353:   Summary: Fixes
                    354: 
1.224     brouard   355:   Revision 1.223  2016/02/19 09:23:35  brouard
                    356:   Summary: temporary
                    357: 
1.223     brouard   358:   Revision 1.222  2016/02/17 08:14:50  brouard
                    359:   Summary: Probably last 0.98 stable version 0.98r6
                    360: 
1.222     brouard   361:   Revision 1.221  2016/02/15 23:35:36  brouard
                    362:   Summary: minor bug
                    363: 
1.220     brouard   364:   Revision 1.219  2016/02/15 00:48:12  brouard
                    365:   *** empty log message ***
                    366: 
1.219     brouard   367:   Revision 1.218  2016/02/12 11:29:23  brouard
                    368:   Summary: 0.99 Back projections
                    369: 
1.218     brouard   370:   Revision 1.217  2015/12/23 17:18:31  brouard
                    371:   Summary: Experimental backcast
                    372: 
1.217     brouard   373:   Revision 1.216  2015/12/18 17:32:11  brouard
                    374:   Summary: 0.98r4 Warning and status=-2
                    375: 
                    376:   Version 0.98r4 is now:
                    377:    - displaying an error when status is -1, date of interview unknown and date of death known;
                    378:    - permitting a status -2 when the vital status is unknown at a known date of right truncation.
                    379:   Older changes concerning s=-2, dating from 2005 have been supersed.
                    380: 
1.216     brouard   381:   Revision 1.215  2015/12/16 08:52:24  brouard
                    382:   Summary: 0.98r4 working
                    383: 
1.215     brouard   384:   Revision 1.214  2015/12/16 06:57:54  brouard
                    385:   Summary: temporary not working
                    386: 
1.214     brouard   387:   Revision 1.213  2015/12/11 18:22:17  brouard
                    388:   Summary: 0.98r4
                    389: 
1.213     brouard   390:   Revision 1.212  2015/11/21 12:47:24  brouard
                    391:   Summary: minor typo
                    392: 
1.212     brouard   393:   Revision 1.211  2015/11/21 12:41:11  brouard
                    394:   Summary: 0.98r3 with some graph of projected cross-sectional
                    395: 
                    396:   Author: Nicolas Brouard
                    397: 
1.211     brouard   398:   Revision 1.210  2015/11/18 17:41:20  brouard
1.252     brouard   399:   Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
1.210     brouard   400:   Summary: Adding ftolpl parameter
                    401:   Author: N Brouard
                    402: 
                    403:   We had difficulties to get smoothed confidence intervals. It was due
                    404:   to the period prevalence which wasn't computed accurately. The inner
                    405:   parameter ftolpl is now an outer parameter of the .imach parameter
                    406:   file after estepm. If ftolpl is small 1.e-4 and estepm too,
                    407:   computation are long.
                    408: 
1.209     brouard   409:   Revision 1.208  2015/11/17 14:31:57  brouard
                    410:   Summary: temporary
                    411: 
1.208     brouard   412:   Revision 1.207  2015/10/27 17:36:57  brouard
                    413:   *** empty log message ***
                    414: 
1.207     brouard   415:   Revision 1.206  2015/10/24 07:14:11  brouard
                    416:   *** empty log message ***
                    417: 
1.206     brouard   418:   Revision 1.205  2015/10/23 15:50:53  brouard
                    419:   Summary: 0.98r3 some clarification for graphs on likelihood contributions
                    420: 
1.205     brouard   421:   Revision 1.204  2015/10/01 16:20:26  brouard
                    422:   Summary: Some new graphs of contribution to likelihood
                    423: 
1.204     brouard   424:   Revision 1.203  2015/09/30 17:45:14  brouard
                    425:   Summary: looking at better estimation of the hessian
                    426: 
                    427:   Also a better criteria for convergence to the period prevalence And
                    428:   therefore adding the number of years needed to converge. (The
                    429:   prevalence in any alive state shold sum to one
                    430: 
1.203     brouard   431:   Revision 1.202  2015/09/22 19:45:16  brouard
                    432:   Summary: Adding some overall graph on contribution to likelihood. Might change
                    433: 
1.202     brouard   434:   Revision 1.201  2015/09/15 17:34:58  brouard
                    435:   Summary: 0.98r0
                    436: 
                    437:   - Some new graphs like suvival functions
                    438:   - Some bugs fixed like model=1+age+V2.
                    439: 
1.201     brouard   440:   Revision 1.200  2015/09/09 16:53:55  brouard
                    441:   Summary: Big bug thanks to Flavia
                    442: 
                    443:   Even model=1+age+V2. did not work anymore
                    444: 
1.200     brouard   445:   Revision 1.199  2015/09/07 14:09:23  brouard
                    446:   Summary: 0.98q6 changing default small png format for graph to vectorized svg.
                    447: 
1.199     brouard   448:   Revision 1.198  2015/09/03 07:14:39  brouard
                    449:   Summary: 0.98q5 Flavia
                    450: 
1.198     brouard   451:   Revision 1.197  2015/09/01 18:24:39  brouard
                    452:   *** empty log message ***
                    453: 
1.197     brouard   454:   Revision 1.196  2015/08/18 23:17:52  brouard
                    455:   Summary: 0.98q5
                    456: 
1.196     brouard   457:   Revision 1.195  2015/08/18 16:28:39  brouard
                    458:   Summary: Adding a hack for testing purpose
                    459: 
                    460:   After reading the title, ftol and model lines, if the comment line has
                    461:   a q, starting with #q, the answer at the end of the run is quit. It
                    462:   permits to run test files in batch with ctest. The former workaround was
                    463:   $ echo q | imach foo.imach
                    464: 
1.195     brouard   465:   Revision 1.194  2015/08/18 13:32:00  brouard
                    466:   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
                    467: 
1.194     brouard   468:   Revision 1.193  2015/08/04 07:17:42  brouard
                    469:   Summary: 0.98q4
                    470: 
1.193     brouard   471:   Revision 1.192  2015/07/16 16:49:02  brouard
                    472:   Summary: Fixing some outputs
                    473: 
1.192     brouard   474:   Revision 1.191  2015/07/14 10:00:33  brouard
                    475:   Summary: Some fixes
                    476: 
1.191     brouard   477:   Revision 1.190  2015/05/05 08:51:13  brouard
                    478:   Summary: Adding digits in output parameters (7 digits instead of 6)
                    479: 
                    480:   Fix 1+age+.
                    481: 
1.190     brouard   482:   Revision 1.189  2015/04/30 14:45:16  brouard
                    483:   Summary: 0.98q2
                    484: 
1.189     brouard   485:   Revision 1.188  2015/04/30 08:27:53  brouard
                    486:   *** empty log message ***
                    487: 
1.188     brouard   488:   Revision 1.187  2015/04/29 09:11:15  brouard
                    489:   *** empty log message ***
                    490: 
1.187     brouard   491:   Revision 1.186  2015/04/23 12:01:52  brouard
                    492:   Summary: V1*age is working now, version 0.98q1
                    493: 
                    494:   Some codes had been disabled in order to simplify and Vn*age was
                    495:   working in the optimization phase, ie, giving correct MLE parameters,
                    496:   but, as usual, outputs were not correct and program core dumped.
                    497: 
1.186     brouard   498:   Revision 1.185  2015/03/11 13:26:42  brouard
                    499:   Summary: Inclusion of compile and links command line for Intel Compiler
                    500: 
1.185     brouard   501:   Revision 1.184  2015/03/11 11:52:39  brouard
                    502:   Summary: Back from Windows 8. Intel Compiler
                    503: 
1.184     brouard   504:   Revision 1.183  2015/03/10 20:34:32  brouard
                    505:   Summary: 0.98q0, trying with directest, mnbrak fixed
                    506: 
                    507:   We use directest instead of original Powell test; probably no
                    508:   incidence on the results, but better justifications;
                    509:   We fixed Numerical Recipes mnbrak routine which was wrong and gave
                    510:   wrong results.
                    511: 
1.183     brouard   512:   Revision 1.182  2015/02/12 08:19:57  brouard
                    513:   Summary: Trying to keep directest which seems simpler and more general
                    514:   Author: Nicolas Brouard
                    515: 
1.182     brouard   516:   Revision 1.181  2015/02/11 23:22:24  brouard
                    517:   Summary: Comments on Powell added
                    518: 
                    519:   Author:
                    520: 
1.181     brouard   521:   Revision 1.180  2015/02/11 17:33:45  brouard
                    522:   Summary: Finishing move from main to function (hpijx and prevalence_limit)
                    523: 
1.180     brouard   524:   Revision 1.179  2015/01/04 09:57:06  brouard
                    525:   Summary: back to OS/X
                    526: 
1.179     brouard   527:   Revision 1.178  2015/01/04 09:35:48  brouard
                    528:   *** empty log message ***
                    529: 
1.178     brouard   530:   Revision 1.177  2015/01/03 18:40:56  brouard
                    531:   Summary: Still testing ilc32 on OSX
                    532: 
1.177     brouard   533:   Revision 1.176  2015/01/03 16:45:04  brouard
                    534:   *** empty log message ***
                    535: 
1.176     brouard   536:   Revision 1.175  2015/01/03 16:33:42  brouard
                    537:   *** empty log message ***
                    538: 
1.175     brouard   539:   Revision 1.174  2015/01/03 16:15:49  brouard
                    540:   Summary: Still in cross-compilation
                    541: 
1.174     brouard   542:   Revision 1.173  2015/01/03 12:06:26  brouard
                    543:   Summary: trying to detect cross-compilation
                    544: 
1.173     brouard   545:   Revision 1.172  2014/12/27 12:07:47  brouard
                    546:   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
                    547: 
1.172     brouard   548:   Revision 1.171  2014/12/23 13:26:59  brouard
                    549:   Summary: Back from Visual C
                    550: 
                    551:   Still problem with utsname.h on Windows
                    552: 
1.171     brouard   553:   Revision 1.170  2014/12/23 11:17:12  brouard
                    554:   Summary: Cleaning some \%% back to %%
                    555: 
                    556:   The escape was mandatory for a specific compiler (which one?), but too many warnings.
                    557: 
1.170     brouard   558:   Revision 1.169  2014/12/22 23:08:31  brouard
                    559:   Summary: 0.98p
                    560: 
                    561:   Outputs some informations on compiler used, OS etc. Testing on different platforms.
                    562: 
1.169     brouard   563:   Revision 1.168  2014/12/22 15:17:42  brouard
1.170     brouard   564:   Summary: update
1.169     brouard   565: 
1.168     brouard   566:   Revision 1.167  2014/12/22 13:50:56  brouard
                    567:   Summary: Testing uname and compiler version and if compiled 32 or 64
                    568: 
                    569:   Testing on Linux 64
                    570: 
1.167     brouard   571:   Revision 1.166  2014/12/22 11:40:47  brouard
                    572:   *** empty log message ***
                    573: 
1.166     brouard   574:   Revision 1.165  2014/12/16 11:20:36  brouard
                    575:   Summary: After compiling on Visual C
                    576: 
                    577:   * imach.c (Module): Merging 1.61 to 1.162
                    578: 
1.165     brouard   579:   Revision 1.164  2014/12/16 10:52:11  brouard
                    580:   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
                    581: 
                    582:   * imach.c (Module): Merging 1.61 to 1.162
                    583: 
1.164     brouard   584:   Revision 1.163  2014/12/16 10:30:11  brouard
                    585:   * imach.c (Module): Merging 1.61 to 1.162
                    586: 
1.163     brouard   587:   Revision 1.162  2014/09/25 11:43:39  brouard
                    588:   Summary: temporary backup 0.99!
                    589: 
1.162     brouard   590:   Revision 1.1  2014/09/16 11:06:58  brouard
                    591:   Summary: With some code (wrong) for nlopt
                    592: 
                    593:   Author:
                    594: 
                    595:   Revision 1.161  2014/09/15 20:41:41  brouard
                    596:   Summary: Problem with macro SQR on Intel compiler
                    597: 
1.161     brouard   598:   Revision 1.160  2014/09/02 09:24:05  brouard
                    599:   *** empty log message ***
                    600: 
1.160     brouard   601:   Revision 1.159  2014/09/01 10:34:10  brouard
                    602:   Summary: WIN32
                    603:   Author: Brouard
                    604: 
1.159     brouard   605:   Revision 1.158  2014/08/27 17:11:51  brouard
                    606:   *** empty log message ***
                    607: 
1.158     brouard   608:   Revision 1.157  2014/08/27 16:26:55  brouard
                    609:   Summary: Preparing windows Visual studio version
                    610:   Author: Brouard
                    611: 
                    612:   In order to compile on Visual studio, time.h is now correct and time_t
                    613:   and tm struct should be used. difftime should be used but sometimes I
                    614:   just make the differences in raw time format (time(&now).
                    615:   Trying to suppress #ifdef LINUX
                    616:   Add xdg-open for __linux in order to open default browser.
                    617: 
1.157     brouard   618:   Revision 1.156  2014/08/25 20:10:10  brouard
                    619:   *** empty log message ***
                    620: 
1.156     brouard   621:   Revision 1.155  2014/08/25 18:32:34  brouard
                    622:   Summary: New compile, minor changes
                    623:   Author: Brouard
                    624: 
1.155     brouard   625:   Revision 1.154  2014/06/20 17:32:08  brouard
                    626:   Summary: Outputs now all graphs of convergence to period prevalence
                    627: 
1.154     brouard   628:   Revision 1.153  2014/06/20 16:45:46  brouard
                    629:   Summary: If 3 live state, convergence to period prevalence on same graph
                    630:   Author: Brouard
                    631: 
1.153     brouard   632:   Revision 1.152  2014/06/18 17:54:09  brouard
                    633:   Summary: open browser, use gnuplot on same dir than imach if not found in the path
                    634: 
1.152     brouard   635:   Revision 1.151  2014/06/18 16:43:30  brouard
                    636:   *** empty log message ***
                    637: 
1.151     brouard   638:   Revision 1.150  2014/06/18 16:42:35  brouard
                    639:   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
                    640:   Author: brouard
                    641: 
1.150     brouard   642:   Revision 1.149  2014/06/18 15:51:14  brouard
                    643:   Summary: Some fixes in parameter files errors
                    644:   Author: Nicolas Brouard
                    645: 
1.149     brouard   646:   Revision 1.148  2014/06/17 17:38:48  brouard
                    647:   Summary: Nothing new
                    648:   Author: Brouard
                    649: 
                    650:   Just a new packaging for OS/X version 0.98nS
                    651: 
1.148     brouard   652:   Revision 1.147  2014/06/16 10:33:11  brouard
                    653:   *** empty log message ***
                    654: 
1.147     brouard   655:   Revision 1.146  2014/06/16 10:20:28  brouard
                    656:   Summary: Merge
                    657:   Author: Brouard
                    658: 
                    659:   Merge, before building revised version.
                    660: 
1.146     brouard   661:   Revision 1.145  2014/06/10 21:23:15  brouard
                    662:   Summary: Debugging with valgrind
                    663:   Author: Nicolas Brouard
                    664: 
                    665:   Lot of changes in order to output the results with some covariates
                    666:   After the Edimburgh REVES conference 2014, it seems mandatory to
                    667:   improve the code.
                    668:   No more memory valgrind error but a lot has to be done in order to
                    669:   continue the work of splitting the code into subroutines.
                    670:   Also, decodemodel has been improved. Tricode is still not
                    671:   optimal. nbcode should be improved. Documentation has been added in
                    672:   the source code.
                    673: 
1.144     brouard   674:   Revision 1.143  2014/01/26 09:45:38  brouard
                    675:   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
                    676: 
                    677:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    678:   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
                    679: 
1.143     brouard   680:   Revision 1.142  2014/01/26 03:57:36  brouard
                    681:   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
                    682: 
                    683:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    684: 
1.142     brouard   685:   Revision 1.141  2014/01/26 02:42:01  brouard
                    686:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    687: 
1.141     brouard   688:   Revision 1.140  2011/09/02 10:37:54  brouard
                    689:   Summary: times.h is ok with mingw32 now.
                    690: 
1.140     brouard   691:   Revision 1.139  2010/06/14 07:50:17  brouard
                    692:   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
                    693:   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
                    694: 
1.139     brouard   695:   Revision 1.138  2010/04/30 18:19:40  brouard
                    696:   *** empty log message ***
                    697: 
1.138     brouard   698:   Revision 1.137  2010/04/29 18:11:38  brouard
                    699:   (Module): Checking covariates for more complex models
                    700:   than V1+V2. A lot of change to be done. Unstable.
                    701: 
1.137     brouard   702:   Revision 1.136  2010/04/26 20:30:53  brouard
                    703:   (Module): merging some libgsl code. Fixing computation
                    704:   of likelione (using inter/intrapolation if mle = 0) in order to
                    705:   get same likelihood as if mle=1.
                    706:   Some cleaning of code and comments added.
                    707: 
1.136     brouard   708:   Revision 1.135  2009/10/29 15:33:14  brouard
                    709:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                    710: 
1.135     brouard   711:   Revision 1.134  2009/10/29 13:18:53  brouard
                    712:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                    713: 
1.134     brouard   714:   Revision 1.133  2009/07/06 10:21:25  brouard
                    715:   just nforces
                    716: 
1.133     brouard   717:   Revision 1.132  2009/07/06 08:22:05  brouard
                    718:   Many tings
                    719: 
1.132     brouard   720:   Revision 1.131  2009/06/20 16:22:47  brouard
                    721:   Some dimensions resccaled
                    722: 
1.131     brouard   723:   Revision 1.130  2009/05/26 06:44:34  brouard
                    724:   (Module): Max Covariate is now set to 20 instead of 8. A
                    725:   lot of cleaning with variables initialized to 0. Trying to make
                    726:   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
                    727: 
1.130     brouard   728:   Revision 1.129  2007/08/31 13:49:27  lievre
                    729:   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
                    730: 
1.129     lievre    731:   Revision 1.128  2006/06/30 13:02:05  brouard
                    732:   (Module): Clarifications on computing e.j
                    733: 
1.128     brouard   734:   Revision 1.127  2006/04/28 18:11:50  brouard
                    735:   (Module): Yes the sum of survivors was wrong since
                    736:   imach-114 because nhstepm was no more computed in the age
                    737:   loop. Now we define nhstepma in the age loop.
                    738:   (Module): In order to speed up (in case of numerous covariates) we
                    739:   compute health expectancies (without variances) in a first step
                    740:   and then all the health expectancies with variances or standard
                    741:   deviation (needs data from the Hessian matrices) which slows the
                    742:   computation.
                    743:   In the future we should be able to stop the program is only health
                    744:   expectancies and graph are needed without standard deviations.
                    745: 
1.127     brouard   746:   Revision 1.126  2006/04/28 17:23:28  brouard
                    747:   (Module): Yes the sum of survivors was wrong since
                    748:   imach-114 because nhstepm was no more computed in the age
                    749:   loop. Now we define nhstepma in the age loop.
                    750:   Version 0.98h
                    751: 
1.126     brouard   752:   Revision 1.125  2006/04/04 15:20:31  lievre
                    753:   Errors in calculation of health expectancies. Age was not initialized.
                    754:   Forecasting file added.
                    755: 
                    756:   Revision 1.124  2006/03/22 17:13:53  lievre
                    757:   Parameters are printed with %lf instead of %f (more numbers after the comma).
                    758:   The log-likelihood is printed in the log file
                    759: 
                    760:   Revision 1.123  2006/03/20 10:52:43  brouard
                    761:   * imach.c (Module): <title> changed, corresponds to .htm file
                    762:   name. <head> headers where missing.
                    763: 
                    764:   * imach.c (Module): Weights can have a decimal point as for
                    765:   English (a comma might work with a correct LC_NUMERIC environment,
                    766:   otherwise the weight is truncated).
                    767:   Modification of warning when the covariates values are not 0 or
                    768:   1.
                    769:   Version 0.98g
                    770: 
                    771:   Revision 1.122  2006/03/20 09:45:41  brouard
                    772:   (Module): Weights can have a decimal point as for
                    773:   English (a comma might work with a correct LC_NUMERIC environment,
                    774:   otherwise the weight is truncated).
                    775:   Modification of warning when the covariates values are not 0 or
                    776:   1.
                    777:   Version 0.98g
                    778: 
                    779:   Revision 1.121  2006/03/16 17:45:01  lievre
                    780:   * imach.c (Module): Comments concerning covariates added
                    781: 
                    782:   * imach.c (Module): refinements in the computation of lli if
                    783:   status=-2 in order to have more reliable computation if stepm is
                    784:   not 1 month. Version 0.98f
                    785: 
                    786:   Revision 1.120  2006/03/16 15:10:38  lievre
                    787:   (Module): refinements in the computation of lli if
                    788:   status=-2 in order to have more reliable computation if stepm is
                    789:   not 1 month. Version 0.98f
                    790: 
                    791:   Revision 1.119  2006/03/15 17:42:26  brouard
                    792:   (Module): Bug if status = -2, the loglikelihood was
                    793:   computed as likelihood omitting the logarithm. Version O.98e
                    794: 
                    795:   Revision 1.118  2006/03/14 18:20:07  brouard
                    796:   (Module): varevsij Comments added explaining the second
                    797:   table of variances if popbased=1 .
                    798:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    799:   (Module): Function pstamp added
                    800:   (Module): Version 0.98d
                    801: 
                    802:   Revision 1.117  2006/03/14 17:16:22  brouard
                    803:   (Module): varevsij Comments added explaining the second
                    804:   table of variances if popbased=1 .
                    805:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    806:   (Module): Function pstamp added
                    807:   (Module): Version 0.98d
                    808: 
                    809:   Revision 1.116  2006/03/06 10:29:27  brouard
                    810:   (Module): Variance-covariance wrong links and
                    811:   varian-covariance of ej. is needed (Saito).
                    812: 
                    813:   Revision 1.115  2006/02/27 12:17:45  brouard
                    814:   (Module): One freematrix added in mlikeli! 0.98c
                    815: 
                    816:   Revision 1.114  2006/02/26 12:57:58  brouard
                    817:   (Module): Some improvements in processing parameter
                    818:   filename with strsep.
                    819: 
                    820:   Revision 1.113  2006/02/24 14:20:24  brouard
                    821:   (Module): Memory leaks checks with valgrind and:
                    822:   datafile was not closed, some imatrix were not freed and on matrix
                    823:   allocation too.
                    824: 
                    825:   Revision 1.112  2006/01/30 09:55:26  brouard
                    826:   (Module): Back to gnuplot.exe instead of wgnuplot.exe
                    827: 
                    828:   Revision 1.111  2006/01/25 20:38:18  brouard
                    829:   (Module): Lots of cleaning and bugs added (Gompertz)
                    830:   (Module): Comments can be added in data file. Missing date values
                    831:   can be a simple dot '.'.
                    832: 
                    833:   Revision 1.110  2006/01/25 00:51:50  brouard
                    834:   (Module): Lots of cleaning and bugs added (Gompertz)
                    835: 
                    836:   Revision 1.109  2006/01/24 19:37:15  brouard
                    837:   (Module): Comments (lines starting with a #) are allowed in data.
                    838: 
                    839:   Revision 1.108  2006/01/19 18:05:42  lievre
                    840:   Gnuplot problem appeared...
                    841:   To be fixed
                    842: 
                    843:   Revision 1.107  2006/01/19 16:20:37  brouard
                    844:   Test existence of gnuplot in imach path
                    845: 
                    846:   Revision 1.106  2006/01/19 13:24:36  brouard
                    847:   Some cleaning and links added in html output
                    848: 
                    849:   Revision 1.105  2006/01/05 20:23:19  lievre
                    850:   *** empty log message ***
                    851: 
                    852:   Revision 1.104  2005/09/30 16:11:43  lievre
                    853:   (Module): sump fixed, loop imx fixed, and simplifications.
                    854:   (Module): If the status is missing at the last wave but we know
                    855:   that the person is alive, then we can code his/her status as -2
                    856:   (instead of missing=-1 in earlier versions) and his/her
                    857:   contributions to the likelihood is 1 - Prob of dying from last
                    858:   health status (= 1-p13= p11+p12 in the easiest case of somebody in
                    859:   the healthy state at last known wave). Version is 0.98
                    860: 
                    861:   Revision 1.103  2005/09/30 15:54:49  lievre
                    862:   (Module): sump fixed, loop imx fixed, and simplifications.
                    863: 
                    864:   Revision 1.102  2004/09/15 17:31:30  brouard
                    865:   Add the possibility to read data file including tab characters.
                    866: 
                    867:   Revision 1.101  2004/09/15 10:38:38  brouard
                    868:   Fix on curr_time
                    869: 
                    870:   Revision 1.100  2004/07/12 18:29:06  brouard
                    871:   Add version for Mac OS X. Just define UNIX in Makefile
                    872: 
                    873:   Revision 1.99  2004/06/05 08:57:40  brouard
                    874:   *** empty log message ***
                    875: 
                    876:   Revision 1.98  2004/05/16 15:05:56  brouard
                    877:   New version 0.97 . First attempt to estimate force of mortality
                    878:   directly from the data i.e. without the need of knowing the health
                    879:   state at each age, but using a Gompertz model: log u =a + b*age .
                    880:   This is the basic analysis of mortality and should be done before any
                    881:   other analysis, in order to test if the mortality estimated from the
                    882:   cross-longitudinal survey is different from the mortality estimated
                    883:   from other sources like vital statistic data.
                    884: 
                    885:   The same imach parameter file can be used but the option for mle should be -3.
                    886: 
1.324     brouard   887:   Agnès, who wrote this part of the code, tried to keep most of the
1.126     brouard   888:   former routines in order to include the new code within the former code.
                    889: 
                    890:   The output is very simple: only an estimate of the intercept and of
                    891:   the slope with 95% confident intervals.
                    892: 
                    893:   Current limitations:
                    894:   A) Even if you enter covariates, i.e. with the
                    895:   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
                    896:   B) There is no computation of Life Expectancy nor Life Table.
                    897: 
                    898:   Revision 1.97  2004/02/20 13:25:42  lievre
                    899:   Version 0.96d. Population forecasting command line is (temporarily)
                    900:   suppressed.
                    901: 
                    902:   Revision 1.96  2003/07/15 15:38:55  brouard
                    903:   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
                    904:   rewritten within the same printf. Workaround: many printfs.
                    905: 
                    906:   Revision 1.95  2003/07/08 07:54:34  brouard
                    907:   * imach.c (Repository):
                    908:   (Repository): Using imachwizard code to output a more meaningful covariance
                    909:   matrix (cov(a12,c31) instead of numbers.
                    910: 
                    911:   Revision 1.94  2003/06/27 13:00:02  brouard
                    912:   Just cleaning
                    913: 
                    914:   Revision 1.93  2003/06/25 16:33:55  brouard
                    915:   (Module): On windows (cygwin) function asctime_r doesn't
                    916:   exist so I changed back to asctime which exists.
                    917:   (Module): Version 0.96b
                    918: 
                    919:   Revision 1.92  2003/06/25 16:30:45  brouard
                    920:   (Module): On windows (cygwin) function asctime_r doesn't
                    921:   exist so I changed back to asctime which exists.
                    922: 
                    923:   Revision 1.91  2003/06/25 15:30:29  brouard
                    924:   * imach.c (Repository): Duplicated warning errors corrected.
                    925:   (Repository): Elapsed time after each iteration is now output. It
                    926:   helps to forecast when convergence will be reached. Elapsed time
                    927:   is stamped in powell.  We created a new html file for the graphs
                    928:   concerning matrix of covariance. It has extension -cov.htm.
                    929: 
                    930:   Revision 1.90  2003/06/24 12:34:15  brouard
                    931:   (Module): Some bugs corrected for windows. Also, when
                    932:   mle=-1 a template is output in file "or"mypar.txt with the design
                    933:   of the covariance matrix to be input.
                    934: 
                    935:   Revision 1.89  2003/06/24 12:30:52  brouard
                    936:   (Module): Some bugs corrected for windows. Also, when
                    937:   mle=-1 a template is output in file "or"mypar.txt with the design
                    938:   of the covariance matrix to be input.
                    939: 
                    940:   Revision 1.88  2003/06/23 17:54:56  brouard
                    941:   * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
                    942: 
                    943:   Revision 1.87  2003/06/18 12:26:01  brouard
                    944:   Version 0.96
                    945: 
                    946:   Revision 1.86  2003/06/17 20:04:08  brouard
                    947:   (Module): Change position of html and gnuplot routines and added
                    948:   routine fileappend.
                    949: 
                    950:   Revision 1.85  2003/06/17 13:12:43  brouard
                    951:   * imach.c (Repository): Check when date of death was earlier that
                    952:   current date of interview. It may happen when the death was just
                    953:   prior to the death. In this case, dh was negative and likelihood
                    954:   was wrong (infinity). We still send an "Error" but patch by
                    955:   assuming that the date of death was just one stepm after the
                    956:   interview.
                    957:   (Repository): Because some people have very long ID (first column)
                    958:   we changed int to long in num[] and we added a new lvector for
                    959:   memory allocation. But we also truncated to 8 characters (left
                    960:   truncation)
                    961:   (Repository): No more line truncation errors.
                    962: 
                    963:   Revision 1.84  2003/06/13 21:44:43  brouard
                    964:   * imach.c (Repository): Replace "freqsummary" at a correct
                    965:   place. It differs from routine "prevalence" which may be called
                    966:   many times. Probs is memory consuming and must be used with
                    967:   parcimony.
                    968:   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
                    969: 
                    970:   Revision 1.83  2003/06/10 13:39:11  lievre
                    971:   *** empty log message ***
                    972: 
                    973:   Revision 1.82  2003/06/05 15:57:20  brouard
                    974:   Add log in  imach.c and  fullversion number is now printed.
                    975: 
                    976: */
                    977: /*
                    978:    Interpolated Markov Chain
                    979: 
                    980:   Short summary of the programme:
                    981:   
1.227     brouard   982:   This program computes Healthy Life Expectancies or State-specific
                    983:   (if states aren't health statuses) Expectancies from
                    984:   cross-longitudinal data. Cross-longitudinal data consist in: 
                    985: 
                    986:   -1- a first survey ("cross") where individuals from different ages
                    987:   are interviewed on their health status or degree of disability (in
                    988:   the case of a health survey which is our main interest)
                    989: 
                    990:   -2- at least a second wave of interviews ("longitudinal") which
                    991:   measure each change (if any) in individual health status.  Health
                    992:   expectancies are computed from the time spent in each health state
                    993:   according to a model. More health states you consider, more time is
                    994:   necessary to reach the Maximum Likelihood of the parameters involved
                    995:   in the model.  The simplest model is the multinomial logistic model
                    996:   where pij is the probability to be observed in state j at the second
                    997:   wave conditional to be observed in state i at the first
                    998:   wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
                    999:   etc , where 'age' is age and 'sex' is a covariate. If you want to
                   1000:   have a more complex model than "constant and age", you should modify
                   1001:   the program where the markup *Covariates have to be included here
                   1002:   again* invites you to do it.  More covariates you add, slower the
1.126     brouard  1003:   convergence.
                   1004: 
                   1005:   The advantage of this computer programme, compared to a simple
                   1006:   multinomial logistic model, is clear when the delay between waves is not
                   1007:   identical for each individual. Also, if a individual missed an
                   1008:   intermediate interview, the information is lost, but taken into
                   1009:   account using an interpolation or extrapolation.  
                   1010: 
                   1011:   hPijx is the probability to be observed in state i at age x+h
                   1012:   conditional to the observed state i at age x. The delay 'h' can be
                   1013:   split into an exact number (nh*stepm) of unobserved intermediate
                   1014:   states. This elementary transition (by month, quarter,
                   1015:   semester or year) is modelled as a multinomial logistic.  The hPx
                   1016:   matrix is simply the matrix product of nh*stepm elementary matrices
                   1017:   and the contribution of each individual to the likelihood is simply
                   1018:   hPijx.
                   1019: 
                   1020:   Also this programme outputs the covariance matrix of the parameters but also
1.218     brouard  1021:   of the life expectancies. It also computes the period (stable) prevalence.
                   1022: 
                   1023: Back prevalence and projections:
1.227     brouard  1024: 
                   1025:  - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
                   1026:    double agemaxpar, double ftolpl, int *ncvyearp, double
                   1027:    dateprev1,double dateprev2, int firstpass, int lastpass, int
                   1028:    mobilavproj)
                   1029: 
                   1030:     Computes the back prevalence limit for any combination of
                   1031:     covariate values k at any age between ageminpar and agemaxpar and
                   1032:     returns it in **bprlim. In the loops,
                   1033: 
                   1034:    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
                   1035:        **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
                   1036: 
                   1037:    - hBijx Back Probability to be in state i at age x-h being in j at x
1.218     brouard  1038:    Computes for any combination of covariates k and any age between bage and fage 
                   1039:    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   1040:                        oldm=oldms;savm=savms;
1.227     brouard  1041: 
1.267     brouard  1042:    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218     brouard  1043:      Computes the transition matrix starting at age 'age' over
                   1044:      'nhstepm*hstepm*stepm' months (i.e. until
                   1045:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
1.227     brouard  1046:      nhstepm*hstepm matrices. 
                   1047: 
                   1048:      Returns p3mat[i][j][h] after calling
                   1049:      p3mat[i][j][h]=matprod2(newm,
                   1050:      bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
                   1051:      dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
                   1052:      oldm);
1.226     brouard  1053: 
                   1054: Important routines
                   1055: 
                   1056: - func (or funcone), computes logit (pij) distinguishing
                   1057:   o fixed variables (single or product dummies or quantitative);
                   1058:   o varying variables by:
                   1059:    (1) wave (single, product dummies, quantitative), 
                   1060:    (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
                   1061:        % fixed dummy (treated) or quantitative (not done because time-consuming);
                   1062:        % varying dummy (not done) or quantitative (not done);
                   1063: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
                   1064:   and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
                   1065: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
1.325     brouard  1066:   o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
1.226     brouard  1067:     race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218     brouard  1068: 
1.226     brouard  1069: 
                   1070:   
1.324     brouard  1071:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                   1072:            Institut national d'études démographiques, Paris.
1.126     brouard  1073:   This software have been partly granted by Euro-REVES, a concerted action
                   1074:   from the European Union.
                   1075:   It is copyrighted identically to a GNU software product, ie programme and
                   1076:   software can be distributed freely for non commercial use. Latest version
                   1077:   can be accessed at http://euroreves.ined.fr/imach .
                   1078: 
                   1079:   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
                   1080:   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
                   1081:   
                   1082:   **********************************************************************/
                   1083: /*
                   1084:   main
                   1085:   read parameterfile
                   1086:   read datafile
                   1087:   concatwav
                   1088:   freqsummary
                   1089:   if (mle >= 1)
                   1090:     mlikeli
                   1091:   print results files
                   1092:   if mle==1 
                   1093:      computes hessian
                   1094:   read end of parameter file: agemin, agemax, bage, fage, estepm
                   1095:       begin-prev-date,...
                   1096:   open gnuplot file
                   1097:   open html file
1.145     brouard  1098:   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
                   1099:    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
                   1100:                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
                   1101:     freexexit2 possible for memory heap.
                   1102: 
                   1103:   h Pij x                         | pij_nom  ficrestpij
                   1104:    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
                   1105:        1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
                   1106:        1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
                   1107: 
                   1108:        1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
                   1109:        1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
                   1110:   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
                   1111:    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
                   1112:    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
                   1113: 
1.126     brouard  1114:   forecasting if prevfcast==1 prevforecast call prevalence()
                   1115:   health expectancies
                   1116:   Variance-covariance of DFLE
                   1117:   prevalence()
                   1118:    movingaverage()
                   1119:   varevsij() 
                   1120:   if popbased==1 varevsij(,popbased)
                   1121:   total life expectancies
                   1122:   Variance of period (stable) prevalence
                   1123:  end
                   1124: */
                   1125: 
1.187     brouard  1126: /* #define DEBUG */
                   1127: /* #define DEBUGBRENT */
1.203     brouard  1128: /* #define DEBUGLINMIN */
                   1129: /* #define DEBUGHESS */
                   1130: #define DEBUGHESSIJ
1.224     brouard  1131: /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165     brouard  1132: #define POWELL /* Instead of NLOPT */
1.224     brouard  1133: #define POWELLNOF3INFF1TEST /* Skip test */
1.186     brouard  1134: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
                   1135: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.319     brouard  1136: /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
1.126     brouard  1137: 
                   1138: #include <math.h>
                   1139: #include <stdio.h>
                   1140: #include <stdlib.h>
                   1141: #include <string.h>
1.226     brouard  1142: #include <ctype.h>
1.159     brouard  1143: 
                   1144: #ifdef _WIN32
                   1145: #include <io.h>
1.172     brouard  1146: #include <windows.h>
                   1147: #include <tchar.h>
1.159     brouard  1148: #else
1.126     brouard  1149: #include <unistd.h>
1.159     brouard  1150: #endif
1.126     brouard  1151: 
                   1152: #include <limits.h>
                   1153: #include <sys/types.h>
1.171     brouard  1154: 
                   1155: #if defined(__GNUC__)
                   1156: #include <sys/utsname.h> /* Doesn't work on Windows */
                   1157: #endif
                   1158: 
1.126     brouard  1159: #include <sys/stat.h>
                   1160: #include <errno.h>
1.159     brouard  1161: /* extern int errno; */
1.126     brouard  1162: 
1.157     brouard  1163: /* #ifdef LINUX */
                   1164: /* #include <time.h> */
                   1165: /* #include "timeval.h" */
                   1166: /* #else */
                   1167: /* #include <sys/time.h> */
                   1168: /* #endif */
                   1169: 
1.126     brouard  1170: #include <time.h>
                   1171: 
1.136     brouard  1172: #ifdef GSL
                   1173: #include <gsl/gsl_errno.h>
                   1174: #include <gsl/gsl_multimin.h>
                   1175: #endif
                   1176: 
1.167     brouard  1177: 
1.162     brouard  1178: #ifdef NLOPT
                   1179: #include <nlopt.h>
                   1180: typedef struct {
                   1181:   double (* function)(double [] );
                   1182: } myfunc_data ;
                   1183: #endif
                   1184: 
1.126     brouard  1185: /* #include <libintl.h> */
                   1186: /* #define _(String) gettext (String) */
                   1187: 
1.251     brouard  1188: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126     brouard  1189: 
                   1190: #define GNUPLOTPROGRAM "gnuplot"
                   1191: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
                   1192: #define FILENAMELENGTH 132
                   1193: 
                   1194: #define        GLOCK_ERROR_NOPATH              -1      /* empty path */
                   1195: #define        GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
                   1196: 
1.144     brouard  1197: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
                   1198: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126     brouard  1199: 
                   1200: #define NINTERVMAX 8
1.144     brouard  1201: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
                   1202: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.325     brouard  1203: #define NCOVMAX 30  /**< Maximum number of covariates used in the model, including generated covariates V1*V2 or V1*age */
1.197     brouard  1204: #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
1.211     brouard  1205: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
                   1206: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
1.290     brouard  1207: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144     brouard  1208: #define YEARM 12. /**< Number of months per year */
1.218     brouard  1209: /* #define AGESUP 130 */
1.288     brouard  1210: /* #define AGESUP 150 */
                   1211: #define AGESUP 200
1.268     brouard  1212: #define AGEINF 0
1.218     brouard  1213: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126     brouard  1214: #define AGEBASE 40
1.194     brouard  1215: #define AGEOVERFLOW 1.e20
1.164     brouard  1216: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157     brouard  1217: #ifdef _WIN32
                   1218: #define DIRSEPARATOR '\\'
                   1219: #define CHARSEPARATOR "\\"
                   1220: #define ODIRSEPARATOR '/'
                   1221: #else
1.126     brouard  1222: #define DIRSEPARATOR '/'
                   1223: #define CHARSEPARATOR "/"
                   1224: #define ODIRSEPARATOR '\\'
                   1225: #endif
                   1226: 
1.328   ! brouard  1227: /* $Id: imach.c,v 1.327 2022/07/27 14:47:35 brouard Exp $ */
1.126     brouard  1228: /* $State: Exp $ */
1.196     brouard  1229: #include "version.h"
                   1230: char version[]=__IMACH_VERSION__;
1.323     brouard  1231: char copyright[]="July 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";
1.328   ! brouard  1232: char fullversion[]="$Revision: 1.327 $ $Date: 2022/07/27 14:47:35 $"; 
1.126     brouard  1233: char strstart[80];
                   1234: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130     brouard  1235: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
1.187     brouard  1236: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145     brouard  1237: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
                   1238: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
                   1239: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225     brouard  1240: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
                   1241: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145     brouard  1242: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
                   1243: int cptcovprodnoage=0; /**< Number of covariate products without age */   
                   1244: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233     brouard  1245: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
                   1246: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232     brouard  1247: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234     brouard  1248: int nsd=0; /**< Total number of single dummy variables (output) */
                   1249: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232     brouard  1250: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225     brouard  1251: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224     brouard  1252: int ntveff=0; /**< ntveff number of effective time varying variables */
                   1253: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145     brouard  1254: int cptcov=0; /* Working variable */
1.290     brouard  1255: int nobs=10;  /* Number of observations in the data lastobs-firstobs */
1.218     brouard  1256: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302     brouard  1257: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126     brouard  1258: int nlstate=2; /* Number of live states */
                   1259: int ndeath=1; /* Number of dead states */
1.130     brouard  1260: int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223     brouard  1261: int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
1.126     brouard  1262: int popbased=0;
                   1263: 
                   1264: int *wav; /* Number of waves for this individuual 0 is possible */
1.130     brouard  1265: int maxwav=0; /* Maxim number of waves */
                   1266: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
                   1267: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
                   1268: int gipmx=0, gsw=0; /* Global variables on the number of contributions 
1.126     brouard  1269:                   to the likelihood and the sum of weights (done by funcone)*/
1.130     brouard  1270: int mle=1, weightopt=0;
1.126     brouard  1271: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
                   1272: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
                   1273: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
                   1274:           * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162     brouard  1275: int countcallfunc=0;  /* Count the number of calls to func */
1.230     brouard  1276: int selected(int kvar); /* Is covariate kvar selected for printing results */
                   1277: 
1.130     brouard  1278: double jmean=1; /* Mean space between 2 waves */
1.145     brouard  1279: double **matprod2(); /* test */
1.126     brouard  1280: double **oldm, **newm, **savm; /* Working pointers to matrices */
                   1281: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218     brouard  1282: double  **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
                   1283: 
1.136     brouard  1284: /*FILE *fic ; */ /* Used in readdata only */
1.217     brouard  1285: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126     brouard  1286: FILE *ficlog, *ficrespow;
1.130     brouard  1287: int globpr=0; /* Global variable for printing or not */
1.126     brouard  1288: double fretone; /* Only one call to likelihood */
1.130     brouard  1289: long ipmx=0; /* Number of contributions */
1.126     brouard  1290: double sw; /* Sum of weights */
                   1291: char filerespow[FILENAMELENGTH];
                   1292: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
                   1293: FILE *ficresilk;
                   1294: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
                   1295: FILE *ficresprobmorprev;
                   1296: FILE *fichtm, *fichtmcov; /* Html File */
                   1297: FILE *ficreseij;
                   1298: char filerese[FILENAMELENGTH];
                   1299: FILE *ficresstdeij;
                   1300: char fileresstde[FILENAMELENGTH];
                   1301: FILE *ficrescveij;
                   1302: char filerescve[FILENAMELENGTH];
                   1303: FILE  *ficresvij;
                   1304: char fileresv[FILENAMELENGTH];
1.269     brouard  1305: 
1.126     brouard  1306: char title[MAXLINE];
1.234     brouard  1307: char model[MAXLINE]; /**< The model line */
1.217     brouard  1308: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
1.126     brouard  1309: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
                   1310: char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
                   1311: char command[FILENAMELENGTH];
                   1312: int  outcmd=0;
                   1313: 
1.217     brouard  1314: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202     brouard  1315: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126     brouard  1316: char filelog[FILENAMELENGTH]; /* Log file */
                   1317: char filerest[FILENAMELENGTH];
                   1318: char fileregp[FILENAMELENGTH];
                   1319: char popfile[FILENAMELENGTH];
                   1320: 
                   1321: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
                   1322: 
1.157     brouard  1323: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
                   1324: /* struct timezone tzp; */
                   1325: /* extern int gettimeofday(); */
                   1326: struct tm tml, *gmtime(), *localtime();
                   1327: 
                   1328: extern time_t time();
                   1329: 
                   1330: struct tm start_time, end_time, curr_time, last_time, forecast_time;
                   1331: time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
                   1332: struct tm tm;
                   1333: 
1.126     brouard  1334: char strcurr[80], strfor[80];
                   1335: 
                   1336: char *endptr;
                   1337: long lval;
                   1338: double dval;
                   1339: 
                   1340: #define NR_END 1
                   1341: #define FREE_ARG char*
                   1342: #define FTOL 1.0e-10
                   1343: 
                   1344: #define NRANSI 
1.240     brouard  1345: #define ITMAX 200
                   1346: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ 
1.126     brouard  1347: 
                   1348: #define TOL 2.0e-4 
                   1349: 
                   1350: #define CGOLD 0.3819660 
                   1351: #define ZEPS 1.0e-10 
                   1352: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
                   1353: 
                   1354: #define GOLD 1.618034 
                   1355: #define GLIMIT 100.0 
                   1356: #define TINY 1.0e-20 
                   1357: 
                   1358: static double maxarg1,maxarg2;
                   1359: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
                   1360: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                   1361:   
                   1362: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
                   1363: #define rint(a) floor(a+0.5)
1.166     brouard  1364: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183     brouard  1365: #define mytinydouble 1.0e-16
1.166     brouard  1366: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
                   1367: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
                   1368: /* static double dsqrarg; */
                   1369: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126     brouard  1370: static double sqrarg;
                   1371: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
                   1372: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                   1373: int agegomp= AGEGOMP;
                   1374: 
                   1375: int imx; 
                   1376: int stepm=1;
                   1377: /* Stepm, step in month: minimum step interpolation*/
                   1378: 
                   1379: int estepm;
                   1380: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
                   1381: 
                   1382: int m,nb;
                   1383: long *num;
1.197     brouard  1384: int firstpass=0, lastpass=4,*cod, *cens;
1.192     brouard  1385: int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                   1386:                   covariate for which somebody answered excluding 
                   1387:                   undefined. Usually 2: 0 and 1. */
                   1388: int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
                   1389:                             covariate for which somebody answered including 
                   1390:                             undefined. Usually 3: -1, 0 and 1. */
1.126     brouard  1391: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218     brouard  1392: double **pmmij, ***probs; /* Global pointer */
1.219     brouard  1393: double ***mobaverage, ***mobaverages; /* New global variable */
1.126     brouard  1394: double *ageexmed,*agecens;
                   1395: double dateintmean=0;
1.296     brouard  1396:   double anprojd, mprojd, jprojd; /* For eventual projections */
                   1397:   double anprojf, mprojf, jprojf;
1.126     brouard  1398: 
1.296     brouard  1399:   double anbackd, mbackd, jbackd; /* For eventual backprojections */
                   1400:   double anbackf, mbackf, jbackf;
                   1401:   double jintmean,mintmean,aintmean;  
1.126     brouard  1402: double *weight;
                   1403: int **s; /* Status */
1.141     brouard  1404: double *agedc;
1.145     brouard  1405: double  **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141     brouard  1406:                  * covar=matrix(0,NCOVMAX,1,n); 
1.187     brouard  1407:                  * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268     brouard  1408: double **coqvar; /* Fixed quantitative covariate nqv */
                   1409: double ***cotvar; /* Time varying covariate ntv */
1.225     brouard  1410: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141     brouard  1411: double  idx; 
                   1412: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.319     brouard  1413: /* Some documentation */
                   1414:       /*   Design original data
                   1415:        *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12 
                   1416:        *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
                   1417:        *                                                             ntv=3     nqtv=1
                   1418:        *  cptcovn number of covariates (not including constant and age) = # of + plus 1 = 10+1=11
                   1419:        * For time varying covariate, quanti or dummies
                   1420:        *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
                   1421:        *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
                   1422:        *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
                   1423:        *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
                   1424:        *       covar[k,i], value of kth fixed covariate dummy or quanti :
                   1425:        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
                   1426:        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
                   1427:        *   k=  1    2      3       4     5       6      7        8   9     10       11 
                   1428:        */
                   1429: /* According to the model, more columns can be added to covar by the product of covariates */
1.318     brouard  1430: /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
                   1431:   # States 1=Coresidence, 2 Living alone, 3 Institution
                   1432:   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
                   1433: */
1.319     brouard  1434: /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1435: /*    k        1  2   3   4     5    6    7     8    9 */
                   1436: /*Typevar[k]=  0  0   0   2     1    0    2     1    0 *//*0 for simple covariate (dummy, quantitative,*/
                   1437:                                                          /* fixed or varying), 1 for age product, 2 for*/
                   1438:                                                          /* product */
                   1439: /*Dummy[k]=    1  0   0   1     3    1    1     2    0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
                   1440:                                                          /*(single or product without age), 2 dummy*/
                   1441:                                                          /* with age product, 3 quant with age product*/
                   1442: /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
                   1443: /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
                   1444: /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
                   1445: /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */
                   1446: /*    nsq      1                     2                 */ /* Counting single quantit tv */
                   1447: /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */
                   1448: /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */
                   1449: /* Tprod[i]=k             1               2            */ /* Position in model of the ith prod without age */
                   1450: /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */
                   1451: /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */
                   1452: /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */
                   1453: /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
1.320     brouard  1454: /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
1.234     brouard  1455: /* Type                    */
                   1456: /* V         1  2  3  4  5 */
                   1457: /*           F  F  V  V  V */
                   1458: /*           D  Q  D  D  Q */
                   1459: /*                         */
                   1460: int *TvarsD;
                   1461: int *TvarsDind;
                   1462: int *TvarsQ;
                   1463: int *TvarsQind;
                   1464: 
1.318     brouard  1465: #define MAXRESULTLINESPONE 10+1
1.235     brouard  1466: int nresult=0;
1.258     brouard  1467: int parameterline=0; /* # of the parameter (type) line */
1.318     brouard  1468: int TKresult[MAXRESULTLINESPONE];
                   1469: int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
                   1470: int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
                   1471: int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */
                   1472: double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
                   1473: double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
                   1474: int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */
                   1475: 
                   1476: /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
                   1477:   # States 1=Coresidence, 2 Living alone, 3 Institution
                   1478:   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
                   1479: */
1.234     brouard  1480: /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
1.232     brouard  1481: int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1482: int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1483: int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1484: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1485: int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1486: int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231     brouard  1487: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1488: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1489: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1490: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1491: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1492: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1493: int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
                   1494: int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
                   1495: 
1.230     brouard  1496: int *Tvarsel; /**< Selected covariates for output */
                   1497: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226     brouard  1498: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
1.227     brouard  1499: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
                   1500: int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
1.238     brouard  1501: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
                   1502: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197     brouard  1503: int *Tage;
1.227     brouard  1504: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
1.228     brouard  1505: int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.230     brouard  1506: int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ 
                   1507: int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
1.145     brouard  1508: int *Ndum; /** Freq of modality (tricode */
1.200     brouard  1509: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227     brouard  1510: int **Tvard;
                   1511: int *Tprod;/**< Gives the k position of the k1 product */
1.238     brouard  1512: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
1.227     brouard  1513: int *Tposprod; /**< Gives the k1 product from the k position */
1.238     brouard  1514:    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
                   1515:    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227     brouard  1516: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126     brouard  1517: double *lsurv, *lpop, *tpop;
                   1518: 
1.231     brouard  1519: #define FD 1; /* Fixed dummy covariate */
                   1520: #define FQ 2; /* Fixed quantitative covariate */
                   1521: #define FP 3; /* Fixed product covariate */
                   1522: #define FPDD 7; /* Fixed product dummy*dummy covariate */
                   1523: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
                   1524: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
                   1525: #define VD 10; /* Varying dummy covariate */
                   1526: #define VQ 11; /* Varying quantitative covariate */
                   1527: #define VP 12; /* Varying product covariate */
                   1528: #define VPDD 13; /* Varying product dummy*dummy covariate */
                   1529: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
                   1530: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
                   1531: #define APFD 16; /* Age product * fixed dummy covariate */
                   1532: #define APFQ 17; /* Age product * fixed quantitative covariate */
                   1533: #define APVD 18; /* Age product * varying dummy covariate */
                   1534: #define APVQ 19; /* Age product * varying quantitative covariate */
                   1535: 
                   1536: #define FTYPE 1; /* Fixed covariate */
                   1537: #define VTYPE 2; /* Varying covariate (loop in wave) */
                   1538: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
                   1539: 
                   1540: struct kmodel{
                   1541:        int maintype; /* main type */
                   1542:        int subtype; /* subtype */
                   1543: };
                   1544: struct kmodel modell[NCOVMAX];
                   1545: 
1.143     brouard  1546: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
                   1547: double ftolhess; /**< Tolerance for computing hessian */
1.126     brouard  1548: 
                   1549: /**************** split *************************/
                   1550: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
                   1551: {
                   1552:   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
                   1553:      the name of the file (name), its extension only (ext) and its first part of the name (finame)
                   1554:   */ 
                   1555:   char *ss;                            /* pointer */
1.186     brouard  1556:   int  l1=0, l2=0;                             /* length counters */
1.126     brouard  1557: 
                   1558:   l1 = strlen(path );                  /* length of path */
                   1559:   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
                   1560:   ss= strrchr( path, DIRSEPARATOR );           /* find last / */
                   1561:   if ( ss == NULL ) {                  /* no directory, so determine current directory */
                   1562:     strcpy( name, path );              /* we got the fullname name because no directory */
                   1563:     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
                   1564:       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
                   1565:     /* get current working directory */
                   1566:     /*    extern  char* getcwd ( char *buf , int len);*/
1.184     brouard  1567: #ifdef WIN32
                   1568:     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
                   1569: #else
                   1570:        if (getcwd(dirc, FILENAME_MAX) == NULL) {
                   1571: #endif
1.126     brouard  1572:       return( GLOCK_ERROR_GETCWD );
                   1573:     }
                   1574:     /* got dirc from getcwd*/
                   1575:     printf(" DIRC = %s \n",dirc);
1.205     brouard  1576:   } else {                             /* strip directory from path */
1.126     brouard  1577:     ss++;                              /* after this, the filename */
                   1578:     l2 = strlen( ss );                 /* length of filename */
                   1579:     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
                   1580:     strcpy( name, ss );                /* save file name */
                   1581:     strncpy( dirc, path, l1 - l2 );    /* now the directory */
1.186     brouard  1582:     dirc[l1-l2] = '\0';                        /* add zero */
1.126     brouard  1583:     printf(" DIRC2 = %s \n",dirc);
                   1584:   }
                   1585:   /* We add a separator at the end of dirc if not exists */
                   1586:   l1 = strlen( dirc );                 /* length of directory */
                   1587:   if( dirc[l1-1] != DIRSEPARATOR ){
                   1588:     dirc[l1] =  DIRSEPARATOR;
                   1589:     dirc[l1+1] = 0; 
                   1590:     printf(" DIRC3 = %s \n",dirc);
                   1591:   }
                   1592:   ss = strrchr( name, '.' );           /* find last / */
                   1593:   if (ss >0){
                   1594:     ss++;
                   1595:     strcpy(ext,ss);                    /* save extension */
                   1596:     l1= strlen( name);
                   1597:     l2= strlen(ss)+1;
                   1598:     strncpy( finame, name, l1-l2);
                   1599:     finame[l1-l2]= 0;
                   1600:   }
                   1601: 
                   1602:   return( 0 );                         /* we're done */
                   1603: }
                   1604: 
                   1605: 
                   1606: /******************************************/
                   1607: 
                   1608: void replace_back_to_slash(char *s, char*t)
                   1609: {
                   1610:   int i;
                   1611:   int lg=0;
                   1612:   i=0;
                   1613:   lg=strlen(t);
                   1614:   for(i=0; i<= lg; i++) {
                   1615:     (s[i] = t[i]);
                   1616:     if (t[i]== '\\') s[i]='/';
                   1617:   }
                   1618: }
                   1619: 
1.132     brouard  1620: char *trimbb(char *out, char *in)
1.137     brouard  1621: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132     brouard  1622:   char *s;
                   1623:   s=out;
                   1624:   while (*in != '\0'){
1.137     brouard  1625:     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132     brouard  1626:       in++;
                   1627:     }
                   1628:     *out++ = *in++;
                   1629:   }
                   1630:   *out='\0';
                   1631:   return s;
                   1632: }
                   1633: 
1.187     brouard  1634: /* char *substrchaine(char *out, char *in, char *chain) */
                   1635: /* { */
                   1636: /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
                   1637: /*   char *s, *t; */
                   1638: /*   t=in;s=out; */
                   1639: /*   while ((*in != *chain) && (*in != '\0')){ */
                   1640: /*     *out++ = *in++; */
                   1641: /*   } */
                   1642: 
                   1643: /*   /\* *in matches *chain *\/ */
                   1644: /*   while ((*in++ == *chain++) && (*in != '\0')){ */
                   1645: /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
                   1646: /*   } */
                   1647: /*   in--; chain--; */
                   1648: /*   while ( (*in != '\0')){ */
                   1649: /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
                   1650: /*     *out++ = *in++; */
                   1651: /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
                   1652: /*   } */
                   1653: /*   *out='\0'; */
                   1654: /*   out=s; */
                   1655: /*   return out; */
                   1656: /* } */
                   1657: char *substrchaine(char *out, char *in, char *chain)
                   1658: {
                   1659:   /* Substract chain 'chain' from 'in', return and output 'out' */
                   1660:   /* in="V1+V1*age+age*age+V2", chain="age*age" */
                   1661: 
                   1662:   char *strloc;
                   1663: 
                   1664:   strcpy (out, in); 
                   1665:   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
                   1666:   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
                   1667:   if(strloc != NULL){ 
                   1668:     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
                   1669:     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
                   1670:     /* strcpy (strloc, strloc +strlen(chain));*/
                   1671:   }
                   1672:   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
                   1673:   return out;
                   1674: }
                   1675: 
                   1676: 
1.145     brouard  1677: char *cutl(char *blocc, char *alocc, char *in, char occ)
                   1678: {
1.187     brouard  1679:   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
1.145     brouard  1680:      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.310     brouard  1681:      gives alocc="abcdef" and blocc="ghi2j".
1.145     brouard  1682:      If occ is not found blocc is null and alocc is equal to in. Returns blocc
                   1683:   */
1.160     brouard  1684:   char *s, *t;
1.145     brouard  1685:   t=in;s=in;
                   1686:   while ((*in != occ) && (*in != '\0')){
                   1687:     *alocc++ = *in++;
                   1688:   }
                   1689:   if( *in == occ){
                   1690:     *(alocc)='\0';
                   1691:     s=++in;
                   1692:   }
                   1693:  
                   1694:   if (s == t) {/* occ not found */
                   1695:     *(alocc-(in-s))='\0';
                   1696:     in=s;
                   1697:   }
                   1698:   while ( *in != '\0'){
                   1699:     *blocc++ = *in++;
                   1700:   }
                   1701: 
                   1702:   *blocc='\0';
                   1703:   return t;
                   1704: }
1.137     brouard  1705: char *cutv(char *blocc, char *alocc, char *in, char occ)
                   1706: {
1.187     brouard  1707:   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
1.137     brouard  1708:      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                   1709:      gives blocc="abcdef2ghi" and alocc="j".
                   1710:      If occ is not found blocc is null and alocc is equal to in. Returns alocc
                   1711:   */
                   1712:   char *s, *t;
                   1713:   t=in;s=in;
                   1714:   while (*in != '\0'){
                   1715:     while( *in == occ){
                   1716:       *blocc++ = *in++;
                   1717:       s=in;
                   1718:     }
                   1719:     *blocc++ = *in++;
                   1720:   }
                   1721:   if (s == t) /* occ not found */
                   1722:     *(blocc-(in-s))='\0';
                   1723:   else
                   1724:     *(blocc-(in-s)-1)='\0';
                   1725:   in=s;
                   1726:   while ( *in != '\0'){
                   1727:     *alocc++ = *in++;
                   1728:   }
                   1729: 
                   1730:   *alocc='\0';
                   1731:   return s;
                   1732: }
                   1733: 
1.126     brouard  1734: int nbocc(char *s, char occ)
                   1735: {
                   1736:   int i,j=0;
                   1737:   int lg=20;
                   1738:   i=0;
                   1739:   lg=strlen(s);
                   1740:   for(i=0; i<= lg; i++) {
1.234     brouard  1741:     if  (s[i] == occ ) j++;
1.126     brouard  1742:   }
                   1743:   return j;
                   1744: }
                   1745: 
1.137     brouard  1746: /* void cutv(char *u,char *v, char*t, char occ) */
                   1747: /* { */
                   1748: /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
                   1749: /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
                   1750: /*      gives u="abcdef2ghi" and v="j" *\/ */
                   1751: /*   int i,lg,j,p=0; */
                   1752: /*   i=0; */
                   1753: /*   lg=strlen(t); */
                   1754: /*   for(j=0; j<=lg-1; j++) { */
                   1755: /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
                   1756: /*   } */
1.126     brouard  1757: 
1.137     brouard  1758: /*   for(j=0; j<p; j++) { */
                   1759: /*     (u[j] = t[j]); */
                   1760: /*   } */
                   1761: /*      u[p]='\0'; */
1.126     brouard  1762: 
1.137     brouard  1763: /*    for(j=0; j<= lg; j++) { */
                   1764: /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
                   1765: /*   } */
                   1766: /* } */
1.126     brouard  1767: 
1.160     brouard  1768: #ifdef _WIN32
                   1769: char * strsep(char **pp, const char *delim)
                   1770: {
                   1771:   char *p, *q;
                   1772:          
                   1773:   if ((p = *pp) == NULL)
                   1774:     return 0;
                   1775:   if ((q = strpbrk (p, delim)) != NULL)
                   1776:   {
                   1777:     *pp = q + 1;
                   1778:     *q = '\0';
                   1779:   }
                   1780:   else
                   1781:     *pp = 0;
                   1782:   return p;
                   1783: }
                   1784: #endif
                   1785: 
1.126     brouard  1786: /********************** nrerror ********************/
                   1787: 
                   1788: void nrerror(char error_text[])
                   1789: {
                   1790:   fprintf(stderr,"ERREUR ...\n");
                   1791:   fprintf(stderr,"%s\n",error_text);
                   1792:   exit(EXIT_FAILURE);
                   1793: }
                   1794: /*********************** vector *******************/
                   1795: double *vector(int nl, int nh)
                   1796: {
                   1797:   double *v;
                   1798:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
                   1799:   if (!v) nrerror("allocation failure in vector");
                   1800:   return v-nl+NR_END;
                   1801: }
                   1802: 
                   1803: /************************ free vector ******************/
                   1804: void free_vector(double*v, int nl, int nh)
                   1805: {
                   1806:   free((FREE_ARG)(v+nl-NR_END));
                   1807: }
                   1808: 
                   1809: /************************ivector *******************************/
                   1810: int *ivector(long nl,long nh)
                   1811: {
                   1812:   int *v;
                   1813:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                   1814:   if (!v) nrerror("allocation failure in ivector");
                   1815:   return v-nl+NR_END;
                   1816: }
                   1817: 
                   1818: /******************free ivector **************************/
                   1819: void free_ivector(int *v, long nl, long nh)
                   1820: {
                   1821:   free((FREE_ARG)(v+nl-NR_END));
                   1822: }
                   1823: 
                   1824: /************************lvector *******************************/
                   1825: long *lvector(long nl,long nh)
                   1826: {
                   1827:   long *v;
                   1828:   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
                   1829:   if (!v) nrerror("allocation failure in ivector");
                   1830:   return v-nl+NR_END;
                   1831: }
                   1832: 
                   1833: /******************free lvector **************************/
                   1834: void free_lvector(long *v, long nl, long nh)
                   1835: {
                   1836:   free((FREE_ARG)(v+nl-NR_END));
                   1837: }
                   1838: 
                   1839: /******************* imatrix *******************************/
                   1840: int **imatrix(long nrl, long nrh, long ncl, long nch) 
                   1841:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
                   1842: { 
                   1843:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
                   1844:   int **m; 
                   1845:   
                   1846:   /* allocate pointers to rows */ 
                   1847:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
                   1848:   if (!m) nrerror("allocation failure 1 in matrix()"); 
                   1849:   m += NR_END; 
                   1850:   m -= nrl; 
                   1851:   
                   1852:   
                   1853:   /* allocate rows and set pointers to them */ 
                   1854:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
                   1855:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
                   1856:   m[nrl] += NR_END; 
                   1857:   m[nrl] -= ncl; 
                   1858:   
                   1859:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
                   1860:   
                   1861:   /* return pointer to array of pointers to rows */ 
                   1862:   return m; 
                   1863: } 
                   1864: 
                   1865: /****************** free_imatrix *************************/
                   1866: void free_imatrix(m,nrl,nrh,ncl,nch)
                   1867:       int **m;
                   1868:       long nch,ncl,nrh,nrl; 
                   1869:      /* free an int matrix allocated by imatrix() */ 
                   1870: { 
                   1871:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
                   1872:   free((FREE_ARG) (m+nrl-NR_END)); 
                   1873: } 
                   1874: 
                   1875: /******************* matrix *******************************/
                   1876: double **matrix(long nrl, long nrh, long ncl, long nch)
                   1877: {
                   1878:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
                   1879:   double **m;
                   1880: 
                   1881:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                   1882:   if (!m) nrerror("allocation failure 1 in matrix()");
                   1883:   m += NR_END;
                   1884:   m -= nrl;
                   1885: 
                   1886:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                   1887:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                   1888:   m[nrl] += NR_END;
                   1889:   m[nrl] -= ncl;
                   1890: 
                   1891:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                   1892:   return m;
1.145     brouard  1893:   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
                   1894: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
                   1895: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126     brouard  1896:    */
                   1897: }
                   1898: 
                   1899: /*************************free matrix ************************/
                   1900: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
                   1901: {
                   1902:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                   1903:   free((FREE_ARG)(m+nrl-NR_END));
                   1904: }
                   1905: 
                   1906: /******************* ma3x *******************************/
                   1907: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
                   1908: {
                   1909:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
                   1910:   double ***m;
                   1911: 
                   1912:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                   1913:   if (!m) nrerror("allocation failure 1 in matrix()");
                   1914:   m += NR_END;
                   1915:   m -= nrl;
                   1916: 
                   1917:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                   1918:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                   1919:   m[nrl] += NR_END;
                   1920:   m[nrl] -= ncl;
                   1921: 
                   1922:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                   1923: 
                   1924:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                   1925:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
                   1926:   m[nrl][ncl] += NR_END;
                   1927:   m[nrl][ncl] -= nll;
                   1928:   for (j=ncl+1; j<=nch; j++) 
                   1929:     m[nrl][j]=m[nrl][j-1]+nlay;
                   1930:   
                   1931:   for (i=nrl+1; i<=nrh; i++) {
                   1932:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
                   1933:     for (j=ncl+1; j<=nch; j++) 
                   1934:       m[i][j]=m[i][j-1]+nlay;
                   1935:   }
                   1936:   return m; 
                   1937:   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                   1938:            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
                   1939:   */
                   1940: }
                   1941: 
                   1942: /*************************free ma3x ************************/
                   1943: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                   1944: {
                   1945:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                   1946:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                   1947:   free((FREE_ARG)(m+nrl-NR_END));
                   1948: }
                   1949: 
                   1950: /*************** function subdirf ***********/
                   1951: char *subdirf(char fileres[])
                   1952: {
                   1953:   /* Caution optionfilefiname is hidden */
                   1954:   strcpy(tmpout,optionfilefiname);
                   1955:   strcat(tmpout,"/"); /* Add to the right */
                   1956:   strcat(tmpout,fileres);
                   1957:   return tmpout;
                   1958: }
                   1959: 
                   1960: /*************** function subdirf2 ***********/
                   1961: char *subdirf2(char fileres[], char *preop)
                   1962: {
1.314     brouard  1963:   /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
                   1964:  Errors in subdirf, 2, 3 while printing tmpout is
1.315     brouard  1965:  rewritten within the same printf. Workaround: many printfs */
1.126     brouard  1966:   /* Caution optionfilefiname is hidden */
                   1967:   strcpy(tmpout,optionfilefiname);
                   1968:   strcat(tmpout,"/");
                   1969:   strcat(tmpout,preop);
                   1970:   strcat(tmpout,fileres);
                   1971:   return tmpout;
                   1972: }
                   1973: 
                   1974: /*************** function subdirf3 ***********/
                   1975: char *subdirf3(char fileres[], char *preop, char *preop2)
                   1976: {
                   1977:   
                   1978:   /* Caution optionfilefiname is hidden */
                   1979:   strcpy(tmpout,optionfilefiname);
                   1980:   strcat(tmpout,"/");
                   1981:   strcat(tmpout,preop);
                   1982:   strcat(tmpout,preop2);
                   1983:   strcat(tmpout,fileres);
                   1984:   return tmpout;
                   1985: }
1.213     brouard  1986:  
                   1987: /*************** function subdirfext ***********/
                   1988: char *subdirfext(char fileres[], char *preop, char *postop)
                   1989: {
                   1990:   
                   1991:   strcpy(tmpout,preop);
                   1992:   strcat(tmpout,fileres);
                   1993:   strcat(tmpout,postop);
                   1994:   return tmpout;
                   1995: }
1.126     brouard  1996: 
1.213     brouard  1997: /*************** function subdirfext3 ***********/
                   1998: char *subdirfext3(char fileres[], char *preop, char *postop)
                   1999: {
                   2000:   
                   2001:   /* Caution optionfilefiname is hidden */
                   2002:   strcpy(tmpout,optionfilefiname);
                   2003:   strcat(tmpout,"/");
                   2004:   strcat(tmpout,preop);
                   2005:   strcat(tmpout,fileres);
                   2006:   strcat(tmpout,postop);
                   2007:   return tmpout;
                   2008: }
                   2009:  
1.162     brouard  2010: char *asc_diff_time(long time_sec, char ascdiff[])
                   2011: {
                   2012:   long sec_left, days, hours, minutes;
                   2013:   days = (time_sec) / (60*60*24);
                   2014:   sec_left = (time_sec) % (60*60*24);
                   2015:   hours = (sec_left) / (60*60) ;
                   2016:   sec_left = (sec_left) %(60*60);
                   2017:   minutes = (sec_left) /60;
                   2018:   sec_left = (sec_left) % (60);
                   2019:   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
                   2020:   return ascdiff;
                   2021: }
                   2022: 
1.126     brouard  2023: /***************** f1dim *************************/
                   2024: extern int ncom; 
                   2025: extern double *pcom,*xicom;
                   2026: extern double (*nrfunc)(double []); 
                   2027:  
                   2028: double f1dim(double x) 
                   2029: { 
                   2030:   int j; 
                   2031:   double f;
                   2032:   double *xt; 
                   2033:  
                   2034:   xt=vector(1,ncom); 
                   2035:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
                   2036:   f=(*nrfunc)(xt); 
                   2037:   free_vector(xt,1,ncom); 
                   2038:   return f; 
                   2039: } 
                   2040: 
                   2041: /*****************brent *************************/
                   2042: double brent(double ax, double bx, double cx, double (*f)(double), double tol,         double *xmin) 
1.187     brouard  2043: {
                   2044:   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
                   2045:    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
                   2046:    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
                   2047:    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
                   2048:    * returned function value. 
                   2049:   */
1.126     brouard  2050:   int iter; 
                   2051:   double a,b,d,etemp;
1.159     brouard  2052:   double fu=0,fv,fw,fx;
1.164     brouard  2053:   double ftemp=0.;
1.126     brouard  2054:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
                   2055:   double e=0.0; 
                   2056:  
                   2057:   a=(ax < cx ? ax : cx); 
                   2058:   b=(ax > cx ? ax : cx); 
                   2059:   x=w=v=bx; 
                   2060:   fw=fv=fx=(*f)(x); 
                   2061:   for (iter=1;iter<=ITMAX;iter++) { 
                   2062:     xm=0.5*(a+b); 
                   2063:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                   2064:     /*         if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                   2065:     printf(".");fflush(stdout);
                   2066:     fprintf(ficlog,".");fflush(ficlog);
1.162     brouard  2067: #ifdef DEBUGBRENT
1.126     brouard  2068:     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
                   2069:     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
                   2070:     /*         if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                   2071: #endif
                   2072:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                   2073:       *xmin=x; 
                   2074:       return fx; 
                   2075:     } 
                   2076:     ftemp=fu;
                   2077:     if (fabs(e) > tol1) { 
                   2078:       r=(x-w)*(fx-fv); 
                   2079:       q=(x-v)*(fx-fw); 
                   2080:       p=(x-v)*q-(x-w)*r; 
                   2081:       q=2.0*(q-r); 
                   2082:       if (q > 0.0) p = -p; 
                   2083:       q=fabs(q); 
                   2084:       etemp=e; 
                   2085:       e=d; 
                   2086:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
1.224     brouard  2087:                                d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
1.126     brouard  2088:       else { 
1.224     brouard  2089:                                d=p/q; 
                   2090:                                u=x+d; 
                   2091:                                if (u-a < tol2 || b-u < tol2) 
                   2092:                                        d=SIGN(tol1,xm-x); 
1.126     brouard  2093:       } 
                   2094:     } else { 
                   2095:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                   2096:     } 
                   2097:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                   2098:     fu=(*f)(u); 
                   2099:     if (fu <= fx) { 
                   2100:       if (u >= x) a=x; else b=x; 
                   2101:       SHFT(v,w,x,u) 
1.183     brouard  2102:       SHFT(fv,fw,fx,fu) 
                   2103:     } else { 
                   2104:       if (u < x) a=u; else b=u; 
                   2105:       if (fu <= fw || w == x) { 
1.224     brouard  2106:                                v=w; 
                   2107:                                w=u; 
                   2108:                                fv=fw; 
                   2109:                                fw=fu; 
1.183     brouard  2110:       } else if (fu <= fv || v == x || v == w) { 
1.224     brouard  2111:                                v=u; 
                   2112:                                fv=fu; 
1.183     brouard  2113:       } 
                   2114:     } 
1.126     brouard  2115:   } 
                   2116:   nrerror("Too many iterations in brent"); 
                   2117:   *xmin=x; 
                   2118:   return fx; 
                   2119: } 
                   2120: 
                   2121: /****************** mnbrak ***********************/
                   2122: 
                   2123: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                   2124:            double (*func)(double)) 
1.183     brouard  2125: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
                   2126: the downhill direction (defined by the function as evaluated at the initial points) and returns
                   2127: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
                   2128: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
                   2129:    */
1.126     brouard  2130:   double ulim,u,r,q, dum;
                   2131:   double fu; 
1.187     brouard  2132: 
                   2133:   double scale=10.;
                   2134:   int iterscale=0;
                   2135: 
                   2136:   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
                   2137:   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
                   2138: 
                   2139: 
                   2140:   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
                   2141:   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
                   2142:   /*   *bx = *ax - (*ax - *bx)/scale; */
                   2143:   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
                   2144:   /* } */
                   2145: 
1.126     brouard  2146:   if (*fb > *fa) { 
                   2147:     SHFT(dum,*ax,*bx,dum) 
1.183     brouard  2148:     SHFT(dum,*fb,*fa,dum) 
                   2149:   } 
1.126     brouard  2150:   *cx=(*bx)+GOLD*(*bx-*ax); 
                   2151:   *fc=(*func)(*cx); 
1.183     brouard  2152: #ifdef DEBUG
1.224     brouard  2153:   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
                   2154:   fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1.183     brouard  2155: #endif
1.224     brouard  2156:   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
1.126     brouard  2157:     r=(*bx-*ax)*(*fb-*fc); 
1.224     brouard  2158:     q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126     brouard  2159:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
1.183     brouard  2160:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
                   2161:     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
                   2162:     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126     brouard  2163:       fu=(*func)(u); 
1.163     brouard  2164: #ifdef DEBUG
                   2165:       /* f(x)=A(x-u)**2+f(u) */
                   2166:       double A, fparabu; 
                   2167:       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
                   2168:       fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224     brouard  2169:       printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
                   2170:       fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
1.183     brouard  2171:       /* And thus,it can be that fu > *fc even if fparabu < *fc */
                   2172:       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
                   2173:         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
                   2174:       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163     brouard  2175: #endif 
1.184     brouard  2176: #ifdef MNBRAKORIGINAL
1.183     brouard  2177: #else
1.191     brouard  2178: /*       if (fu > *fc) { */
                   2179: /* #ifdef DEBUG */
                   2180: /*       printf("mnbrak4  fu > fc \n"); */
                   2181: /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
                   2182: /* #endif */
                   2183: /*     /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
                   2184: /*     /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
                   2185: /*     dum=u; /\* Shifting c and u *\/ */
                   2186: /*     u = *cx; */
                   2187: /*     *cx = dum; */
                   2188: /*     dum = fu; */
                   2189: /*     fu = *fc; */
                   2190: /*     *fc =dum; */
                   2191: /*       } else { /\* end *\/ */
                   2192: /* #ifdef DEBUG */
                   2193: /*       printf("mnbrak3  fu < fc \n"); */
                   2194: /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
                   2195: /* #endif */
                   2196: /*     dum=u; /\* Shifting c and u *\/ */
                   2197: /*     u = *cx; */
                   2198: /*     *cx = dum; */
                   2199: /*     dum = fu; */
                   2200: /*     fu = *fc; */
                   2201: /*     *fc =dum; */
                   2202: /*       } */
1.224     brouard  2203: #ifdef DEBUGMNBRAK
                   2204:                 double A, fparabu; 
                   2205:      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
                   2206:      fparabu= *fa - A*(*ax-u)*(*ax-u);
                   2207:      printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
                   2208:      fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
1.183     brouard  2209: #endif
1.191     brouard  2210:       dum=u; /* Shifting c and u */
                   2211:       u = *cx;
                   2212:       *cx = dum;
                   2213:       dum = fu;
                   2214:       fu = *fc;
                   2215:       *fc =dum;
1.183     brouard  2216: #endif
1.162     brouard  2217:     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183     brouard  2218: #ifdef DEBUG
1.224     brouard  2219:       printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
                   2220:       fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
1.183     brouard  2221: #endif
1.126     brouard  2222:       fu=(*func)(u); 
                   2223:       if (fu < *fc) { 
1.183     brouard  2224: #ifdef DEBUG
1.224     brouard  2225:                                printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
                   2226:                          fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
                   2227: #endif
                   2228:                          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                   2229:                                SHFT(*fb,*fc,fu,(*func)(u)) 
                   2230: #ifdef DEBUG
                   2231:                                        printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183     brouard  2232: #endif
                   2233:       } 
1.162     brouard  2234:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183     brouard  2235: #ifdef DEBUG
1.224     brouard  2236:       printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
                   2237:       fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183     brouard  2238: #endif
1.126     brouard  2239:       u=ulim; 
                   2240:       fu=(*func)(u); 
1.183     brouard  2241:     } else { /* u could be left to b (if r > q parabola has a maximum) */
                   2242: #ifdef DEBUG
1.224     brouard  2243:       printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
                   2244:       fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1.183     brouard  2245: #endif
1.126     brouard  2246:       u=(*cx)+GOLD*(*cx-*bx); 
                   2247:       fu=(*func)(u); 
1.224     brouard  2248: #ifdef DEBUG
                   2249:       printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
                   2250:       fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
                   2251: #endif
1.183     brouard  2252:     } /* end tests */
1.126     brouard  2253:     SHFT(*ax,*bx,*cx,u) 
1.183     brouard  2254:     SHFT(*fa,*fb,*fc,fu) 
                   2255: #ifdef DEBUG
1.224     brouard  2256:       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
                   2257:       fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1.183     brouard  2258: #endif
                   2259:   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1.126     brouard  2260: } 
                   2261: 
                   2262: /*************** linmin ************************/
1.162     brouard  2263: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
                   2264: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
                   2265: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
                   2266: the value of func at the returned location p . This is actually all accomplished by calling the
                   2267: routines mnbrak and brent .*/
1.126     brouard  2268: int ncom; 
                   2269: double *pcom,*xicom;
                   2270: double (*nrfunc)(double []); 
                   2271:  
1.224     brouard  2272: #ifdef LINMINORIGINAL
1.126     brouard  2273: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
1.224     brouard  2274: #else
                   2275: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
                   2276: #endif
1.126     brouard  2277: { 
                   2278:   double brent(double ax, double bx, double cx, 
                   2279:               double (*f)(double), double tol, double *xmin); 
                   2280:   double f1dim(double x); 
                   2281:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                   2282:              double *fc, double (*func)(double)); 
                   2283:   int j; 
                   2284:   double xx,xmin,bx,ax; 
                   2285:   double fx,fb,fa;
1.187     brouard  2286: 
1.203     brouard  2287: #ifdef LINMINORIGINAL
                   2288: #else
                   2289:   double scale=10., axs, xxs; /* Scale added for infinity */
                   2290: #endif
                   2291:   
1.126     brouard  2292:   ncom=n; 
                   2293:   pcom=vector(1,n); 
                   2294:   xicom=vector(1,n); 
                   2295:   nrfunc=func; 
                   2296:   for (j=1;j<=n;j++) { 
                   2297:     pcom[j]=p[j]; 
1.202     brouard  2298:     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126     brouard  2299:   } 
1.187     brouard  2300: 
1.203     brouard  2301: #ifdef LINMINORIGINAL
                   2302:   xx=1.;
                   2303: #else
                   2304:   axs=0.0;
                   2305:   xxs=1.;
                   2306:   do{
                   2307:     xx= xxs;
                   2308: #endif
1.187     brouard  2309:     ax=0.;
                   2310:     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
                   2311:     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
                   2312:     /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
                   2313:     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
                   2314:     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
                   2315:     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
                   2316:     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
1.203     brouard  2317: #ifdef LINMINORIGINAL
                   2318: #else
                   2319:     if (fx != fx){
1.224     brouard  2320:                        xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
                   2321:                        printf("|");
                   2322:                        fprintf(ficlog,"|");
1.203     brouard  2323: #ifdef DEBUGLINMIN
1.224     brouard  2324:                        printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
1.203     brouard  2325: #endif
                   2326:     }
1.224     brouard  2327:   }while(fx != fx && xxs > 1.e-5);
1.203     brouard  2328: #endif
                   2329:   
1.191     brouard  2330: #ifdef DEBUGLINMIN
                   2331:   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
1.202     brouard  2332:   fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
1.191     brouard  2333: #endif
1.224     brouard  2334: #ifdef LINMINORIGINAL
                   2335: #else
1.317     brouard  2336:   if(fb == fx){ /* Flat function in the direction */
                   2337:     xmin=xx;
1.224     brouard  2338:     *flat=1;
1.317     brouard  2339:   }else{
1.224     brouard  2340:     *flat=0;
                   2341: #endif
                   2342:                /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187     brouard  2343:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
                   2344:   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
                   2345:   /* fmin = f(p[j] + xmin * xi[j]) */
                   2346:   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
                   2347:   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126     brouard  2348: #ifdef DEBUG
1.224     brouard  2349:   printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
                   2350:   fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
                   2351: #endif
                   2352: #ifdef LINMINORIGINAL
                   2353: #else
                   2354:                        }
1.126     brouard  2355: #endif
1.191     brouard  2356: #ifdef DEBUGLINMIN
                   2357:   printf("linmin end ");
1.202     brouard  2358:   fprintf(ficlog,"linmin end ");
1.191     brouard  2359: #endif
1.126     brouard  2360:   for (j=1;j<=n;j++) { 
1.203     brouard  2361: #ifdef LINMINORIGINAL
                   2362:     xi[j] *= xmin; 
                   2363: #else
                   2364: #ifdef DEBUGLINMIN
                   2365:     if(xxs <1.0)
                   2366:       printf(" before xi[%d]=%12.8f", j,xi[j]);
                   2367: #endif
                   2368:     xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
                   2369: #ifdef DEBUGLINMIN
                   2370:     if(xxs <1.0)
                   2371:       printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
                   2372: #endif
                   2373: #endif
1.187     brouard  2374:     p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126     brouard  2375:   } 
1.191     brouard  2376: #ifdef DEBUGLINMIN
1.203     brouard  2377:   printf("\n");
1.191     brouard  2378:   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202     brouard  2379:   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.191     brouard  2380:   for (j=1;j<=n;j++) { 
1.202     brouard  2381:     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
                   2382:     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
                   2383:     if(j % ncovmodel == 0){
1.191     brouard  2384:       printf("\n");
1.202     brouard  2385:       fprintf(ficlog,"\n");
                   2386:     }
1.191     brouard  2387:   }
1.203     brouard  2388: #else
1.191     brouard  2389: #endif
1.126     brouard  2390:   free_vector(xicom,1,n); 
                   2391:   free_vector(pcom,1,n); 
                   2392: } 
                   2393: 
                   2394: 
                   2395: /*************** powell ************************/
1.162     brouard  2396: /*
1.317     brouard  2397: Minimization of a function func of n variables. Input consists in an initial starting point
                   2398: p[1..n] ; an initial matrix xi[1..n][1..n]  whose columns contain the initial set of di-
                   2399: rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
                   2400: such that failure to decrease by more than this amount in one iteration signals doneness. On
1.162     brouard  2401: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
                   2402: function value at p , and iter is the number of iterations taken. The routine linmin is used.
                   2403:  */
1.224     brouard  2404: #ifdef LINMINORIGINAL
                   2405: #else
                   2406:        int *flatdir; /* Function is vanishing in that direction */
1.225     brouard  2407:        int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224     brouard  2408: #endif
1.126     brouard  2409: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                   2410:            double (*func)(double [])) 
                   2411: { 
1.224     brouard  2412: #ifdef LINMINORIGINAL
                   2413:  void linmin(double p[], double xi[], int n, double *fret, 
1.126     brouard  2414:              double (*func)(double [])); 
1.224     brouard  2415: #else 
1.241     brouard  2416:  void linmin(double p[], double xi[], int n, double *fret,
                   2417:             double (*func)(double []),int *flat); 
1.224     brouard  2418: #endif
1.239     brouard  2419:  int i,ibig,j,jk,k; 
1.126     brouard  2420:   double del,t,*pt,*ptt,*xit;
1.181     brouard  2421:   double directest;
1.126     brouard  2422:   double fp,fptt;
                   2423:   double *xits;
                   2424:   int niterf, itmp;
                   2425: 
                   2426:   pt=vector(1,n); 
                   2427:   ptt=vector(1,n); 
                   2428:   xit=vector(1,n); 
                   2429:   xits=vector(1,n); 
                   2430:   *fret=(*func)(p); 
                   2431:   for (j=1;j<=n;j++) pt[j]=p[j]; 
1.202     brouard  2432:   rcurr_time = time(NULL);  
1.126     brouard  2433:   for (*iter=1;;++(*iter)) { 
                   2434:     ibig=0; 
                   2435:     del=0.0; 
1.157     brouard  2436:     rlast_time=rcurr_time;
                   2437:     /* (void) gettimeofday(&curr_time,&tzp); */
                   2438:     rcurr_time = time(NULL);  
                   2439:     curr_time = *localtime(&rcurr_time);
1.324     brouard  2440:     printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
                   2441:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1.157     brouard  2442: /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.324     brouard  2443:     fp=(*fret); /* From former iteration or initial value */
1.192     brouard  2444:     for (i=1;i<=n;i++) {
1.126     brouard  2445:       fprintf(ficrespow," %.12lf", p[i]);
                   2446:     }
1.239     brouard  2447:     fprintf(ficrespow,"\n");fflush(ficrespow);
                   2448:     printf("\n#model=  1      +     age ");
                   2449:     fprintf(ficlog,"\n#model=  1      +     age ");
                   2450:     if(nagesqr==1){
1.241     brouard  2451:        printf("  + age*age  ");
                   2452:        fprintf(ficlog,"  + age*age  ");
1.239     brouard  2453:     }
                   2454:     for(j=1;j <=ncovmodel-2;j++){
                   2455:       if(Typevar[j]==0) {
                   2456:        printf("  +      V%d  ",Tvar[j]);
                   2457:        fprintf(ficlog,"  +      V%d  ",Tvar[j]);
                   2458:       }else if(Typevar[j]==1) {
                   2459:        printf("  +    V%d*age ",Tvar[j]);
                   2460:        fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
                   2461:       }else if(Typevar[j]==2) {
                   2462:        printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   2463:        fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   2464:       }
                   2465:     }
1.126     brouard  2466:     printf("\n");
1.239     brouard  2467: /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
                   2468: /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
1.126     brouard  2469:     fprintf(ficlog,"\n");
1.239     brouard  2470:     for(i=1,jk=1; i <=nlstate; i++){
                   2471:       for(k=1; k <=(nlstate+ndeath); k++){
                   2472:        if (k != i) {
                   2473:          printf("%d%d ",i,k);
                   2474:          fprintf(ficlog,"%d%d ",i,k);
                   2475:          for(j=1; j <=ncovmodel; j++){
                   2476:            printf("%12.7f ",p[jk]);
                   2477:            fprintf(ficlog,"%12.7f ",p[jk]);
                   2478:            jk++; 
                   2479:          }
                   2480:          printf("\n");
                   2481:          fprintf(ficlog,"\n");
                   2482:        }
                   2483:       }
                   2484:     }
1.241     brouard  2485:     if(*iter <=3 && *iter >1){
1.157     brouard  2486:       tml = *localtime(&rcurr_time);
                   2487:       strcpy(strcurr,asctime(&tml));
                   2488:       rforecast_time=rcurr_time; 
1.126     brouard  2489:       itmp = strlen(strcurr);
                   2490:       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
1.241     brouard  2491:        strcurr[itmp-1]='\0';
1.162     brouard  2492:       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157     brouard  2493:       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126     brouard  2494:       for(niterf=10;niterf<=30;niterf+=10){
1.241     brouard  2495:        rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                   2496:        forecast_time = *localtime(&rforecast_time);
                   2497:        strcpy(strfor,asctime(&forecast_time));
                   2498:        itmp = strlen(strfor);
                   2499:        if(strfor[itmp-1]=='\n')
                   2500:          strfor[itmp-1]='\0';
                   2501:        printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
                   2502:        fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1.126     brouard  2503:       }
                   2504:     }
1.187     brouard  2505:     for (i=1;i<=n;i++) { /* For each direction i */
                   2506:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126     brouard  2507:       fptt=(*fret); 
                   2508: #ifdef DEBUG
1.203     brouard  2509:       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
                   2510:       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126     brouard  2511: #endif
1.203     brouard  2512:       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126     brouard  2513:       fprintf(ficlog,"%d",i);fflush(ficlog);
1.224     brouard  2514: #ifdef LINMINORIGINAL
1.188     brouard  2515:       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224     brouard  2516: #else
                   2517:       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                   2518:                        flatdir[i]=flat; /* Function is vanishing in that direction i */
                   2519: #endif
                   2520:                        /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188     brouard  2521:       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224     brouard  2522:                                /* because that direction will be replaced unless the gain del is small */
                   2523:                                /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
                   2524:                                /* Unless the n directions are conjugate some gain in the determinant may be obtained */
                   2525:                                /* with the new direction. */
                   2526:                                del=fabs(fptt-(*fret)); 
                   2527:                                ibig=i; 
1.126     brouard  2528:       } 
                   2529: #ifdef DEBUG
                   2530:       printf("%d %.12e",i,(*fret));
                   2531:       fprintf(ficlog,"%d %.12e",i,(*fret));
                   2532:       for (j=1;j<=n;j++) {
1.224     brouard  2533:                                xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                   2534:                                printf(" x(%d)=%.12e",j,xit[j]);
                   2535:                                fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126     brouard  2536:       }
                   2537:       for(j=1;j<=n;j++) {
1.225     brouard  2538:                                printf(" p(%d)=%.12e",j,p[j]);
                   2539:                                fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126     brouard  2540:       }
                   2541:       printf("\n");
                   2542:       fprintf(ficlog,"\n");
                   2543: #endif
1.187     brouard  2544:     } /* end loop on each direction i */
                   2545:     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
1.188     brouard  2546:     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
1.187     brouard  2547:     /* New value of last point Pn is not computed, P(n-1) */
1.319     brouard  2548:     for(j=1;j<=n;j++) {
                   2549:       if(flatdir[j] >0){
                   2550:         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                   2551:         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
1.302     brouard  2552:       }
1.319     brouard  2553:       /* printf("\n"); */
                   2554:       /* fprintf(ficlog,"\n"); */
                   2555:     }
1.243     brouard  2556:     /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
                   2557:     if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188     brouard  2558:       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
                   2559:       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
                   2560:       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
                   2561:       /* decreased of more than 3.84  */
                   2562:       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
                   2563:       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
                   2564:       /* By adding 10 parameters more the gain should be 18.31 */
1.224     brouard  2565:                        
1.188     brouard  2566:       /* Starting the program with initial values given by a former maximization will simply change */
                   2567:       /* the scales of the directions and the directions, because the are reset to canonical directions */
                   2568:       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
                   2569:       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
1.126     brouard  2570: #ifdef DEBUG
                   2571:       int k[2],l;
                   2572:       k[0]=1;
                   2573:       k[1]=-1;
                   2574:       printf("Max: %.12e",(*func)(p));
                   2575:       fprintf(ficlog,"Max: %.12e",(*func)(p));
                   2576:       for (j=1;j<=n;j++) {
                   2577:        printf(" %.12e",p[j]);
                   2578:        fprintf(ficlog," %.12e",p[j]);
                   2579:       }
                   2580:       printf("\n");
                   2581:       fprintf(ficlog,"\n");
                   2582:       for(l=0;l<=1;l++) {
                   2583:        for (j=1;j<=n;j++) {
                   2584:          ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                   2585:          printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   2586:          fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   2587:        }
                   2588:        printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   2589:        fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   2590:       }
                   2591: #endif
                   2592: 
                   2593:       free_vector(xit,1,n); 
                   2594:       free_vector(xits,1,n); 
                   2595:       free_vector(ptt,1,n); 
                   2596:       free_vector(pt,1,n); 
                   2597:       return; 
1.192     brouard  2598:     } /* enough precision */ 
1.240     brouard  2599:     if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); 
1.181     brouard  2600:     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126     brouard  2601:       ptt[j]=2.0*p[j]-pt[j]; 
                   2602:       xit[j]=p[j]-pt[j]; 
                   2603:       pt[j]=p[j]; 
                   2604:     } 
1.181     brouard  2605:     fptt=(*func)(ptt); /* f_3 */
1.224     brouard  2606: #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   2607:                if (*iter <=4) {
1.225     brouard  2608: #else
                   2609: #endif
1.224     brouard  2610: #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
1.192     brouard  2611: #else
1.161     brouard  2612:     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192     brouard  2613: #endif
1.162     brouard  2614:       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161     brouard  2615:       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162     brouard  2616:       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
                   2617:       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
                   2618:       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224     brouard  2619:       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
                   2620:       /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
                   2621:       /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161     brouard  2622:       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224     brouard  2623:       /*  Even if f3 <f1, directest can be negative and t >0 */
                   2624:       /* mu² and del² are equal when f3=f1 */
                   2625:                        /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
                   2626:                        /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
                   2627:                        /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
                   2628:                        /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
1.183     brouard  2629: #ifdef NRCORIGINAL
                   2630:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
                   2631: #else
                   2632:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1.161     brouard  2633:       t= t- del*SQR(fp-fptt);
1.183     brouard  2634: #endif
1.202     brouard  2635:       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161     brouard  2636: #ifdef DEBUG
1.181     brouard  2637:       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
                   2638:       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1.161     brouard  2639:       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                   2640:             (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
                   2641:       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                   2642:             (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
                   2643:       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
                   2644:       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
                   2645: #endif
1.183     brouard  2646: #ifdef POWELLORIGINAL
                   2647:       if (t < 0.0) { /* Then we use it for new direction */
                   2648: #else
1.182     brouard  2649:       if (directest*t < 0.0) { /* Contradiction between both tests */
1.224     brouard  2650:                                printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.192     brouard  2651:         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.224     brouard  2652:         fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.192     brouard  2653:         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
                   2654:       } 
1.181     brouard  2655:       if (directest < 0.0) { /* Then we use it for new direction */
                   2656: #endif
1.191     brouard  2657: #ifdef DEBUGLINMIN
1.234     brouard  2658:        printf("Before linmin in direction P%d-P0\n",n);
                   2659:        for (j=1;j<=n;j++) {
                   2660:          printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2661:          fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2662:          if(j % ncovmodel == 0){
                   2663:            printf("\n");
                   2664:            fprintf(ficlog,"\n");
                   2665:          }
                   2666:        }
1.224     brouard  2667: #endif
                   2668: #ifdef LINMINORIGINAL
1.234     brouard  2669:        linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224     brouard  2670: #else
1.234     brouard  2671:        linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
                   2672:        flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191     brouard  2673: #endif
1.234     brouard  2674:        
1.191     brouard  2675: #ifdef DEBUGLINMIN
1.234     brouard  2676:        for (j=1;j<=n;j++) { 
                   2677:          printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2678:          fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2679:          if(j % ncovmodel == 0){
                   2680:            printf("\n");
                   2681:            fprintf(ficlog,"\n");
                   2682:          }
                   2683:        }
1.224     brouard  2684: #endif
1.234     brouard  2685:        for (j=1;j<=n;j++) { 
                   2686:          xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                   2687:          xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                   2688:        }
1.224     brouard  2689: #ifdef LINMINORIGINAL
                   2690: #else
1.234     brouard  2691:        for (j=1, flatd=0;j<=n;j++) {
                   2692:          if(flatdir[j]>0)
                   2693:            flatd++;
                   2694:        }
                   2695:        if(flatd >0){
1.255     brouard  2696:          printf("%d flat directions: ",flatd);
                   2697:          fprintf(ficlog,"%d flat directions :",flatd);
1.234     brouard  2698:          for (j=1;j<=n;j++) { 
                   2699:            if(flatdir[j]>0){
                   2700:              printf("%d ",j);
                   2701:              fprintf(ficlog,"%d ",j);
                   2702:            }
                   2703:          }
                   2704:          printf("\n");
                   2705:          fprintf(ficlog,"\n");
1.319     brouard  2706: #ifdef FLATSUP
                   2707:           free_vector(xit,1,n); 
                   2708:           free_vector(xits,1,n); 
                   2709:           free_vector(ptt,1,n); 
                   2710:           free_vector(pt,1,n); 
                   2711:           return;
                   2712: #endif
1.234     brouard  2713:        }
1.191     brouard  2714: #endif
1.234     brouard  2715:        printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                   2716:        fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                   2717:        
1.126     brouard  2718: #ifdef DEBUG
1.234     brouard  2719:        printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                   2720:        fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                   2721:        for(j=1;j<=n;j++){
                   2722:          printf(" %lf",xit[j]);
                   2723:          fprintf(ficlog," %lf",xit[j]);
                   2724:        }
                   2725:        printf("\n");
                   2726:        fprintf(ficlog,"\n");
1.126     brouard  2727: #endif
1.192     brouard  2728:       } /* end of t or directest negative */
1.224     brouard  2729: #ifdef POWELLNOF3INFF1TEST
1.192     brouard  2730: #else
1.234     brouard  2731:       } /* end if (fptt < fp)  */
1.192     brouard  2732: #endif
1.225     brouard  2733: #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
1.234     brouard  2734:     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
1.225     brouard  2735: #else
1.224     brouard  2736: #endif
1.234     brouard  2737:                } /* loop iteration */ 
1.126     brouard  2738: } 
1.234     brouard  2739:   
1.126     brouard  2740: /**** Prevalence limit (stable or period prevalence)  ****************/
1.234     brouard  2741:   
1.235     brouard  2742:   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
1.234     brouard  2743:   {
1.279     brouard  2744:     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij 
                   2745:      *   (and selected quantitative values in nres)
                   2746:      *  by left multiplying the unit
                   2747:      *  matrix by transitions matrix until convergence is reached with precision ftolpl 
                   2748:      * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
                   2749:      * Wx is row vector: population in state 1, population in state 2, population dead
                   2750:      * or prevalence in state 1, prevalence in state 2, 0
                   2751:      * newm is the matrix after multiplications, its rows are identical at a factor.
                   2752:      * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
                   2753:      * Output is prlim.
                   2754:      * Initial matrix pimij 
                   2755:      */
1.206     brouard  2756:   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
                   2757:   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
                   2758:   /*  0,                   0                  , 1} */
                   2759:   /*
                   2760:    * and after some iteration: */
                   2761:   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
                   2762:   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
                   2763:   /*  0,                   0                  , 1} */
                   2764:   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
                   2765:   /* {0.51571254859325999, 0.4842874514067399, */
                   2766:   /*  0.51326036147820708, 0.48673963852179264} */
                   2767:   /* If we start from prlim again, prlim tends to a constant matrix */
1.234     brouard  2768:     
1.126     brouard  2769:   int i, ii,j,k;
1.209     brouard  2770:   double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145     brouard  2771:   /* double **matprod2(); */ /* test */
1.218     brouard  2772:   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126     brouard  2773:   double **newm;
1.209     brouard  2774:   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203     brouard  2775:   int ncvloop=0;
1.288     brouard  2776:   int first=0;
1.169     brouard  2777:   
1.209     brouard  2778:   min=vector(1,nlstate);
                   2779:   max=vector(1,nlstate);
                   2780:   meandiff=vector(1,nlstate);
                   2781: 
1.218     brouard  2782:        /* Starting with matrix unity */
1.126     brouard  2783:   for (ii=1;ii<=nlstate+ndeath;ii++)
                   2784:     for (j=1;j<=nlstate+ndeath;j++){
                   2785:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2786:     }
1.169     brouard  2787:   
                   2788:   cov[1]=1.;
                   2789:   
                   2790:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202     brouard  2791:   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126     brouard  2792:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202     brouard  2793:     ncvloop++;
1.126     brouard  2794:     newm=savm;
                   2795:     /* Covariates have to be included here again */
1.138     brouard  2796:     cov[2]=agefin;
1.319     brouard  2797:      if(nagesqr==1){
                   2798:       cov[3]= agefin*agefin;
                   2799:      }
1.234     brouard  2800:     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                   2801:                        /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                   2802:       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.319     brouard  2803:       /* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */
1.235     brouard  2804:       /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
1.234     brouard  2805:     }
                   2806:     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                   2807:                        /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.319     brouard  2808:       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
                   2809:       /* cov[++k1]=Tqresult[nres][k];  */
1.235     brouard  2810:       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
1.138     brouard  2811:     }
1.237     brouard  2812:     for (k=1; k<=cptcovage;k++){  /* For product with age */
1.319     brouard  2813:       if(Dummy[Tage[k]]==2){ /* dummy with age */
1.234     brouard  2814:        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319     brouard  2815:        /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
                   2816:       } else if(Dummy[Tage[k]]==3){ /* quantitative with age */
                   2817:        cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
                   2818:        /* cov[++k1]=Tqresult[nres][k];  */
1.234     brouard  2819:       }
1.235     brouard  2820:       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
1.234     brouard  2821:     }
1.237     brouard  2822:     for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235     brouard  2823:       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
1.237     brouard  2824:       if(Dummy[Tvard[k][1]==0]){
                   2825:        if(Dummy[Tvard[k][2]==0]){
                   2826:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.319     brouard  2827:          /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.237     brouard  2828:        }else{
                   2829:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
1.319     brouard  2830:          /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
1.237     brouard  2831:        }
                   2832:       }else{
                   2833:        if(Dummy[Tvard[k][2]==0]){
                   2834:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
1.319     brouard  2835:          /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
1.237     brouard  2836:        }else{
                   2837:          cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
1.319     brouard  2838:          /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
1.237     brouard  2839:        }
                   2840:       }
1.234     brouard  2841:     }
1.138     brouard  2842:     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                   2843:     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                   2844:     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145     brouard  2845:     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   2846:     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.319     brouard  2847:     /* age and covariate values of ij are in 'cov' */
1.142     brouard  2848:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138     brouard  2849:     
1.126     brouard  2850:     savm=oldm;
                   2851:     oldm=newm;
1.209     brouard  2852: 
                   2853:     for(j=1; j<=nlstate; j++){
                   2854:       max[j]=0.;
                   2855:       min[j]=1.;
                   2856:     }
                   2857:     for(i=1;i<=nlstate;i++){
                   2858:       sumnew=0;
                   2859:       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                   2860:       for(j=1; j<=nlstate; j++){ 
                   2861:        prlim[i][j]= newm[i][j]/(1-sumnew);
                   2862:        max[j]=FMAX(max[j],prlim[i][j]);
                   2863:        min[j]=FMIN(min[j],prlim[i][j]);
                   2864:       }
                   2865:     }
                   2866: 
1.126     brouard  2867:     maxmax=0.;
1.209     brouard  2868:     for(j=1; j<=nlstate; j++){
                   2869:       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
                   2870:       maxmax=FMAX(maxmax,meandiff[j]);
                   2871:       /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
1.169     brouard  2872:     } /* j loop */
1.203     brouard  2873:     *ncvyear= (int)age- (int)agefin;
1.208     brouard  2874:     /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126     brouard  2875:     if(maxmax < ftolpl){
1.209     brouard  2876:       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
                   2877:       free_vector(min,1,nlstate);
                   2878:       free_vector(max,1,nlstate);
                   2879:       free_vector(meandiff,1,nlstate);
1.126     brouard  2880:       return prlim;
                   2881:     }
1.288     brouard  2882:   } /* agefin loop */
1.208     brouard  2883:     /* After some age loop it doesn't converge */
1.288     brouard  2884:   if(!first){
                   2885:     first=1;
                   2886:     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
1.317     brouard  2887:     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
                   2888:   }else if (first >=1 && first <10){
                   2889:     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
                   2890:     first++;
                   2891:   }else if (first ==10){
                   2892:     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
                   2893:     printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
                   2894:     fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
                   2895:     first++;
1.288     brouard  2896:   }
                   2897: 
1.209     brouard  2898:   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
                   2899:   free_vector(min,1,nlstate);
                   2900:   free_vector(max,1,nlstate);
                   2901:   free_vector(meandiff,1,nlstate);
1.208     brouard  2902:   
1.169     brouard  2903:   return prlim; /* should not reach here */
1.126     brouard  2904: }
                   2905: 
1.217     brouard  2906: 
                   2907:  /**** Back Prevalence limit (stable or period prevalence)  ****************/
                   2908: 
1.218     brouard  2909:  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
                   2910:  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
1.242     brouard  2911:   double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217     brouard  2912: {
1.264     brouard  2913:   /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
1.217     brouard  2914:      matrix by transitions matrix until convergence is reached with precision ftolpl */
                   2915:   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
                   2916:   /* Wx is row vector: population in state 1, population in state 2, population dead */
                   2917:   /* or prevalence in state 1, prevalence in state 2, 0 */
                   2918:   /* newm is the matrix after multiplications, its rows are identical at a factor */
                   2919:   /* Initial matrix pimij */
                   2920:   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
                   2921:   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
                   2922:   /*  0,                   0                  , 1} */
                   2923:   /*
                   2924:    * and after some iteration: */
                   2925:   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
                   2926:   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
                   2927:   /*  0,                   0                  , 1} */
                   2928:   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
                   2929:   /* {0.51571254859325999, 0.4842874514067399, */
                   2930:   /*  0.51326036147820708, 0.48673963852179264} */
                   2931:   /* If we start from prlim again, prlim tends to a constant matrix */
                   2932: 
                   2933:   int i, ii,j,k;
1.247     brouard  2934:   int first=0;
1.217     brouard  2935:   double *min, *max, *meandiff, maxmax,sumnew=0.;
                   2936:   /* double **matprod2(); */ /* test */
                   2937:   double **out, cov[NCOVMAX+1], **bmij();
                   2938:   double **newm;
1.218     brouard  2939:   double        **dnewm, **doldm, **dsavm;  /* for use */
                   2940:   double        **oldm, **savm;  /* for use */
                   2941: 
1.217     brouard  2942:   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
                   2943:   int ncvloop=0;
                   2944:   
                   2945:   min=vector(1,nlstate);
                   2946:   max=vector(1,nlstate);
                   2947:   meandiff=vector(1,nlstate);
                   2948: 
1.266     brouard  2949:   dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
                   2950:   oldm=oldms; savm=savms;
                   2951:   
                   2952:   /* Starting with matrix unity */
                   2953:   for (ii=1;ii<=nlstate+ndeath;ii++)
                   2954:     for (j=1;j<=nlstate+ndeath;j++){
1.217     brouard  2955:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2956:     }
                   2957:   
                   2958:   cov[1]=1.;
                   2959:   
                   2960:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   2961:   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218     brouard  2962:   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288     brouard  2963:   /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
                   2964:   for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217     brouard  2965:     ncvloop++;
1.218     brouard  2966:     newm=savm; /* oldm should be kept from previous iteration or unity at start */
                   2967:                /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217     brouard  2968:     /* Covariates have to be included here again */
                   2969:     cov[2]=agefin;
1.319     brouard  2970:     if(nagesqr==1){
1.217     brouard  2971:       cov[3]= agefin*agefin;;
1.319     brouard  2972:     }
1.242     brouard  2973:     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                   2974:                        /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                   2975:       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264     brouard  2976:       /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
1.242     brouard  2977:     }
                   2978:     /* for (k=1; k<=cptcovn;k++) { */
                   2979:     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
                   2980:     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
                   2981:     /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
                   2982:     /* } */
                   2983:     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                   2984:                        /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
                   2985:       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
                   2986:       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
                   2987:     }
                   2988:     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
                   2989:     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
                   2990:     /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
                   2991:     /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
                   2992:     for (k=1; k<=cptcovage;k++){  /* For product with age */
1.319     brouard  2993:       /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ ERROR ???*/
                   2994:       if(Dummy[Tage[k]]== 2){ /* dummy with age */
1.242     brouard  2995:        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319     brouard  2996:       } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
                   2997:        cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.242     brouard  2998:       }
                   2999:       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
                   3000:     }
                   3001:     for (k=1; k<=cptcovprod;k++){ /* For product without age */
                   3002:       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
                   3003:       if(Dummy[Tvard[k][1]==0]){
                   3004:        if(Dummy[Tvard[k][2]==0]){
                   3005:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
                   3006:        }else{
                   3007:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
                   3008:        }
                   3009:       }else{
                   3010:        if(Dummy[Tvard[k][2]==0]){
                   3011:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
                   3012:        }else{
                   3013:          cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
                   3014:        }
                   3015:       }
1.217     brouard  3016:     }
                   3017:     
                   3018:     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                   3019:     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                   3020:     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
                   3021:     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   3022:     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218     brouard  3023:                /* ij should be linked to the correct index of cov */
                   3024:                /* age and covariate values ij are in 'cov', but we need to pass
                   3025:                 * ij for the observed prevalence at age and status and covariate
                   3026:                 * number:  prevacurrent[(int)agefin][ii][ij]
                   3027:                 */
                   3028:     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
                   3029:     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
                   3030:     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
1.268     brouard  3031:     /* if((int)age == 86 || (int)age == 87){ */
1.266     brouard  3032:     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
                   3033:     /*   for(i=1; i<=nlstate+ndeath; i++) { */
                   3034:     /*         printf("%d newm= ",i); */
                   3035:     /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3036:     /*           printf("%f ",newm[i][j]); */
                   3037:     /*         } */
                   3038:     /*         printf("oldm * "); */
                   3039:     /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3040:     /*           printf("%f ",oldm[i][j]); */
                   3041:     /*         } */
1.268     brouard  3042:     /*         printf(" bmmij "); */
1.266     brouard  3043:     /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3044:     /*           printf("%f ",pmmij[i][j]); */
                   3045:     /*         } */
                   3046:     /*         printf("\n"); */
                   3047:     /*   } */
                   3048:     /* } */
1.217     brouard  3049:     savm=oldm;
                   3050:     oldm=newm;
1.266     brouard  3051: 
1.217     brouard  3052:     for(j=1; j<=nlstate; j++){
                   3053:       max[j]=0.;
                   3054:       min[j]=1.;
                   3055:     }
                   3056:     for(j=1; j<=nlstate; j++){ 
                   3057:       for(i=1;i<=nlstate;i++){
1.234     brouard  3058:        /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                   3059:        bprlim[i][j]= newm[i][j];
                   3060:        max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                   3061:        min[i]=FMIN(min[i],bprlim[i][j]);
1.217     brouard  3062:       }
                   3063:     }
1.218     brouard  3064:                
1.217     brouard  3065:     maxmax=0.;
                   3066:     for(i=1; i<=nlstate; i++){
1.318     brouard  3067:       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column, could be nan! */
1.217     brouard  3068:       maxmax=FMAX(maxmax,meandiff[i]);
                   3069:       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
1.268     brouard  3070:     } /* i loop */
1.217     brouard  3071:     *ncvyear= -( (int)age- (int)agefin);
1.268     brouard  3072:     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217     brouard  3073:     if(maxmax < ftolpl){
1.220     brouard  3074:       /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217     brouard  3075:       free_vector(min,1,nlstate);
                   3076:       free_vector(max,1,nlstate);
                   3077:       free_vector(meandiff,1,nlstate);
                   3078:       return bprlim;
                   3079:     }
1.288     brouard  3080:   } /* agefin loop */
1.217     brouard  3081:     /* After some age loop it doesn't converge */
1.288     brouard  3082:   if(!first){
1.247     brouard  3083:     first=1;
                   3084:     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
                   3085: Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
                   3086:   }
                   3087:   fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.217     brouard  3088: Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
                   3089:   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
                   3090:   free_vector(min,1,nlstate);
                   3091:   free_vector(max,1,nlstate);
                   3092:   free_vector(meandiff,1,nlstate);
                   3093:   
                   3094:   return bprlim; /* should not reach here */
                   3095: }
                   3096: 
1.126     brouard  3097: /*************** transition probabilities ***************/ 
                   3098: 
                   3099: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                   3100: {
1.138     brouard  3101:   /* According to parameters values stored in x and the covariate's values stored in cov,
1.266     brouard  3102:      computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138     brouard  3103:      model to the ncovmodel covariates (including constant and age).
                   3104:      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
                   3105:      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
                   3106:      ncth covariate in the global vector x is given by the formula:
                   3107:      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
                   3108:      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
                   3109:      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
                   3110:      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266     brouard  3111:      Outputs ps[i][j] or probability to be observed in j being in i according to
1.138     brouard  3112:      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266     brouard  3113:      Sum on j ps[i][j] should equal to 1.
1.138     brouard  3114:   */
                   3115:   double s1, lnpijopii;
1.126     brouard  3116:   /*double t34;*/
1.164     brouard  3117:   int i,j, nc, ii, jj;
1.126     brouard  3118: 
1.223     brouard  3119:   for(i=1; i<= nlstate; i++){
                   3120:     for(j=1; j<i;j++){
                   3121:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   3122:        /*lnpijopii += param[i][j][nc]*cov[nc];*/
                   3123:        lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                   3124:        /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   3125:       }
                   3126:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   3127:       /*       printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   3128:     }
                   3129:     for(j=i+1; j<=nlstate+ndeath;j++){
                   3130:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   3131:        /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                   3132:        lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                   3133:        /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                   3134:       }
                   3135:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   3136:     }
                   3137:   }
1.218     brouard  3138:   
1.223     brouard  3139:   for(i=1; i<= nlstate; i++){
                   3140:     s1=0;
                   3141:     for(j=1; j<i; j++){
                   3142:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   3143:       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   3144:     }
                   3145:     for(j=i+1; j<=nlstate+ndeath; j++){
                   3146:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   3147:       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   3148:     }
                   3149:     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   3150:     ps[i][i]=1./(s1+1.);
                   3151:     /* Computing other pijs */
                   3152:     for(j=1; j<i; j++)
1.325     brouard  3153:       ps[i][j]= exp(ps[i][j])*ps[i][i];/* Bug valgrind */
1.223     brouard  3154:     for(j=i+1; j<=nlstate+ndeath; j++)
                   3155:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   3156:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                   3157:   } /* end i */
1.218     brouard  3158:   
1.223     brouard  3159:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   3160:     for(jj=1; jj<= nlstate+ndeath; jj++){
                   3161:       ps[ii][jj]=0;
                   3162:       ps[ii][ii]=1;
                   3163:     }
                   3164:   }
1.294     brouard  3165: 
                   3166: 
1.223     brouard  3167:   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
                   3168:   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
                   3169:   /*   printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
                   3170:   /*   } */
                   3171:   /*   printf("\n "); */
                   3172:   /* } */
                   3173:   /* printf("\n ");printf("%lf ",cov[2]);*/
                   3174:   /*
                   3175:     for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218     brouard  3176:                goto end;*/
1.266     brouard  3177:   return ps; /* Pointer is unchanged since its call */
1.126     brouard  3178: }
                   3179: 
1.218     brouard  3180: /*************** backward transition probabilities ***************/ 
                   3181: 
                   3182:  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
                   3183: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
                   3184:  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
                   3185: {
1.302     brouard  3186:   /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
1.266     brouard  3187:    * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
1.222     brouard  3188:    */
1.218     brouard  3189:   int i, ii, j,k;
1.222     brouard  3190:   
                   3191:   double **out, **pmij();
                   3192:   double sumnew=0.;
1.218     brouard  3193:   double agefin;
1.292     brouard  3194:   double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
1.222     brouard  3195:   double **dnewm, **dsavm, **doldm;
                   3196:   double **bbmij;
                   3197:   
1.218     brouard  3198:   doldm=ddoldms; /* global pointers */
1.222     brouard  3199:   dnewm=ddnewms;
                   3200:   dsavm=ddsavms;
1.318     brouard  3201: 
                   3202:   /* Debug */
                   3203:   /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
1.222     brouard  3204:   agefin=cov[2];
1.268     brouard  3205:   /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222     brouard  3206:   /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266     brouard  3207:      the observed prevalence (with this covariate ij) at beginning of transition */
                   3208:   /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268     brouard  3209: 
                   3210:   /* P_x */
1.325     brouard  3211:   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm *//* Bug valgrind */
1.268     brouard  3212:   /* outputs pmmij which is a stochastic matrix in row */
                   3213: 
                   3214:   /* Diag(w_x) */
1.292     brouard  3215:   /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268     brouard  3216:   sumnew=0.;
1.269     brouard  3217:   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268     brouard  3218:   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297     brouard  3219:     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268     brouard  3220:     sumnew+=prevacurrent[(int)agefin][ii][ij];
                   3221:   }
                   3222:   if(sumnew >0.01){  /* At least some value in the prevalence */
                   3223:     for (ii=1;ii<=nlstate+ndeath;ii++){
                   3224:       for (j=1;j<=nlstate+ndeath;j++)
1.269     brouard  3225:        doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268     brouard  3226:     }
                   3227:   }else{
                   3228:     for (ii=1;ii<=nlstate+ndeath;ii++){
                   3229:       for (j=1;j<=nlstate+ndeath;j++)
                   3230:       doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
                   3231:     }
                   3232:     /* if(sumnew <0.9){ */
                   3233:     /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
                   3234:     /* } */
                   3235:   }
                   3236:   k3=0.0;  /* We put the last diagonal to 0 */
                   3237:   for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
                   3238:       doldm[ii][ii]= k3;
                   3239:   }
                   3240:   /* End doldm, At the end doldm is diag[(w_i)] */
                   3241:   
1.292     brouard  3242:   /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
                   3243:   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268     brouard  3244: 
1.292     brouard  3245:   /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268     brouard  3246:   /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
1.222     brouard  3247:   for (j=1;j<=nlstate+ndeath;j++){
1.268     brouard  3248:     sumnew=0.;
1.222     brouard  3249:     for (ii=1;ii<=nlstate;ii++){
1.266     brouard  3250:       /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268     brouard  3251:       sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222     brouard  3252:     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268     brouard  3253:     for (ii=1;ii<=nlstate+ndeath;ii++){
1.222     brouard  3254:        /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268     brouard  3255:        /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222     brouard  3256:        /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268     brouard  3257:        /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222     brouard  3258:        /* }else */
1.268     brouard  3259:       dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
                   3260:     } /*End ii */
                   3261:   } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
                   3262: 
1.292     brouard  3263:   ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268     brouard  3264:   /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222     brouard  3265:   /* end bmij */
1.266     brouard  3266:   return ps; /*pointer is unchanged */
1.218     brouard  3267: }
1.217     brouard  3268: /*************** transition probabilities ***************/ 
                   3269: 
1.218     brouard  3270: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217     brouard  3271: {
                   3272:   /* According to parameters values stored in x and the covariate's values stored in cov,
                   3273:      computes the probability to be observed in state j being in state i by appying the
                   3274:      model to the ncovmodel covariates (including constant and age).
                   3275:      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
                   3276:      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
                   3277:      ncth covariate in the global vector x is given by the formula:
                   3278:      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
                   3279:      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
                   3280:      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
                   3281:      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
                   3282:      Outputs ps[i][j] the probability to be observed in j being in j according to
                   3283:      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
                   3284:   */
                   3285:   double s1, lnpijopii;
                   3286:   /*double t34;*/
                   3287:   int i,j, nc, ii, jj;
                   3288: 
1.234     brouard  3289:   for(i=1; i<= nlstate; i++){
                   3290:     for(j=1; j<i;j++){
                   3291:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   3292:        /*lnpijopii += param[i][j][nc]*cov[nc];*/
                   3293:        lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                   3294:        /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   3295:       }
                   3296:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   3297:       /*       printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   3298:     }
                   3299:     for(j=i+1; j<=nlstate+ndeath;j++){
                   3300:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   3301:        /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                   3302:        lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                   3303:        /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                   3304:       }
                   3305:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   3306:     }
                   3307:   }
                   3308:   
                   3309:   for(i=1; i<= nlstate; i++){
                   3310:     s1=0;
                   3311:     for(j=1; j<i; j++){
                   3312:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   3313:       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   3314:     }
                   3315:     for(j=i+1; j<=nlstate+ndeath; j++){
                   3316:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   3317:       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   3318:     }
                   3319:     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   3320:     ps[i][i]=1./(s1+1.);
                   3321:     /* Computing other pijs */
                   3322:     for(j=1; j<i; j++)
                   3323:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   3324:     for(j=i+1; j<=nlstate+ndeath; j++)
                   3325:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   3326:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                   3327:   } /* end i */
                   3328:   
                   3329:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   3330:     for(jj=1; jj<= nlstate+ndeath; jj++){
                   3331:       ps[ii][jj]=0;
                   3332:       ps[ii][ii]=1;
                   3333:     }
                   3334:   }
1.296     brouard  3335:   /* Added for prevbcast */ /* Transposed matrix too */
1.234     brouard  3336:   for(jj=1; jj<= nlstate+ndeath; jj++){
                   3337:     s1=0.;
                   3338:     for(ii=1; ii<= nlstate+ndeath; ii++){
                   3339:       s1+=ps[ii][jj];
                   3340:     }
                   3341:     for(ii=1; ii<= nlstate; ii++){
                   3342:       ps[ii][jj]=ps[ii][jj]/s1;
                   3343:     }
                   3344:   }
                   3345:   /* Transposition */
                   3346:   for(jj=1; jj<= nlstate+ndeath; jj++){
                   3347:     for(ii=jj; ii<= nlstate+ndeath; ii++){
                   3348:       s1=ps[ii][jj];
                   3349:       ps[ii][jj]=ps[jj][ii];
                   3350:       ps[jj][ii]=s1;
                   3351:     }
                   3352:   }
                   3353:   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
                   3354:   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
                   3355:   /*   printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
                   3356:   /*   } */
                   3357:   /*   printf("\n "); */
                   3358:   /* } */
                   3359:   /* printf("\n ");printf("%lf ",cov[2]);*/
                   3360:   /*
                   3361:     for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   3362:     goto end;*/
                   3363:   return ps;
1.217     brouard  3364: }
                   3365: 
                   3366: 
1.126     brouard  3367: /**************** Product of 2 matrices ******************/
                   3368: 
1.145     brouard  3369: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126     brouard  3370: {
                   3371:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                   3372:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                   3373:   /* in, b, out are matrice of pointers which should have been initialized 
                   3374:      before: only the contents of out is modified. The function returns
                   3375:      a pointer to pointers identical to out */
1.145     brouard  3376:   int i, j, k;
1.126     brouard  3377:   for(i=nrl; i<= nrh; i++)
1.145     brouard  3378:     for(k=ncolol; k<=ncoloh; k++){
                   3379:       out[i][k]=0.;
                   3380:       for(j=ncl; j<=nch; j++)
                   3381:        out[i][k] +=in[i][j]*b[j][k];
                   3382:     }
1.126     brouard  3383:   return out;
                   3384: }
                   3385: 
                   3386: 
                   3387: /************* Higher Matrix Product ***************/
                   3388: 
1.235     brouard  3389: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
1.126     brouard  3390: {
1.218     brouard  3391:   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
1.126     brouard  3392:      'nhstepm*hstepm*stepm' months (i.e. until
                   3393:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                   3394:      nhstepm*hstepm matrices. 
                   3395:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
                   3396:      (typically every 2 years instead of every month which is too big 
                   3397:      for the memory).
                   3398:      Model is determined by parameters x and covariates have to be 
                   3399:      included manually here. 
                   3400: 
                   3401:      */
                   3402: 
                   3403:   int i, j, d, h, k;
1.131     brouard  3404:   double **out, cov[NCOVMAX+1];
1.126     brouard  3405:   double **newm;
1.187     brouard  3406:   double agexact;
1.214     brouard  3407:   double agebegin, ageend;
1.126     brouard  3408: 
                   3409:   /* Hstepm could be zero and should return the unit matrix */
                   3410:   for (i=1;i<=nlstate+ndeath;i++)
                   3411:     for (j=1;j<=nlstate+ndeath;j++){
                   3412:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   3413:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   3414:     }
                   3415:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   3416:   for(h=1; h <=nhstepm; h++){
                   3417:     for(d=1; d <=hstepm; d++){
                   3418:       newm=savm;
                   3419:       /* Covariates have to be included here again */
                   3420:       cov[1]=1.;
1.214     brouard  3421:       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187     brouard  3422:       cov[2]=agexact;
1.319     brouard  3423:       if(nagesqr==1){
1.227     brouard  3424:        cov[3]= agexact*agexact;
1.319     brouard  3425:       }
1.235     brouard  3426:       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
1.319     brouard  3427: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                   3428:        /* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 */
                   3429: /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   3430: /*    k        1  2   3   4     5    6    7     8    9 */
                   3431: /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
                   3432: /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
                   3433: /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
                   3434: /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */
1.235     brouard  3435:        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
                   3436:        /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
                   3437:       }
                   3438:       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                   3439:        /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.319     brouard  3440:        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
1.235     brouard  3441:        /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
                   3442:       }
1.319     brouard  3443:       for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1*age +V4 +age*V3 */
                   3444:        /* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/
                   3445:        /* */
                   3446:        if(Dummy[Tage[k]]== 2){ /* dummy with age */
                   3447:        /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ */
1.235     brouard  3448:          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319     brouard  3449:        } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
                   3450:          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.235     brouard  3451:        }
                   3452:        /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
                   3453:       }
1.319     brouard  3454:       for (k=1; k<=cptcovprod;k++){ /*  For product without age */
1.235     brouard  3455:        /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
1.319     brouard  3456:        /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
                   3457:        if(Dummy[Tvard[k][1]==0]){
                   3458:          if(Dummy[Tvard[k][2]==0]){
                   3459:            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
                   3460:          }else{
                   3461:            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
                   3462:          }
                   3463:        }else{
                   3464:          if(Dummy[Tvard[k][2]==0]){
                   3465:            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
                   3466:          }else{
                   3467:            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
                   3468:          }
                   3469:        }
1.235     brouard  3470:       }
                   3471:       /* for (k=1; k<=cptcovn;k++)  */
                   3472:       /*       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
                   3473:       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
                   3474:       /*       cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
                   3475:       /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
                   3476:       /*       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227     brouard  3477:       
                   3478:       
1.126     brouard  3479:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   3480:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.319     brouard  3481:       /* right multiplication of oldm by the current matrix */
1.126     brouard  3482:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                   3483:                   pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217     brouard  3484:       /* if((int)age == 70){ */
                   3485:       /*       printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
                   3486:       /*       for(i=1; i<=nlstate+ndeath; i++) { */
                   3487:       /*         printf("%d pmmij ",i); */
                   3488:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3489:       /*           printf("%f ",pmmij[i][j]); */
                   3490:       /*         } */
                   3491:       /*         printf(" oldm "); */
                   3492:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3493:       /*           printf("%f ",oldm[i][j]); */
                   3494:       /*         } */
                   3495:       /*         printf("\n"); */
                   3496:       /*       } */
                   3497:       /* } */
1.126     brouard  3498:       savm=oldm;
                   3499:       oldm=newm;
                   3500:     }
                   3501:     for(i=1; i<=nlstate+ndeath; i++)
                   3502:       for(j=1;j<=nlstate+ndeath;j++) {
1.267     brouard  3503:        po[i][j][h]=newm[i][j];
                   3504:        /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126     brouard  3505:       }
1.128     brouard  3506:     /*printf("h=%d ",h);*/
1.126     brouard  3507:   } /* end h */
1.267     brouard  3508:   /*     printf("\n H=%d \n",h); */
1.126     brouard  3509:   return po;
                   3510: }
                   3511: 
1.217     brouard  3512: /************* Higher Back Matrix Product ***************/
1.218     brouard  3513: /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
1.267     brouard  3514: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
1.217     brouard  3515: {
1.266     brouard  3516:   /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217     brouard  3517:      'nhstepm*hstepm*stepm' months (i.e. until
1.218     brouard  3518:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
                   3519:      nhstepm*hstepm matrices.
                   3520:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
                   3521:      (typically every 2 years instead of every month which is too big
1.217     brouard  3522:      for the memory).
1.218     brouard  3523:      Model is determined by parameters x and covariates have to be
1.266     brouard  3524:      included manually here. Then we use a call to bmij(x and cov)
                   3525:      The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222     brouard  3526:   */
1.217     brouard  3527: 
                   3528:   int i, j, d, h, k;
1.266     brouard  3529:   double **out, cov[NCOVMAX+1], **bmij();
                   3530:   double **newm, ***newmm;
1.217     brouard  3531:   double agexact;
                   3532:   double agebegin, ageend;
1.222     brouard  3533:   double **oldm, **savm;
1.217     brouard  3534: 
1.266     brouard  3535:   newmm=po; /* To be saved */
                   3536:   oldm=oldms;savm=savms; /* Global pointers */
1.217     brouard  3537:   /* Hstepm could be zero and should return the unit matrix */
                   3538:   for (i=1;i<=nlstate+ndeath;i++)
                   3539:     for (j=1;j<=nlstate+ndeath;j++){
                   3540:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   3541:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   3542:     }
                   3543:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   3544:   for(h=1; h <=nhstepm; h++){
                   3545:     for(d=1; d <=hstepm; d++){
                   3546:       newm=savm;
                   3547:       /* Covariates have to be included here again */
                   3548:       cov[1]=1.;
1.271     brouard  3549:       agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217     brouard  3550:       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
1.318     brouard  3551:         /* Debug */
                   3552:       /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
1.217     brouard  3553:       cov[2]=agexact;
                   3554:       if(nagesqr==1)
1.222     brouard  3555:        cov[3]= agexact*agexact;
1.325     brouard  3556:       for (k=1; k<=nsd;k++){ /* For single dummy covariates only *//* cptcovn error */
1.266     brouard  3557:       /*       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
                   3558:       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
1.325     brouard  3559:        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];/* Bug valgrind */
1.266     brouard  3560:         /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
                   3561:       }
1.267     brouard  3562:       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                   3563:        /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
                   3564:        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
                   3565:        /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
                   3566:       }
1.319     brouard  3567:       for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 *//* For product with age */
                   3568:        /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!*\/ */
                   3569:        if(Dummy[Tage[k]]== 2){ /* dummy with age */
1.267     brouard  3570:          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319     brouard  3571:        } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
1.267     brouard  3572:          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
                   3573:        }
                   3574:        /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
                   3575:       }
                   3576:       for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222     brouard  3577:        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.325     brouard  3578:        if(Dummy[Tvard[k][1]==0]){
                   3579:          if(Dummy[Tvard[k][2]==0]){
                   3580:            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
                   3581:          }else{
                   3582:            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
                   3583:          }
                   3584:        }else{
                   3585:          if(Dummy[Tvard[k][2]==0]){
                   3586:            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
                   3587:          }else{
                   3588:            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
                   3589:          }
                   3590:        }
1.267     brouard  3591:       }                        
1.217     brouard  3592:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   3593:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267     brouard  3594: 
1.218     brouard  3595:       /* Careful transposed matrix */
1.266     brouard  3596:       /* age is in cov[2], prevacurrent at beginning of transition. */
1.218     brouard  3597:       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222     brouard  3598:       /*                                                1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218     brouard  3599:       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.325     brouard  3600:                   1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */
1.217     brouard  3601:       /* if((int)age == 70){ */
                   3602:       /*       printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
                   3603:       /*       for(i=1; i<=nlstate+ndeath; i++) { */
                   3604:       /*         printf("%d pmmij ",i); */
                   3605:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3606:       /*           printf("%f ",pmmij[i][j]); */
                   3607:       /*         } */
                   3608:       /*         printf(" oldm "); */
                   3609:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3610:       /*           printf("%f ",oldm[i][j]); */
                   3611:       /*         } */
                   3612:       /*         printf("\n"); */
                   3613:       /*       } */
                   3614:       /* } */
                   3615:       savm=oldm;
                   3616:       oldm=newm;
                   3617:     }
                   3618:     for(i=1; i<=nlstate+ndeath; i++)
                   3619:       for(j=1;j<=nlstate+ndeath;j++) {
1.222     brouard  3620:        po[i][j][h]=newm[i][j];
1.268     brouard  3621:        /* if(h==nhstepm) */
                   3622:        /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217     brouard  3623:       }
1.268     brouard  3624:     /* printf("h=%d %.1f ",h, agexact); */
1.217     brouard  3625:   } /* end h */
1.268     brouard  3626:   /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217     brouard  3627:   return po;
                   3628: }
                   3629: 
                   3630: 
1.162     brouard  3631: #ifdef NLOPT
                   3632:   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
                   3633:   double fret;
                   3634:   double *xt;
                   3635:   int j;
                   3636:   myfunc_data *d2 = (myfunc_data *) pd;
                   3637: /* xt = (p1-1); */
                   3638:   xt=vector(1,n); 
                   3639:   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
                   3640: 
                   3641:   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
                   3642:   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
                   3643:   printf("Function = %.12lf ",fret);
                   3644:   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
                   3645:   printf("\n");
                   3646:  free_vector(xt,1,n);
                   3647:   return fret;
                   3648: }
                   3649: #endif
1.126     brouard  3650: 
                   3651: /*************** log-likelihood *************/
                   3652: double func( double *x)
                   3653: {
1.226     brouard  3654:   int i, ii, j, k, mi, d, kk;
                   3655:   int ioffset=0;
                   3656:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
                   3657:   double **out;
                   3658:   double lli; /* Individual log likelihood */
                   3659:   int s1, s2;
1.228     brouard  3660:   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
1.226     brouard  3661:   double bbh, survp;
                   3662:   long ipmx;
                   3663:   double agexact;
                   3664:   /*extern weight */
                   3665:   /* We are differentiating ll according to initial status */
                   3666:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   3667:   /*for(i=1;i<imx;i++) 
                   3668:     printf(" %d\n",s[4][i]);
                   3669:   */
1.162     brouard  3670: 
1.226     brouard  3671:   ++countcallfunc;
1.162     brouard  3672: 
1.226     brouard  3673:   cov[1]=1.;
1.126     brouard  3674: 
1.226     brouard  3675:   for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224     brouard  3676:   ioffset=0;
1.226     brouard  3677:   if(mle==1){
                   3678:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3679:       /* Computes the values of the ncovmodel covariates of the model
                   3680:         depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
                   3681:         Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
                   3682:         to be observed in j being in i according to the model.
                   3683:       */
1.243     brouard  3684:       ioffset=2+nagesqr ;
1.233     brouard  3685:    /* Fixed */
1.319     brouard  3686:       for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */
                   3687:        /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
                   3688:         /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   3689:        /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
1.320     brouard  3690:         /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
1.319     brouard  3691:        cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
                   3692:        /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
1.234     brouard  3693:       }
1.226     brouard  3694:       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
1.319     brouard  3695:         is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6 
1.226     brouard  3696:         has been calculated etc */
                   3697:       /* For an individual i, wav[i] gives the number of effective waves */
                   3698:       /* We compute the contribution to Likelihood of each effective transition
                   3699:         mw[mi][i] is real wave of the mi th effectve wave */
                   3700:       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
                   3701:         s2=s[mw[mi+1][i]][i];
                   3702:         And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
                   3703:         But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
                   3704:         meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
                   3705:       */
                   3706:       for(mi=1; mi<= wav[i]-1; mi++){
1.319     brouard  3707:        for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
                   3708:          /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
1.242     brouard  3709:          cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234     brouard  3710:        }
                   3711:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3712:          for (j=1;j<=nlstate+ndeath;j++){
                   3713:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3714:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3715:          }
                   3716:        for(d=0; d<dh[mi][i]; d++){
                   3717:          newm=savm;
                   3718:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3719:          cov[2]=agexact;
                   3720:          if(nagesqr==1)
                   3721:            cov[3]= agexact*agexact;  /* Should be changed here */
                   3722:          for (kk=1; kk<=cptcovage;kk++) {
1.318     brouard  3723:            if(!FixedV[Tvar[Tage[kk]]])
                   3724:              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
                   3725:            else
                   3726:              cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234     brouard  3727:          }
                   3728:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3729:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3730:          savm=oldm;
                   3731:          oldm=newm;
                   3732:        } /* end mult */
                   3733:        
                   3734:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   3735:        /* But now since version 0.9 we anticipate for bias at large stepm.
                   3736:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   3737:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   3738:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   3739:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   3740:         * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                   3741:         * probability in order to take into account the bias as a fraction of the way
1.231     brouard  3742:                                 * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                   3743:                                 * -stepm/2 to stepm/2 .
                   3744:                                 * For stepm=1 the results are the same as for previous versions of Imach.
                   3745:                                 * For stepm > 1 the results are less biased than in previous versions. 
                   3746:                                 */
1.234     brouard  3747:        s1=s[mw[mi][i]][i];
                   3748:        s2=s[mw[mi+1][i]][i];
                   3749:        bbh=(double)bh[mi][i]/(double)stepm; 
                   3750:        /* bias bh is positive if real duration
                   3751:         * is higher than the multiple of stepm and negative otherwise.
                   3752:         */
                   3753:        /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                   3754:        if( s2 > nlstate){ 
                   3755:          /* i.e. if s2 is a death state and if the date of death is known 
                   3756:             then the contribution to the likelihood is the probability to 
                   3757:             die between last step unit time and current  step unit time, 
                   3758:             which is also equal to probability to die before dh 
                   3759:             minus probability to die before dh-stepm . 
                   3760:             In version up to 0.92 likelihood was computed
                   3761:             as if date of death was unknown. Death was treated as any other
                   3762:             health state: the date of the interview describes the actual state
                   3763:             and not the date of a change in health state. The former idea was
                   3764:             to consider that at each interview the state was recorded
                   3765:             (healthy, disable or death) and IMaCh was corrected; but when we
                   3766:             introduced the exact date of death then we should have modified
                   3767:             the contribution of an exact death to the likelihood. This new
                   3768:             contribution is smaller and very dependent of the step unit
                   3769:             stepm. It is no more the probability to die between last interview
                   3770:             and month of death but the probability to survive from last
                   3771:             interview up to one month before death multiplied by the
                   3772:             probability to die within a month. Thanks to Chris
                   3773:             Jackson for correcting this bug.  Former versions increased
                   3774:             mortality artificially. The bad side is that we add another loop
                   3775:             which slows down the processing. The difference can be up to 10%
                   3776:             lower mortality.
                   3777:          */
                   3778:          /* If, at the beginning of the maximization mostly, the
                   3779:             cumulative probability or probability to be dead is
                   3780:             constant (ie = 1) over time d, the difference is equal to
                   3781:             0.  out[s1][3] = savm[s1][3]: probability, being at state
                   3782:             s1 at precedent wave, to be dead a month before current
                   3783:             wave is equal to probability, being at state s1 at
                   3784:             precedent wave, to be dead at mont of the current
                   3785:             wave. Then the observed probability (that this person died)
                   3786:             is null according to current estimated parameter. In fact,
                   3787:             it should be very low but not zero otherwise the log go to
                   3788:             infinity.
                   3789:          */
1.183     brouard  3790: /* #ifdef INFINITYORIGINAL */
                   3791: /*         lli=log(out[s1][s2] - savm[s1][s2]); */
                   3792: /* #else */
                   3793: /*       if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
                   3794: /*         lli=log(mytinydouble); */
                   3795: /*       else */
                   3796: /*         lli=log(out[s1][s2] - savm[s1][s2]); */
                   3797: /* #endif */
1.226     brouard  3798:          lli=log(out[s1][s2] - savm[s1][s2]);
1.216     brouard  3799:          
1.226     brouard  3800:        } else if  ( s2==-1 ) { /* alive */
                   3801:          for (j=1,survp=0. ; j<=nlstate; j++) 
                   3802:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   3803:          /*survp += out[s1][j]; */
                   3804:          lli= log(survp);
                   3805:        }
                   3806:        else if  (s2==-4) { 
                   3807:          for (j=3,survp=0. ; j<=nlstate; j++)  
                   3808:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   3809:          lli= log(survp); 
                   3810:        } 
                   3811:        else if  (s2==-5) { 
                   3812:          for (j=1,survp=0. ; j<=2; j++)  
                   3813:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   3814:          lli= log(survp); 
                   3815:        } 
                   3816:        else{
                   3817:          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   3818:          /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                   3819:        } 
                   3820:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   3821:        /*if(lli ==000.0)*/
                   3822:        /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                   3823:        ipmx +=1;
                   3824:        sw += weight[i];
                   3825:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3826:        /* if (lli < log(mytinydouble)){ */
                   3827:        /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
                   3828:        /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
                   3829:        /* } */
                   3830:       } /* end of wave */
                   3831:     } /* end of individual */
                   3832:   }  else if(mle==2){
                   3833:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.319     brouard  3834:       ioffset=2+nagesqr ;
                   3835:       for (k=1; k<=ncovf;k++)
                   3836:        cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
1.226     brouard  3837:       for(mi=1; mi<= wav[i]-1; mi++){
1.319     brouard  3838:        for(k=1; k <= ncovv ; k++){
                   3839:          cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
                   3840:        }
1.226     brouard  3841:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3842:          for (j=1;j<=nlstate+ndeath;j++){
                   3843:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3844:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3845:          }
                   3846:        for(d=0; d<=dh[mi][i]; d++){
                   3847:          newm=savm;
                   3848:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3849:          cov[2]=agexact;
                   3850:          if(nagesqr==1)
                   3851:            cov[3]= agexact*agexact;
                   3852:          for (kk=1; kk<=cptcovage;kk++) {
                   3853:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3854:          }
                   3855:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3856:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3857:          savm=oldm;
                   3858:          oldm=newm;
                   3859:        } /* end mult */
                   3860:       
                   3861:        s1=s[mw[mi][i]][i];
                   3862:        s2=s[mw[mi+1][i]][i];
                   3863:        bbh=(double)bh[mi][i]/(double)stepm; 
                   3864:        lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                   3865:        ipmx +=1;
                   3866:        sw += weight[i];
                   3867:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3868:       } /* end of wave */
                   3869:     } /* end of individual */
                   3870:   }  else if(mle==3){  /* exponential inter-extrapolation */
                   3871:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3872:       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   3873:       for(mi=1; mi<= wav[i]-1; mi++){
                   3874:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3875:          for (j=1;j<=nlstate+ndeath;j++){
                   3876:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3877:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3878:          }
                   3879:        for(d=0; d<dh[mi][i]; d++){
                   3880:          newm=savm;
                   3881:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3882:          cov[2]=agexact;
                   3883:          if(nagesqr==1)
                   3884:            cov[3]= agexact*agexact;
                   3885:          for (kk=1; kk<=cptcovage;kk++) {
                   3886:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3887:          }
                   3888:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3889:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3890:          savm=oldm;
                   3891:          oldm=newm;
                   3892:        } /* end mult */
                   3893:       
                   3894:        s1=s[mw[mi][i]][i];
                   3895:        s2=s[mw[mi+1][i]][i];
                   3896:        bbh=(double)bh[mi][i]/(double)stepm; 
                   3897:        lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
                   3898:        ipmx +=1;
                   3899:        sw += weight[i];
                   3900:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3901:       } /* end of wave */
                   3902:     } /* end of individual */
                   3903:   }else if (mle==4){  /* ml=4 no inter-extrapolation */
                   3904:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3905:       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   3906:       for(mi=1; mi<= wav[i]-1; mi++){
                   3907:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3908:          for (j=1;j<=nlstate+ndeath;j++){
                   3909:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3910:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3911:          }
                   3912:        for(d=0; d<dh[mi][i]; d++){
                   3913:          newm=savm;
                   3914:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3915:          cov[2]=agexact;
                   3916:          if(nagesqr==1)
                   3917:            cov[3]= agexact*agexact;
                   3918:          for (kk=1; kk<=cptcovage;kk++) {
                   3919:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3920:          }
1.126     brouard  3921:        
1.226     brouard  3922:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3923:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3924:          savm=oldm;
                   3925:          oldm=newm;
                   3926:        } /* end mult */
                   3927:       
                   3928:        s1=s[mw[mi][i]][i];
                   3929:        s2=s[mw[mi+1][i]][i];
                   3930:        if( s2 > nlstate){ 
                   3931:          lli=log(out[s1][s2] - savm[s1][s2]);
                   3932:        } else if  ( s2==-1 ) { /* alive */
                   3933:          for (j=1,survp=0. ; j<=nlstate; j++) 
                   3934:            survp += out[s1][j];
                   3935:          lli= log(survp);
                   3936:        }else{
                   3937:          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   3938:        }
                   3939:        ipmx +=1;
                   3940:        sw += weight[i];
                   3941:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126     brouard  3942: /*     printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.226     brouard  3943:       } /* end of wave */
                   3944:     } /* end of individual */
                   3945:   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                   3946:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3947:       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   3948:       for(mi=1; mi<= wav[i]-1; mi++){
                   3949:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3950:          for (j=1;j<=nlstate+ndeath;j++){
                   3951:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3952:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3953:          }
                   3954:        for(d=0; d<dh[mi][i]; d++){
                   3955:          newm=savm;
                   3956:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3957:          cov[2]=agexact;
                   3958:          if(nagesqr==1)
                   3959:            cov[3]= agexact*agexact;
                   3960:          for (kk=1; kk<=cptcovage;kk++) {
                   3961:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3962:          }
1.126     brouard  3963:        
1.226     brouard  3964:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3965:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3966:          savm=oldm;
                   3967:          oldm=newm;
                   3968:        } /* end mult */
                   3969:       
                   3970:        s1=s[mw[mi][i]][i];
                   3971:        s2=s[mw[mi+1][i]][i];
                   3972:        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   3973:        ipmx +=1;
                   3974:        sw += weight[i];
                   3975:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3976:        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
                   3977:       } /* end of wave */
                   3978:     } /* end of individual */
                   3979:   } /* End of if */
                   3980:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   3981:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   3982:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   3983:   return -l;
1.126     brouard  3984: }
                   3985: 
                   3986: /*************** log-likelihood *************/
                   3987: double funcone( double *x)
                   3988: {
1.228     brouard  3989:   /* Same as func but slower because of a lot of printf and if */
1.126     brouard  3990:   int i, ii, j, k, mi, d, kk;
1.228     brouard  3991:   int ioffset=0;
1.131     brouard  3992:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126     brouard  3993:   double **out;
                   3994:   double lli; /* Individual log likelihood */
                   3995:   double llt;
                   3996:   int s1, s2;
1.228     brouard  3997:   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
                   3998: 
1.126     brouard  3999:   double bbh, survp;
1.187     brouard  4000:   double agexact;
1.214     brouard  4001:   double agebegin, ageend;
1.126     brouard  4002:   /*extern weight */
                   4003:   /* We are differentiating ll according to initial status */
                   4004:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   4005:   /*for(i=1;i<imx;i++) 
                   4006:     printf(" %d\n",s[4][i]);
                   4007:   */
                   4008:   cov[1]=1.;
                   4009: 
                   4010:   for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224     brouard  4011:   ioffset=0;
                   4012:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243     brouard  4013:     /* ioffset=2+nagesqr+cptcovage; */
                   4014:     ioffset=2+nagesqr;
1.232     brouard  4015:     /* Fixed */
1.224     brouard  4016:     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232     brouard  4017:     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
1.311     brouard  4018:     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
1.232     brouard  4019:       cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
                   4020: /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
                   4021: /*    cov[2+6]=covar[Tvar[6]][i];  */
                   4022: /*    cov[2+6]=covar[2][i]; V2  */
                   4023: /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
                   4024: /*    cov[2+7]=covar[Tvar[7]][i];  */
                   4025: /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
                   4026: /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
                   4027: /*    cov[2+9]=covar[Tvar[9]][i];  */
                   4028: /*    cov[2+9]=covar[1][i]; V1  */
1.225     brouard  4029:     }
1.232     brouard  4030:     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
                   4031:     /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
                   4032:     /* } */
1.231     brouard  4033:     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
                   4034:     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
                   4035:     /* } */
1.225     brouard  4036:     
1.233     brouard  4037: 
                   4038:     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
1.232     brouard  4039:     /* Wave varying (but not age varying) */
                   4040:       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
1.242     brouard  4041:        /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
                   4042:        cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
                   4043:       }
1.232     brouard  4044:       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242     brouard  4045:       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
                   4046:       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
                   4047:       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
                   4048:       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
                   4049:       /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
1.232     brouard  4050:       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242     brouard  4051:       /*       iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
                   4052:       /*       /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
                   4053:       /*       cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232     brouard  4054:       /* } */
1.126     brouard  4055:       for (ii=1;ii<=nlstate+ndeath;ii++)
1.242     brouard  4056:        for (j=1;j<=nlstate+ndeath;j++){
                   4057:          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   4058:          savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   4059:        }
1.214     brouard  4060:       
                   4061:       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
                   4062:       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
                   4063:       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
1.247     brouard  4064:       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242     brouard  4065:        /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   4066:          and mw[mi+1][i]. dh depends on stepm.*/
                   4067:        newm=savm;
1.247     brouard  4068:        agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
1.242     brouard  4069:        cov[2]=agexact;
                   4070:        if(nagesqr==1)
                   4071:          cov[3]= agexact*agexact;
                   4072:        for (kk=1; kk<=cptcovage;kk++) {
                   4073:          if(!FixedV[Tvar[Tage[kk]]])
                   4074:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   4075:          else
                   4076:            cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
                   4077:        }
                   4078:        /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
                   4079:        /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   4080:        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   4081:                     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   4082:        /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                   4083:        /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
                   4084:        savm=oldm;
                   4085:        oldm=newm;
1.126     brouard  4086:       } /* end mult */
                   4087:       
                   4088:       s1=s[mw[mi][i]][i];
                   4089:       s2=s[mw[mi+1][i]][i];
1.217     brouard  4090:       /* if(s2==-1){ */
1.268     brouard  4091:       /*       printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217     brouard  4092:       /*       /\* exit(1); *\/ */
                   4093:       /* } */
1.126     brouard  4094:       bbh=(double)bh[mi][i]/(double)stepm; 
                   4095:       /* bias is positive if real duration
                   4096:        * is higher than the multiple of stepm and negative otherwise.
                   4097:        */
                   4098:       if( s2 > nlstate && (mle <5) ){  /* Jackson */
1.242     brouard  4099:        lli=log(out[s1][s2] - savm[s1][s2]);
1.216     brouard  4100:       } else if  ( s2==-1 ) { /* alive */
1.242     brouard  4101:        for (j=1,survp=0. ; j<=nlstate; j++) 
                   4102:          survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   4103:        lli= log(survp);
1.126     brouard  4104:       }else if (mle==1){
1.242     brouard  4105:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126     brouard  4106:       } else if(mle==2){
1.242     brouard  4107:        lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.126     brouard  4108:       } else if(mle==3){  /* exponential inter-extrapolation */
1.242     brouard  4109:        lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.126     brouard  4110:       } else if (mle==4){  /* mle=4 no inter-extrapolation */
1.242     brouard  4111:        lli=log(out[s1][s2]); /* Original formula */
1.136     brouard  4112:       } else{  /* mle=0 back to 1 */
1.242     brouard  4113:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   4114:        /*lli=log(out[s1][s2]); */ /* Original formula */
1.126     brouard  4115:       } /* End of if */
                   4116:       ipmx +=1;
                   4117:       sw += weight[i];
                   4118:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132     brouard  4119:       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.126     brouard  4120:       if(globpr){
1.246     brouard  4121:        fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126     brouard  4122:  %11.6f %11.6f %11.6f ", \
1.242     brouard  4123:                num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.268     brouard  4124:                2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242     brouard  4125:        for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   4126:          llt +=ll[k]*gipmx/gsw;
                   4127:          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                   4128:        }
                   4129:        fprintf(ficresilk," %10.6f\n", -llt);
1.126     brouard  4130:       }
1.232     brouard  4131:        } /* end of wave */
                   4132: } /* end of individual */
                   4133: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   4134: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   4135: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   4136: if(globpr==0){ /* First time we count the contributions and weights */
                   4137:        gipmx=ipmx;
                   4138:        gsw=sw;
                   4139: }
                   4140: return -l;
1.126     brouard  4141: }
                   4142: 
                   4143: 
                   4144: /*************** function likelione ***********/
1.292     brouard  4145: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126     brouard  4146: {
                   4147:   /* This routine should help understanding what is done with 
                   4148:      the selection of individuals/waves and
                   4149:      to check the exact contribution to the likelihood.
                   4150:      Plotting could be done.
                   4151:    */
                   4152:   int k;
                   4153: 
                   4154:   if(*globpri !=0){ /* Just counts and sums, no printings */
1.201     brouard  4155:     strcpy(fileresilk,"ILK_"); 
1.202     brouard  4156:     strcat(fileresilk,fileresu);
1.126     brouard  4157:     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                   4158:       printf("Problem with resultfile: %s\n", fileresilk);
                   4159:       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
                   4160:     }
1.214     brouard  4161:     fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
                   4162:     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126     brouard  4163:     /*         i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                   4164:     for(k=1; k<=nlstate; k++) 
                   4165:       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                   4166:     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
                   4167:   }
                   4168: 
1.292     brouard  4169:   *fretone=(*func)(p);
1.126     brouard  4170:   if(*globpri !=0){
                   4171:     fclose(ficresilk);
1.205     brouard  4172:     if (mle ==0)
                   4173:       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
                   4174:     else if(mle >=1)
                   4175:       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
                   4176:     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.274     brouard  4177:     fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model); 
1.208     brouard  4178:       
                   4179:     for (k=1; k<= nlstate ; k++) {
1.211     brouard  4180:       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
1.208     brouard  4181: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
                   4182:     }
1.207     brouard  4183:     fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
1.204     brouard  4184: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207     brouard  4185:     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204     brouard  4186: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207     brouard  4187:     fflush(fichtm);
1.205     brouard  4188:   }
1.126     brouard  4189:   return;
                   4190: }
                   4191: 
                   4192: 
                   4193: /*********** Maximum Likelihood Estimation ***************/
                   4194: 
                   4195: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                   4196: {
1.319     brouard  4197:   int i,j,k, jk, jkk=0, iter=0;
1.126     brouard  4198:   double **xi;
                   4199:   double fret;
                   4200:   double fretone; /* Only one call to likelihood */
                   4201:   /*  char filerespow[FILENAMELENGTH];*/
1.162     brouard  4202: 
                   4203: #ifdef NLOPT
                   4204:   int creturn;
                   4205:   nlopt_opt opt;
                   4206:   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
                   4207:   double *lb;
                   4208:   double minf; /* the minimum objective value, upon return */
                   4209:   double * p1; /* Shifted parameters from 0 instead of 1 */
                   4210:   myfunc_data dinst, *d = &dinst;
                   4211: #endif
                   4212: 
                   4213: 
1.126     brouard  4214:   xi=matrix(1,npar,1,npar);
                   4215:   for (i=1;i<=npar;i++)
                   4216:     for (j=1;j<=npar;j++)
                   4217:       xi[i][j]=(i==j ? 1.0 : 0.0);
                   4218:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.201     brouard  4219:   strcpy(filerespow,"POW_"); 
1.126     brouard  4220:   strcat(filerespow,fileres);
                   4221:   if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   4222:     printf("Problem with resultfile: %s\n", filerespow);
                   4223:     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   4224:   }
                   4225:   fprintf(ficrespow,"# Powell\n# iter -2*LL");
                   4226:   for (i=1;i<=nlstate;i++)
                   4227:     for(j=1;j<=nlstate+ndeath;j++)
                   4228:       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   4229:   fprintf(ficrespow,"\n");
1.162     brouard  4230: #ifdef POWELL
1.319     brouard  4231: #ifdef LINMINORIGINAL
                   4232: #else /* LINMINORIGINAL */
                   4233:   
                   4234:   flatdir=ivector(1,npar); 
                   4235:   for (j=1;j<=npar;j++) flatdir[j]=0; 
                   4236: #endif /*LINMINORIGINAL */
                   4237: 
                   4238: #ifdef FLATSUP
                   4239:   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
                   4240:   /* reorganizing p by suppressing flat directions */
                   4241:   for(i=1, jk=1; i <=nlstate; i++){
                   4242:     for(k=1; k <=(nlstate+ndeath); k++){
                   4243:       if (k != i) {
                   4244:         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
                   4245:         if(flatdir[jk]==1){
                   4246:           printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
                   4247:         }
                   4248:         for(j=1; j <=ncovmodel; j++){
                   4249:           printf("%12.7f ",p[jk]);
                   4250:           jk++; 
                   4251:         }
                   4252:         printf("\n");
                   4253:       }
                   4254:     }
                   4255:   }
                   4256: /* skipping */
                   4257:   /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
                   4258:   for(i=1, jk=1, jkk=1;i <=nlstate; i++){
                   4259:     for(k=1; k <=(nlstate+ndeath); k++){
                   4260:       if (k != i) {
                   4261:         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
                   4262:         if(flatdir[jk]==1){
                   4263:           printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
                   4264:           for(j=1; j <=ncovmodel;  jk++,j++){
                   4265:             printf(" p[%d]=%12.7f",jk, p[jk]);
                   4266:             /*q[jjk]=p[jk];*/
                   4267:           }
                   4268:         }else{
                   4269:           printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
                   4270:           for(j=1; j <=ncovmodel;  jk++,jkk++,j++){
                   4271:             printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
                   4272:             /*q[jjk]=p[jk];*/
                   4273:           }
                   4274:         }
                   4275:         printf("\n");
                   4276:       }
                   4277:       fflush(stdout);
                   4278:     }
                   4279:   }
                   4280:   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
                   4281: #else  /* FLATSUP */
1.126     brouard  4282:   powell(p,xi,npar,ftol,&iter,&fret,func);
1.319     brouard  4283: #endif  /* FLATSUP */
                   4284: 
                   4285: #ifdef LINMINORIGINAL
                   4286: #else
                   4287:       free_ivector(flatdir,1,npar); 
                   4288: #endif  /* LINMINORIGINAL*/
                   4289: #endif /* POWELL */
1.126     brouard  4290: 
1.162     brouard  4291: #ifdef NLOPT
                   4292: #ifdef NEWUOA
                   4293:   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
                   4294: #else
                   4295:   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
                   4296: #endif
                   4297:   lb=vector(0,npar-1);
                   4298:   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
                   4299:   nlopt_set_lower_bounds(opt, lb);
                   4300:   nlopt_set_initial_step1(opt, 0.1);
                   4301:   
                   4302:   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
                   4303:   d->function = func;
                   4304:   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
                   4305:   nlopt_set_min_objective(opt, myfunc, d);
                   4306:   nlopt_set_xtol_rel(opt, ftol);
                   4307:   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
                   4308:     printf("nlopt failed! %d\n",creturn); 
                   4309:   }
                   4310:   else {
                   4311:     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
                   4312:     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
                   4313:     iter=1; /* not equal */
                   4314:   }
                   4315:   nlopt_destroy(opt);
                   4316: #endif
1.319     brouard  4317: #ifdef FLATSUP
                   4318:   /* npared = npar -flatd/ncovmodel; */
                   4319:   /* xired= matrix(1,npared,1,npared); */
                   4320:   /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
                   4321:   /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
                   4322:   /* free_matrix(xire,1,npared,1,npared); */
                   4323: #else  /* FLATSUP */
                   4324: #endif /* FLATSUP */
1.126     brouard  4325:   free_matrix(xi,1,npar,1,npar);
                   4326:   fclose(ficrespow);
1.203     brouard  4327:   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   4328:   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180     brouard  4329:   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126     brouard  4330: 
                   4331: }
                   4332: 
                   4333: /**** Computes Hessian and covariance matrix ***/
1.203     brouard  4334: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126     brouard  4335: {
                   4336:   double  **a,**y,*x,pd;
1.203     brouard  4337:   /* double **hess; */
1.164     brouard  4338:   int i, j;
1.126     brouard  4339:   int *indx;
                   4340: 
                   4341:   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203     brouard  4342:   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126     brouard  4343:   void lubksb(double **a, int npar, int *indx, double b[]) ;
                   4344:   void ludcmp(double **a, int npar, int *indx, double *d) ;
                   4345:   double gompertz(double p[]);
1.203     brouard  4346:   /* hess=matrix(1,npar,1,npar); */
1.126     brouard  4347: 
                   4348:   printf("\nCalculation of the hessian matrix. Wait...\n");
                   4349:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                   4350:   for (i=1;i<=npar;i++){
1.203     brouard  4351:     printf("%d-",i);fflush(stdout);
                   4352:     fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126     brouard  4353:    
                   4354:      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                   4355:     
                   4356:     /*  printf(" %f ",p[i]);
                   4357:        printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
                   4358:   }
                   4359:   
                   4360:   for (i=1;i<=npar;i++) {
                   4361:     for (j=1;j<=npar;j++)  {
                   4362:       if (j>i) { 
1.203     brouard  4363:        printf(".%d-%d",i,j);fflush(stdout);
                   4364:        fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
                   4365:        hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126     brouard  4366:        
                   4367:        hess[j][i]=hess[i][j];    
                   4368:        /*printf(" %lf ",hess[i][j]);*/
                   4369:       }
                   4370:     }
                   4371:   }
                   4372:   printf("\n");
                   4373:   fprintf(ficlog,"\n");
                   4374: 
                   4375:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
                   4376:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                   4377:   
                   4378:   a=matrix(1,npar,1,npar);
                   4379:   y=matrix(1,npar,1,npar);
                   4380:   x=vector(1,npar);
                   4381:   indx=ivector(1,npar);
                   4382:   for (i=1;i<=npar;i++)
                   4383:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   4384:   ludcmp(a,npar,indx,&pd);
                   4385: 
                   4386:   for (j=1;j<=npar;j++) {
                   4387:     for (i=1;i<=npar;i++) x[i]=0;
                   4388:     x[j]=1;
                   4389:     lubksb(a,npar,indx,x);
                   4390:     for (i=1;i<=npar;i++){ 
                   4391:       matcov[i][j]=x[i];
                   4392:     }
                   4393:   }
                   4394: 
                   4395:   printf("\n#Hessian matrix#\n");
                   4396:   fprintf(ficlog,"\n#Hessian matrix#\n");
                   4397:   for (i=1;i<=npar;i++) { 
                   4398:     for (j=1;j<=npar;j++) { 
1.203     brouard  4399:       printf("%.6e ",hess[i][j]);
                   4400:       fprintf(ficlog,"%.6e ",hess[i][j]);
1.126     brouard  4401:     }
                   4402:     printf("\n");
                   4403:     fprintf(ficlog,"\n");
                   4404:   }
                   4405: 
1.203     brouard  4406:   /* printf("\n#Covariance matrix#\n"); */
                   4407:   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
                   4408:   /* for (i=1;i<=npar;i++) {  */
                   4409:   /*   for (j=1;j<=npar;j++) {  */
                   4410:   /*     printf("%.6e ",matcov[i][j]); */
                   4411:   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
                   4412:   /*   } */
                   4413:   /*   printf("\n"); */
                   4414:   /*   fprintf(ficlog,"\n"); */
                   4415:   /* } */
                   4416: 
1.126     brouard  4417:   /* Recompute Inverse */
1.203     brouard  4418:   /* for (i=1;i<=npar;i++) */
                   4419:   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
                   4420:   /* ludcmp(a,npar,indx,&pd); */
                   4421: 
                   4422:   /*  printf("\n#Hessian matrix recomputed#\n"); */
                   4423: 
                   4424:   /* for (j=1;j<=npar;j++) { */
                   4425:   /*   for (i=1;i<=npar;i++) x[i]=0; */
                   4426:   /*   x[j]=1; */
                   4427:   /*   lubksb(a,npar,indx,x); */
                   4428:   /*   for (i=1;i<=npar;i++){  */
                   4429:   /*     y[i][j]=x[i]; */
                   4430:   /*     printf("%.3e ",y[i][j]); */
                   4431:   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
                   4432:   /*   } */
                   4433:   /*   printf("\n"); */
                   4434:   /*   fprintf(ficlog,"\n"); */
                   4435:   /* } */
                   4436: 
                   4437:   /* Verifying the inverse matrix */
                   4438: #ifdef DEBUGHESS
                   4439:   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126     brouard  4440: 
1.203     brouard  4441:    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
                   4442:    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126     brouard  4443: 
                   4444:   for (j=1;j<=npar;j++) {
                   4445:     for (i=1;i<=npar;i++){ 
1.203     brouard  4446:       printf("%.2f ",y[i][j]);
                   4447:       fprintf(ficlog,"%.2f ",y[i][j]);
1.126     brouard  4448:     }
                   4449:     printf("\n");
                   4450:     fprintf(ficlog,"\n");
                   4451:   }
1.203     brouard  4452: #endif
1.126     brouard  4453: 
                   4454:   free_matrix(a,1,npar,1,npar);
                   4455:   free_matrix(y,1,npar,1,npar);
                   4456:   free_vector(x,1,npar);
                   4457:   free_ivector(indx,1,npar);
1.203     brouard  4458:   /* free_matrix(hess,1,npar,1,npar); */
1.126     brouard  4459: 
                   4460: 
                   4461: }
                   4462: 
                   4463: /*************** hessian matrix ****************/
                   4464: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203     brouard  4465: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126     brouard  4466:   int i;
                   4467:   int l=1, lmax=20;
1.203     brouard  4468:   double k1,k2, res, fx;
1.132     brouard  4469:   double p2[MAXPARM+1]; /* identical to x */
1.126     brouard  4470:   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   4471:   int k=0,kmax=10;
                   4472:   double l1;
                   4473: 
                   4474:   fx=func(x);
                   4475:   for (i=1;i<=npar;i++) p2[i]=x[i];
1.145     brouard  4476:   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
1.126     brouard  4477:     l1=pow(10,l);
                   4478:     delts=delt;
                   4479:     for(k=1 ; k <kmax; k=k+1){
                   4480:       delt = delta*(l1*k);
                   4481:       p2[theta]=x[theta] +delt;
1.145     brouard  4482:       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
1.126     brouard  4483:       p2[theta]=x[theta]-delt;
                   4484:       k2=func(p2)-fx;
                   4485:       /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203     brouard  4486:       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126     brouard  4487:       
1.203     brouard  4488: #ifdef DEBUGHESSII
1.126     brouard  4489:       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                   4490:       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                   4491: #endif
                   4492:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                   4493:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   4494:        k=kmax;
                   4495:       }
                   4496:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164     brouard  4497:        k=kmax; l=lmax*10;
1.126     brouard  4498:       }
                   4499:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                   4500:        delts=delt;
                   4501:       }
1.203     brouard  4502:     } /* End loop k */
1.126     brouard  4503:   }
                   4504:   delti[theta]=delts;
                   4505:   return res; 
                   4506:   
                   4507: }
                   4508: 
1.203     brouard  4509: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126     brouard  4510: {
                   4511:   int i;
1.164     brouard  4512:   int l=1, lmax=20;
1.126     brouard  4513:   double k1,k2,k3,k4,res,fx;
1.132     brouard  4514:   double p2[MAXPARM+1];
1.203     brouard  4515:   int k, kmax=1;
                   4516:   double v1, v2, cv12, lc1, lc2;
1.208     brouard  4517: 
                   4518:   int firstime=0;
1.203     brouard  4519:   
1.126     brouard  4520:   fx=func(x);
1.203     brouard  4521:   for (k=1; k<=kmax; k=k+10) {
1.126     brouard  4522:     for (i=1;i<=npar;i++) p2[i]=x[i];
1.203     brouard  4523:     p2[thetai]=x[thetai]+delti[thetai]*k;
                   4524:     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126     brouard  4525:     k1=func(p2)-fx;
                   4526:   
1.203     brouard  4527:     p2[thetai]=x[thetai]+delti[thetai]*k;
                   4528:     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126     brouard  4529:     k2=func(p2)-fx;
                   4530:   
1.203     brouard  4531:     p2[thetai]=x[thetai]-delti[thetai]*k;
                   4532:     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126     brouard  4533:     k3=func(p2)-fx;
                   4534:   
1.203     brouard  4535:     p2[thetai]=x[thetai]-delti[thetai]*k;
                   4536:     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126     brouard  4537:     k4=func(p2)-fx;
1.203     brouard  4538:     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
                   4539:     if(k1*k2*k3*k4 <0.){
1.208     brouard  4540:       firstime=1;
1.203     brouard  4541:       kmax=kmax+10;
1.208     brouard  4542:     }
                   4543:     if(kmax >=10 || firstime ==1){
1.246     brouard  4544:       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
                   4545:       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
1.203     brouard  4546:       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                   4547:       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                   4548:     }
                   4549: #ifdef DEBUGHESSIJ
                   4550:     v1=hess[thetai][thetai];
                   4551:     v2=hess[thetaj][thetaj];
                   4552:     cv12=res;
                   4553:     /* Computing eigen value of Hessian matrix */
                   4554:     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   4555:     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   4556:     if ((lc2 <0) || (lc1 <0) ){
                   4557:       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
                   4558:       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
                   4559:       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                   4560:       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                   4561:     }
1.126     brouard  4562: #endif
                   4563:   }
                   4564:   return res;
                   4565: }
                   4566: 
1.203     brouard  4567:     /* Not done yet: Was supposed to fix if not exactly at the maximum */
                   4568: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
                   4569: /* { */
                   4570: /*   int i; */
                   4571: /*   int l=1, lmax=20; */
                   4572: /*   double k1,k2,k3,k4,res,fx; */
                   4573: /*   double p2[MAXPARM+1]; */
                   4574: /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
                   4575: /*   int k=0,kmax=10; */
                   4576: /*   double l1; */
                   4577:   
                   4578: /*   fx=func(x); */
                   4579: /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
                   4580: /*     l1=pow(10,l); */
                   4581: /*     delts=delt; */
                   4582: /*     for(k=1 ; k <kmax; k=k+1){ */
                   4583: /*       delt = delti*(l1*k); */
                   4584: /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
                   4585: /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
                   4586: /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
                   4587: /*       k1=func(p2)-fx; */
                   4588:       
                   4589: /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
                   4590: /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
                   4591: /*       k2=func(p2)-fx; */
                   4592:       
                   4593: /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
                   4594: /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
                   4595: /*       k3=func(p2)-fx; */
                   4596:       
                   4597: /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
                   4598: /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
                   4599: /*       k4=func(p2)-fx; */
                   4600: /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
                   4601: /* #ifdef DEBUGHESSIJ */
                   4602: /*       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
                   4603: /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
                   4604: /* #endif */
                   4605: /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
                   4606: /*     k=kmax; */
                   4607: /*       } */
                   4608: /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
                   4609: /*     k=kmax; l=lmax*10; */
                   4610: /*       } */
                   4611: /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
                   4612: /*     delts=delt; */
                   4613: /*       } */
                   4614: /*     } /\* End loop k *\/ */
                   4615: /*   } */
                   4616: /*   delti[theta]=delts; */
                   4617: /*   return res;  */
                   4618: /* } */
                   4619: 
                   4620: 
1.126     brouard  4621: /************** Inverse of matrix **************/
                   4622: void ludcmp(double **a, int n, int *indx, double *d) 
                   4623: { 
                   4624:   int i,imax,j,k; 
                   4625:   double big,dum,sum,temp; 
                   4626:   double *vv; 
                   4627:  
                   4628:   vv=vector(1,n); 
                   4629:   *d=1.0; 
                   4630:   for (i=1;i<=n;i++) { 
                   4631:     big=0.0; 
                   4632:     for (j=1;j<=n;j++) 
                   4633:       if ((temp=fabs(a[i][j])) > big) big=temp; 
1.256     brouard  4634:     if (big == 0.0){
                   4635:       printf(" Singular Hessian matrix at row %d:\n",i);
                   4636:       for (j=1;j<=n;j++) {
                   4637:        printf(" a[%d][%d]=%f,",i,j,a[i][j]);
                   4638:        fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
                   4639:       }
                   4640:       fflush(ficlog);
                   4641:       fclose(ficlog);
                   4642:       nrerror("Singular matrix in routine ludcmp"); 
                   4643:     }
1.126     brouard  4644:     vv[i]=1.0/big; 
                   4645:   } 
                   4646:   for (j=1;j<=n;j++) { 
                   4647:     for (i=1;i<j;i++) { 
                   4648:       sum=a[i][j]; 
                   4649:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                   4650:       a[i][j]=sum; 
                   4651:     } 
                   4652:     big=0.0; 
                   4653:     for (i=j;i<=n;i++) { 
                   4654:       sum=a[i][j]; 
                   4655:       for (k=1;k<j;k++) 
                   4656:        sum -= a[i][k]*a[k][j]; 
                   4657:       a[i][j]=sum; 
                   4658:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   4659:        big=dum; 
                   4660:        imax=i; 
                   4661:       } 
                   4662:     } 
                   4663:     if (j != imax) { 
                   4664:       for (k=1;k<=n;k++) { 
                   4665:        dum=a[imax][k]; 
                   4666:        a[imax][k]=a[j][k]; 
                   4667:        a[j][k]=dum; 
                   4668:       } 
                   4669:       *d = -(*d); 
                   4670:       vv[imax]=vv[j]; 
                   4671:     } 
                   4672:     indx[j]=imax; 
                   4673:     if (a[j][j] == 0.0) a[j][j]=TINY; 
                   4674:     if (j != n) { 
                   4675:       dum=1.0/(a[j][j]); 
                   4676:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                   4677:     } 
                   4678:   } 
                   4679:   free_vector(vv,1,n);  /* Doesn't work */
                   4680: ;
                   4681: } 
                   4682: 
                   4683: void lubksb(double **a, int n, int *indx, double b[]) 
                   4684: { 
                   4685:   int i,ii=0,ip,j; 
                   4686:   double sum; 
                   4687:  
                   4688:   for (i=1;i<=n;i++) { 
                   4689:     ip=indx[i]; 
                   4690:     sum=b[ip]; 
                   4691:     b[ip]=b[i]; 
                   4692:     if (ii) 
                   4693:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                   4694:     else if (sum) ii=i; 
                   4695:     b[i]=sum; 
                   4696:   } 
                   4697:   for (i=n;i>=1;i--) { 
                   4698:     sum=b[i]; 
                   4699:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   4700:     b[i]=sum/a[i][i]; 
                   4701:   } 
                   4702: } 
                   4703: 
                   4704: void pstamp(FILE *fichier)
                   4705: {
1.196     brouard  4706:   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126     brouard  4707: }
                   4708: 
1.297     brouard  4709: void date2dmy(double date,double *day, double *month, double *year){
                   4710:   double yp=0., yp1=0., yp2=0.;
                   4711:   
                   4712:   yp1=modf(date,&yp);/* extracts integral of date in yp  and
                   4713:                        fractional in yp1 */
                   4714:   *year=yp;
                   4715:   yp2=modf((yp1*12),&yp);
                   4716:   *month=yp;
                   4717:   yp1=modf((yp2*30.5),&yp);
                   4718:   *day=yp;
                   4719:   if(*day==0) *day=1;
                   4720:   if(*month==0) *month=1;
                   4721: }
                   4722: 
1.253     brouard  4723: 
                   4724: 
1.126     brouard  4725: /************ Frequencies ********************/
1.251     brouard  4726: void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226     brouard  4727:                  int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   4728:                  int firstpass,  int lastpass, int stepm, int weightopt, char model[])
1.250     brouard  4729: {  /* Some frequencies as well as proposing some starting values */
1.226     brouard  4730:   
1.265     brouard  4731:   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226     brouard  4732:   int iind=0, iage=0;
                   4733:   int mi; /* Effective wave */
                   4734:   int first;
                   4735:   double ***freq; /* Frequencies */
1.268     brouard  4736:   double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
                   4737:   int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
1.284     brouard  4738:   double *meanq, *stdq, *idq;
1.226     brouard  4739:   double **meanqt;
                   4740:   double *pp, **prop, *posprop, *pospropt;
                   4741:   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
                   4742:   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
                   4743:   double agebegin, ageend;
                   4744:     
                   4745:   pp=vector(1,nlstate);
1.251     brouard  4746:   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
1.226     brouard  4747:   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
                   4748:   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
                   4749:   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
                   4750:   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284     brouard  4751:   stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283     brouard  4752:   idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226     brouard  4753:   meanqt=matrix(1,lastpass,1,nqtveff);
                   4754:   strcpy(fileresp,"P_");
                   4755:   strcat(fileresp,fileresu);
                   4756:   /*strcat(fileresphtm,fileresu);*/
                   4757:   if((ficresp=fopen(fileresp,"w"))==NULL) {
                   4758:     printf("Problem with prevalence resultfile: %s\n", fileresp);
                   4759:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                   4760:     exit(0);
                   4761:   }
1.240     brouard  4762:   
1.226     brouard  4763:   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
                   4764:   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
                   4765:     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
                   4766:     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
                   4767:     fflush(ficlog);
                   4768:     exit(70); 
                   4769:   }
                   4770:   else{
                   4771:     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240     brouard  4772: <hr size=\"2\" color=\"#EC5E5E\"> \n                                   \
1.214     brouard  4773: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226     brouard  4774:            fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   4775:   }
1.319     brouard  4776:   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);
1.240     brouard  4777:   
1.226     brouard  4778:   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
                   4779:   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
                   4780:     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
                   4781:     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
                   4782:     fflush(ficlog);
                   4783:     exit(70); 
1.240     brouard  4784:   } else{
1.226     brouard  4785:     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.319     brouard  4786: ,<hr size=\"2\" color=\"#EC5E5E\"> \n                                  \
1.214     brouard  4787: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226     brouard  4788:            fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   4789:   }
1.319     brouard  4790:   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);
1.240     brouard  4791:   
1.253     brouard  4792:   y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
                   4793:   x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251     brouard  4794:   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226     brouard  4795:   j1=0;
1.126     brouard  4796:   
1.227     brouard  4797:   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
                   4798:   j=cptcoveff;  /* Only dummy covariates of the model */
1.226     brouard  4799:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240     brouard  4800:   
                   4801:   
1.226     brouard  4802:   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
                   4803:      reference=low_education V1=0,V2=0
                   4804:      med_educ                V1=1 V2=0, 
                   4805:      high_educ               V1=0 V2=1
                   4806:      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
                   4807:   */
1.249     brouard  4808:   dateintsum=0;
                   4809:   k2cpt=0;
                   4810: 
1.253     brouard  4811:   if(cptcoveff == 0 )
1.265     brouard  4812:     nl=1;  /* Constant and age model only */
1.253     brouard  4813:   else
                   4814:     nl=2;
1.265     brouard  4815: 
                   4816:   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
                   4817:   /* Loop on nj=1 or 2 if dummy covariates j!=0
                   4818:    *   Loop on j1(1 to 2**cptcoveff) covariate combination
                   4819:    *     freq[s1][s2][iage] =0.
                   4820:    *     Loop on iind
                   4821:    *       ++freq[s1][s2][iage] weighted
                   4822:    *     end iind
                   4823:    *     if covariate and j!0
                   4824:    *       headers Variable on one line
                   4825:    *     endif cov j!=0
                   4826:    *     header of frequency table by age
                   4827:    *     Loop on age
                   4828:    *       pp[s1]+=freq[s1][s2][iage] weighted
                   4829:    *       pos+=freq[s1][s2][iage] weighted
                   4830:    *       Loop on s1 initial state
                   4831:    *         fprintf(ficresp
                   4832:    *       end s1
                   4833:    *     end age
                   4834:    *     if j!=0 computes starting values
                   4835:    *     end compute starting values
                   4836:    *   end j1
                   4837:    * end nl 
                   4838:    */
1.253     brouard  4839:   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
                   4840:     if(nj==1)
                   4841:       j=0;  /* First pass for the constant */
1.265     brouard  4842:     else{
1.253     brouard  4843:       j=cptcoveff; /* Other passes for the covariate values */
1.265     brouard  4844:     }
1.251     brouard  4845:     first=1;
1.265     brouard  4846:     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
1.251     brouard  4847:       posproptt=0.;
                   4848:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                   4849:        scanf("%d", i);*/
                   4850:       for (i=-5; i<=nlstate+ndeath; i++)  
1.265     brouard  4851:        for (s2=-5; s2<=nlstate+ndeath; s2++)  
1.251     brouard  4852:          for(m=iagemin; m <= iagemax+3; m++)
1.265     brouard  4853:            freq[i][s2][m]=0;
1.251     brouard  4854:       
                   4855:       for (i=1; i<=nlstate; i++)  {
1.240     brouard  4856:        for(m=iagemin; m <= iagemax+3; m++)
1.251     brouard  4857:          prop[i][m]=0;
                   4858:        posprop[i]=0;
                   4859:        pospropt[i]=0;
                   4860:       }
1.283     brouard  4861:       for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284     brouard  4862:         idq[z1]=0.;
                   4863:         meanq[z1]=0.;
                   4864:         stdq[z1]=0.;
1.283     brouard  4865:       }
                   4866:       /* for (z1=1; z1<= nqtveff; z1++) { */
1.251     brouard  4867:       /*   for(m=1;m<=lastpass;m++){ */
1.283     brouard  4868:       /*         meanqt[m][z1]=0.; */
                   4869:       /*       } */
                   4870:       /* }       */
1.251     brouard  4871:       /* dateintsum=0; */
                   4872:       /* k2cpt=0; */
                   4873:       
1.265     brouard  4874:       /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251     brouard  4875:       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
                   4876:        bool=1;
                   4877:        if(j !=0){
                   4878:          if(anyvaryingduminmodel==0){ /* If All fixed covariates */
                   4879:            if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                   4880:              for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                   4881:                /* if(Tvaraff[z1] ==-20){ */
                   4882:                /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                   4883:                /* }else  if(Tvaraff[z1] ==-10){ */
                   4884:                /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                   4885:                /* }else  */
                   4886:                if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265     brouard  4887:                  /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251     brouard  4888:                  bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
                   4889:                  /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                   4890:                     bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                   4891:                     j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                   4892:                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                   4893:                } /* Onlyf fixed */
                   4894:              } /* end z1 */
                   4895:            } /* cptcovn > 0 */
                   4896:          } /* end any */
                   4897:        }/* end j==0 */
1.265     brouard  4898:        if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251     brouard  4899:          /* for(m=firstpass; m<=lastpass; m++){ */
1.284     brouard  4900:          for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251     brouard  4901:            m=mw[mi][iind];
                   4902:            if(j!=0){
                   4903:              if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                   4904:                for (z1=1; z1<=cptcoveff; z1++) {
                   4905:                  if( Fixed[Tmodelind[z1]]==1){
                   4906:                    iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                   4907:                    if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's 
                   4908:                                                                                      value is -1, we don't select. It differs from the 
                   4909:                                                                                      constant and age model which counts them. */
                   4910:                      bool=0; /* not selected */
                   4911:                  }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                   4912:                    if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                   4913:                      bool=0;
                   4914:                    }
                   4915:                  }
                   4916:                }
                   4917:              }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
                   4918:            } /* end j==0 */
                   4919:            /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284     brouard  4920:            if(bool==1){ /*Selected */
1.251     brouard  4921:              /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                   4922:                 and mw[mi+1][iind]. dh depends on stepm. */
                   4923:              agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
                   4924:              ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
                   4925:              if(m >=firstpass && m <=lastpass){
                   4926:                k2=anint[m][iind]+(mint[m][iind]/12.);
                   4927:                /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                   4928:                if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                   4929:                if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                   4930:                if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                   4931:                  prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                   4932:                if (m<lastpass) {
                   4933:                  /* if(s[m][iind]==4 && s[m+1][iind]==4) */
                   4934:                  /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
                   4935:                  if(s[m][iind]==-1)
                   4936:                    printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                   4937:                  freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
1.311     brouard  4938:                  for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
                   4939:                    if(!isnan(covar[ncovcol+z1][iind])){
                   4940:                        idq[z1]=idq[z1]+weight[iind];
                   4941:                        meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
                   4942:                        /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
                   4943:                        stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
                   4944:                    }
1.284     brouard  4945:                  }
1.251     brouard  4946:                  /* if((int)agev[m][iind] == 55) */
                   4947:                  /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
                   4948:                  /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                   4949:                  freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
1.234     brouard  4950:                }
1.251     brouard  4951:              } /* end if between passes */  
                   4952:              if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
                   4953:                dateintsum=dateintsum+k2; /* on all covariates ?*/
                   4954:                k2cpt++;
                   4955:                /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234     brouard  4956:              }
1.251     brouard  4957:            }else{
                   4958:              bool=1;
                   4959:            }/* end bool 2 */
                   4960:          } /* end m */
1.284     brouard  4961:          /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
                   4962:          /*   idq[z1]=idq[z1]+weight[iind]; */
                   4963:          /*   meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /\* Computes mean of quantitative with selected filter *\/ */
                   4964:          /*   stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/  /\* Computes mean of quantitative with selected filter *\/ */
                   4965:          /* } */
1.251     brouard  4966:        } /* end bool */
                   4967:       } /* end iind = 1 to imx */
1.319     brouard  4968:       /* prop[s][age] is fed for any initial and valid live state as well as
1.251     brouard  4969:         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
                   4970:       
                   4971:       
                   4972:       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265     brouard  4973:       if(cptcoveff==0 && nj==1) /* no covariate and first pass */
                   4974:         pstamp(ficresp);
1.251     brouard  4975:       if  (cptcoveff>0 && j!=0){
1.265     brouard  4976:         pstamp(ficresp);
1.251     brouard  4977:        printf( "\n#********** Variable "); 
                   4978:        fprintf(ficresp, "\n#********** Variable "); 
                   4979:        fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
                   4980:        fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
                   4981:        fprintf(ficlog, "\n#********** Variable "); 
                   4982:        for (z1=1; z1<=cptcoveff; z1++){
                   4983:          if(!FixedV[Tvaraff[z1]]){
                   4984:            printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4985:            fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4986:            fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4987:            fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4988:            fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250     brouard  4989:          }else{
1.251     brouard  4990:            printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4991:            fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4992:            fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4993:            fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4994:            fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4995:          }
                   4996:        }
                   4997:        printf( "**********\n#");
                   4998:        fprintf(ficresp, "**********\n#");
                   4999:        fprintf(ficresphtm, "**********</h3>\n");
                   5000:        fprintf(ficresphtmfr, "**********</h3>\n");
                   5001:        fprintf(ficlog, "**********\n");
                   5002:       }
1.284     brouard  5003:       /*
                   5004:        Printing means of quantitative variables if any
                   5005:       */
                   5006:       for (z1=1; z1<= nqfveff; z1++) {
1.311     brouard  5007:        fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.312     brouard  5008:        fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
1.284     brouard  5009:        if(weightopt==1){
                   5010:          printf(" Weighted mean and standard deviation of");
                   5011:          fprintf(ficlog," Weighted mean and standard deviation of");
                   5012:          fprintf(ficresphtmfr," Weighted mean and standard deviation of");
                   5013:        }
1.311     brouard  5014:        /* mu = \frac{w x}{\sum w}
                   5015:            var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2 
                   5016:        */
                   5017:        printf(" fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
                   5018:        fprintf(ficlog," fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
                   5019:        fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
1.284     brouard  5020:       }
                   5021:       /* for (z1=1; z1<= nqtveff; z1++) { */
                   5022:       /*       for(m=1;m<=lastpass;m++){ */
                   5023:       /*         fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
                   5024:       /*   } */
                   5025:       /* } */
1.283     brouard  5026: 
1.251     brouard  5027:       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265     brouard  5028:       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
                   5029:         fprintf(ficresp, " Age");
                   5030:       if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.251     brouard  5031:       for(i=1; i<=nlstate;i++) {
1.265     brouard  5032:        if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
1.251     brouard  5033:        fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
                   5034:       }
1.265     brouard  5035:       if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251     brouard  5036:       fprintf(ficresphtm, "\n");
                   5037:       
                   5038:       /* Header of frequency table by age */
                   5039:       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
                   5040:       fprintf(ficresphtmfr,"<th>Age</th> ");
1.265     brouard  5041:       for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251     brouard  5042:        for(m=-1; m <=nlstate+ndeath; m++){
1.265     brouard  5043:          if(s2!=0 && m!=0)
                   5044:            fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240     brouard  5045:        }
1.226     brouard  5046:       }
1.251     brouard  5047:       fprintf(ficresphtmfr, "\n");
                   5048:     
                   5049:       /* For each age */
                   5050:       for(iage=iagemin; iage <= iagemax+3; iage++){
                   5051:        fprintf(ficresphtm,"<tr>");
                   5052:        if(iage==iagemax+1){
                   5053:          fprintf(ficlog,"1");
                   5054:          fprintf(ficresphtmfr,"<tr><th>0</th> ");
                   5055:        }else if(iage==iagemax+2){
                   5056:          fprintf(ficlog,"0");
                   5057:          fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
                   5058:        }else if(iage==iagemax+3){
                   5059:          fprintf(ficlog,"Total");
                   5060:          fprintf(ficresphtmfr,"<tr><th>Total</th> ");
                   5061:        }else{
1.240     brouard  5062:          if(first==1){
1.251     brouard  5063:            first=0;
                   5064:            printf("See log file for details...\n");
                   5065:          }
                   5066:          fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
                   5067:          fprintf(ficlog,"Age %d", iage);
                   5068:        }
1.265     brouard  5069:        for(s1=1; s1 <=nlstate ; s1++){
                   5070:          for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
                   5071:            pp[s1] += freq[s1][m][iage]; 
1.251     brouard  5072:        }
1.265     brouard  5073:        for(s1=1; s1 <=nlstate ; s1++){
1.251     brouard  5074:          for(m=-1, pos=0; m <=0 ; m++)
1.265     brouard  5075:            pos += freq[s1][m][iage];
                   5076:          if(pp[s1]>=1.e-10){
1.251     brouard  5077:            if(first==1){
1.265     brouard  5078:              printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251     brouard  5079:            }
1.265     brouard  5080:            fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251     brouard  5081:          }else{
                   5082:            if(first==1)
1.265     brouard  5083:              printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
                   5084:            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240     brouard  5085:          }
                   5086:        }
                   5087:       
1.265     brouard  5088:        for(s1=1; s1 <=nlstate ; s1++){ 
                   5089:          /* posprop[s1]=0; */
                   5090:          for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
                   5091:            pp[s1] += freq[s1][m][iage];
                   5092:        }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
                   5093:       
                   5094:        for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
                   5095:          pos += pp[s1]; /* pos is the total number of transitions until this age */
                   5096:          posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
                   5097:                                            from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                   5098:          pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
                   5099:                                          from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                   5100:        }
                   5101:        
                   5102:        /* Writing ficresp */
                   5103:        if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
                   5104:           if( iage <= iagemax){
                   5105:            fprintf(ficresp," %d",iage);
                   5106:           }
                   5107:         }else if( nj==2){
                   5108:           if( iage <= iagemax){
                   5109:            fprintf(ficresp," %d",iage);
                   5110:             for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   5111:           }
1.240     brouard  5112:        }
1.265     brouard  5113:        for(s1=1; s1 <=nlstate ; s1++){
1.240     brouard  5114:          if(pos>=1.e-5){
1.251     brouard  5115:            if(first==1)
1.265     brouard  5116:              printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
                   5117:            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251     brouard  5118:          }else{
                   5119:            if(first==1)
1.265     brouard  5120:              printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
                   5121:            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251     brouard  5122:          }
                   5123:          if( iage <= iagemax){
                   5124:            if(pos>=1.e-5){
1.265     brouard  5125:              if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
                   5126:                fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                   5127:               }else if( nj==2){
                   5128:                fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                   5129:               }
                   5130:              fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                   5131:              /*probs[iage][s1][j1]= pp[s1]/pos;*/
                   5132:              /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
                   5133:            } else{
                   5134:              if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
                   5135:              fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251     brouard  5136:            }
1.240     brouard  5137:          }
1.265     brouard  5138:          pospropt[s1] +=posprop[s1];
                   5139:        } /* end loop s1 */
1.251     brouard  5140:        /* pospropt=0.; */
1.265     brouard  5141:        for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251     brouard  5142:          for(m=-1; m <=nlstate+ndeath; m++){
1.265     brouard  5143:            if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251     brouard  5144:              if(first==1){
1.265     brouard  5145:                printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251     brouard  5146:              }
1.265     brouard  5147:              /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
                   5148:              fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251     brouard  5149:            }
1.265     brouard  5150:            if(s1!=0 && m!=0)
                   5151:              fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240     brouard  5152:          }
1.265     brouard  5153:        } /* end loop s1 */
1.251     brouard  5154:        posproptt=0.; 
1.265     brouard  5155:        for(s1=1; s1 <=nlstate; s1++){
                   5156:          posproptt += pospropt[s1];
1.251     brouard  5157:        }
                   5158:        fprintf(ficresphtmfr,"</tr>\n ");
1.265     brouard  5159:        fprintf(ficresphtm,"</tr>\n");
                   5160:        if((cptcoveff==0 && nj==1)|| nj==2 ) {
                   5161:          if(iage <= iagemax)
                   5162:            fprintf(ficresp,"\n");
1.240     brouard  5163:        }
1.251     brouard  5164:        if(first==1)
                   5165:          printf("Others in log...\n");
                   5166:        fprintf(ficlog,"\n");
                   5167:       } /* end loop age iage */
1.265     brouard  5168:       
1.251     brouard  5169:       fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265     brouard  5170:       for(s1=1; s1 <=nlstate ; s1++){
1.251     brouard  5171:        if(posproptt < 1.e-5){
1.265     brouard  5172:          fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt); 
1.251     brouard  5173:        }else{
1.265     brouard  5174:          fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);  
1.240     brouard  5175:        }
1.226     brouard  5176:       }
1.251     brouard  5177:       fprintf(ficresphtm,"</tr>\n");
                   5178:       fprintf(ficresphtm,"</table>\n");
                   5179:       fprintf(ficresphtmfr,"</table>\n");
1.226     brouard  5180:       if(posproptt < 1.e-5){
1.251     brouard  5181:        fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
                   5182:        fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260     brouard  5183:        fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
                   5184:        printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
1.251     brouard  5185:        invalidvarcomb[j1]=1;
1.226     brouard  5186:       }else{
1.251     brouard  5187:        fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
                   5188:        invalidvarcomb[j1]=0;
1.226     brouard  5189:       }
1.251     brouard  5190:       fprintf(ficresphtmfr,"</table>\n");
                   5191:       fprintf(ficlog,"\n");
                   5192:       if(j!=0){
                   5193:        printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265     brouard  5194:        for(i=1,s1=1; i <=nlstate; i++){
1.251     brouard  5195:          for(k=1; k <=(nlstate+ndeath); k++){
                   5196:            if (k != i) {
1.265     brouard  5197:              for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253     brouard  5198:                if(jj==1){  /* Constant case (in fact cste + age) */
1.251     brouard  5199:                  if(j1==1){ /* All dummy covariates to zero */
                   5200:                    freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
                   5201:                    freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252     brouard  5202:                    printf("%d%d ",i,k);
                   5203:                    fprintf(ficlog,"%d%d ",i,k);
1.265     brouard  5204:                    printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
                   5205:                    fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   5206:                    pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251     brouard  5207:                  }
1.253     brouard  5208:                }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
                   5209:                  for(iage=iagemin; iage <= iagemax+3; iage++){
                   5210:                    x[iage]= (double)iage;
                   5211:                    y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265     brouard  5212:                    /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
1.253     brouard  5213:                  }
1.268     brouard  5214:                  /* Some are not finite, but linreg will ignore these ages */
                   5215:                  no=0;
1.253     brouard  5216:                  linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265     brouard  5217:                  pstart[s1]=b;
                   5218:                  pstart[s1-1]=a;
1.252     brouard  5219:                }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ 
                   5220:                  printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                   5221:                  printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
1.265     brouard  5222:                  pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
1.252     brouard  5223:                  printf("%d%d ",i,k);
                   5224:                  fprintf(ficlog,"%d%d ",i,k);
1.265     brouard  5225:                  printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
1.251     brouard  5226:                }else{ /* Other cases, like quantitative fixed or varying covariates */
                   5227:                  ;
                   5228:                }
                   5229:                /* printf("%12.7f )", param[i][jj][k]); */
                   5230:                /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265     brouard  5231:                s1++; 
1.251     brouard  5232:              } /* end jj */
                   5233:            } /* end k!= i */
                   5234:          } /* end k */
1.265     brouard  5235:        } /* end i, s1 */
1.251     brouard  5236:       } /* end j !=0 */
                   5237:     } /* end selected combination of covariate j1 */
                   5238:     if(j==0){ /* We can estimate starting values from the occurences in each case */
                   5239:       printf("#Freqsummary: Starting values for the constants:\n");
                   5240:       fprintf(ficlog,"\n");
1.265     brouard  5241:       for(i=1,s1=1; i <=nlstate; i++){
1.251     brouard  5242:        for(k=1; k <=(nlstate+ndeath); k++){
                   5243:          if (k != i) {
                   5244:            printf("%d%d ",i,k);
                   5245:            fprintf(ficlog,"%d%d ",i,k);
                   5246:            for(jj=1; jj <=ncovmodel; jj++){
1.265     brouard  5247:              pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253     brouard  5248:              if(jj==1){ /* Age has to be done */
1.265     brouard  5249:                pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                   5250:                printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   5251:                fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
1.251     brouard  5252:              }
                   5253:              /* printf("%12.7f )", param[i][jj][k]); */
                   5254:              /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265     brouard  5255:              s1++; 
1.250     brouard  5256:            }
1.251     brouard  5257:            printf("\n");
                   5258:            fprintf(ficlog,"\n");
1.250     brouard  5259:          }
                   5260:        }
1.284     brouard  5261:       } /* end of state i */
1.251     brouard  5262:       printf("#Freqsummary\n");
                   5263:       fprintf(ficlog,"\n");
1.265     brouard  5264:       for(s1=-1; s1 <=nlstate+ndeath; s1++){
                   5265:        for(s2=-1; s2 <=nlstate+ndeath; s2++){
                   5266:          /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
                   5267:          printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
                   5268:          fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
                   5269:          /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
                   5270:          /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
                   5271:          /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251     brouard  5272:          /* } */
                   5273:        }
1.265     brouard  5274:       } /* end loop s1 */
1.251     brouard  5275:       
                   5276:       printf("\n");
                   5277:       fprintf(ficlog,"\n");
                   5278:     } /* end j=0 */
1.249     brouard  5279:   } /* end j */
1.252     brouard  5280: 
1.253     brouard  5281:   if(mle == -2){  /* We want to use these values as starting values */
1.252     brouard  5282:     for(i=1, jk=1; i <=nlstate; i++){
                   5283:       for(j=1; j <=nlstate+ndeath; j++){
                   5284:        if(j!=i){
                   5285:          /*ca[0]= k+'a'-1;ca[1]='\0';*/
                   5286:          printf("%1d%1d",i,j);
                   5287:          fprintf(ficparo,"%1d%1d",i,j);
                   5288:          for(k=1; k<=ncovmodel;k++){
                   5289:            /*    printf(" %lf",param[i][j][k]); */
                   5290:            /*    fprintf(ficparo," %lf",param[i][j][k]); */
                   5291:            p[jk]=pstart[jk];
                   5292:            printf(" %f ",pstart[jk]);
                   5293:            fprintf(ficparo," %f ",pstart[jk]);
                   5294:            jk++;
                   5295:          }
                   5296:          printf("\n");
                   5297:          fprintf(ficparo,"\n");
                   5298:        }
                   5299:       }
                   5300:     }
                   5301:   } /* end mle=-2 */
1.226     brouard  5302:   dateintmean=dateintsum/k2cpt; 
1.296     brouard  5303:   date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240     brouard  5304:   
1.226     brouard  5305:   fclose(ficresp);
                   5306:   fclose(ficresphtm);
                   5307:   fclose(ficresphtmfr);
1.283     brouard  5308:   free_vector(idq,1,nqfveff);
1.226     brouard  5309:   free_vector(meanq,1,nqfveff);
1.284     brouard  5310:   free_vector(stdq,1,nqfveff);
1.226     brouard  5311:   free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253     brouard  5312:   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
                   5313:   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251     brouard  5314:   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226     brouard  5315:   free_vector(pospropt,1,nlstate);
                   5316:   free_vector(posprop,1,nlstate);
1.251     brouard  5317:   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226     brouard  5318:   free_vector(pp,1,nlstate);
                   5319:   /* End of freqsummary */
                   5320: }
1.126     brouard  5321: 
1.268     brouard  5322: /* Simple linear regression */
                   5323: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
                   5324: 
                   5325:   /* y=a+bx regression */
                   5326:   double   sumx = 0.0;                        /* sum of x                      */
                   5327:   double   sumx2 = 0.0;                       /* sum of x**2                   */
                   5328:   double   sumxy = 0.0;                       /* sum of x * y                  */
                   5329:   double   sumy = 0.0;                        /* sum of y                      */
                   5330:   double   sumy2 = 0.0;                       /* sum of y**2                   */
                   5331:   double   sume2 = 0.0;                       /* sum of square or residuals */
                   5332:   double yhat;
                   5333:   
                   5334:   double denom=0;
                   5335:   int i;
                   5336:   int ne=*no;
                   5337:   
                   5338:   for ( i=ifi, ne=0;i<=ila;i++) {
                   5339:     if(!isfinite(x[i]) || !isfinite(y[i])){
                   5340:       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
                   5341:       continue;
                   5342:     }
                   5343:     ne=ne+1;
                   5344:     sumx  += x[i];       
                   5345:     sumx2 += x[i]*x[i];  
                   5346:     sumxy += x[i] * y[i];
                   5347:     sumy  += y[i];      
                   5348:     sumy2 += y[i]*y[i]; 
                   5349:     denom = (ne * sumx2 - sumx*sumx);
                   5350:     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
                   5351:   } 
                   5352:   
                   5353:   denom = (ne * sumx2 - sumx*sumx);
                   5354:   if (denom == 0) {
                   5355:     // vertical, slope m is infinity
                   5356:     *b = INFINITY;
                   5357:     *a = 0;
                   5358:     if (r) *r = 0;
                   5359:     return 1;
                   5360:   }
                   5361:   
                   5362:   *b = (ne * sumxy  -  sumx * sumy) / denom;
                   5363:   *a = (sumy * sumx2  -  sumx * sumxy) / denom;
                   5364:   if (r!=NULL) {
                   5365:     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
                   5366:       sqrt((sumx2 - sumx*sumx/ne) *
                   5367:           (sumy2 - sumy*sumy/ne));
                   5368:   }
                   5369:   *no=ne;
                   5370:   for ( i=ifi, ne=0;i<=ila;i++) {
                   5371:     if(!isfinite(x[i]) || !isfinite(y[i])){
                   5372:       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
                   5373:       continue;
                   5374:     }
                   5375:     ne=ne+1;
                   5376:     yhat = y[i] - *a -*b* x[i];
                   5377:     sume2  += yhat * yhat ;       
                   5378:     
                   5379:     denom = (ne * sumx2 - sumx*sumx);
                   5380:     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
                   5381:   } 
                   5382:   *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
                   5383:   *sa= *sb * sqrt(sumx2/ne);
                   5384:   
                   5385:   return 0; 
                   5386: }
                   5387: 
1.126     brouard  5388: /************ Prevalence ********************/
1.227     brouard  5389: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
                   5390: {  
                   5391:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   5392:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   5393:      We still use firstpass and lastpass as another selection.
                   5394:   */
1.126     brouard  5395:  
1.227     brouard  5396:   int i, m, jk, j1, bool, z1,j, iv;
                   5397:   int mi; /* Effective wave */
                   5398:   int iage;
                   5399:   double agebegin, ageend;
                   5400: 
                   5401:   double **prop;
                   5402:   double posprop; 
                   5403:   double  y2; /* in fractional years */
                   5404:   int iagemin, iagemax;
                   5405:   int first; /** to stop verbosity which is redirected to log file */
                   5406: 
                   5407:   iagemin= (int) agemin;
                   5408:   iagemax= (int) agemax;
                   5409:   /*pp=vector(1,nlstate);*/
1.251     brouard  5410:   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
1.227     brouard  5411:   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                   5412:   j1=0;
1.222     brouard  5413:   
1.227     brouard  5414:   /*j=cptcoveff;*/
                   5415:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222     brouard  5416:   
1.288     brouard  5417:   first=0;
1.227     brouard  5418:   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
                   5419:     for (i=1; i<=nlstate; i++)  
1.251     brouard  5420:       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227     brouard  5421:        prop[i][iage]=0.0;
                   5422:     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
                   5423:     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
                   5424:     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
                   5425:     
                   5426:     for (i=1; i<=imx; i++) { /* Each individual */
                   5427:       bool=1;
                   5428:       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
                   5429:       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
                   5430:        m=mw[mi][i];
                   5431:        /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
                   5432:        /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
                   5433:        for (z1=1; z1<=cptcoveff; z1++){
                   5434:          if( Fixed[Tmodelind[z1]]==1){
                   5435:            iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                   5436:            if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                   5437:              bool=0;
                   5438:          }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
                   5439:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                   5440:              bool=0;
                   5441:            }
                   5442:        }
                   5443:        if(bool==1){ /* Otherwise we skip that wave/person */
                   5444:          agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
                   5445:          /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                   5446:          if(m >=firstpass && m <=lastpass){
                   5447:            y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   5448:            if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                   5449:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   5450:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251     brouard  5451:              if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227     brouard  5452:                printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                   5453:                exit(1);
                   5454:              }
                   5455:              if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   5456:                /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   5457:                prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                   5458:                prop[s[m][i]][iagemax+3] += weight[i]; 
                   5459:              } /* end valid statuses */ 
                   5460:            } /* end selection of dates */
                   5461:          } /* end selection of waves */
                   5462:        } /* end bool */
                   5463:       } /* end wave */
                   5464:     } /* end individual */
                   5465:     for(i=iagemin; i <= iagemax+3; i++){  
                   5466:       for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   5467:        posprop += prop[jk][i]; 
                   5468:       } 
                   5469:       
                   5470:       for(jk=1; jk <=nlstate ; jk++){      
                   5471:        if( i <=  iagemax){ 
                   5472:          if(posprop>=1.e-5){ 
                   5473:            probs[i][jk][j1]= prop[jk][i]/posprop;
                   5474:          } else{
1.288     brouard  5475:            if(!first){
                   5476:              first=1;
1.266     brouard  5477:              printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
                   5478:            }else{
1.288     brouard  5479:              fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
1.227     brouard  5480:            }
                   5481:          }
                   5482:        } 
                   5483:       }/* end jk */ 
                   5484:     }/* end i */ 
1.222     brouard  5485:      /*} *//* end i1 */
1.227     brouard  5486:   } /* end j1 */
1.222     brouard  5487:   
1.227     brouard  5488:   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   5489:   /*free_vector(pp,1,nlstate);*/
1.251     brouard  5490:   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227     brouard  5491: }  /* End of prevalence */
1.126     brouard  5492: 
                   5493: /************* Waves Concatenation ***************/
                   5494: 
                   5495: void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
                   5496: {
1.298     brouard  5497:   /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
1.126     brouard  5498:      Death is a valid wave (if date is known).
                   5499:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
                   5500:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298     brouard  5501:      and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227     brouard  5502:   */
1.126     brouard  5503: 
1.224     brouard  5504:   int i=0, mi=0, m=0, mli=0;
1.126     brouard  5505:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                   5506:      double sum=0., jmean=0.;*/
1.224     brouard  5507:   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126     brouard  5508:   int j, k=0,jk, ju, jl;
                   5509:   double sum=0.;
                   5510:   first=0;
1.214     brouard  5511:   firstwo=0;
1.217     brouard  5512:   firsthree=0;
1.218     brouard  5513:   firstfour=0;
1.164     brouard  5514:   jmin=100000;
1.126     brouard  5515:   jmax=-1;
                   5516:   jmean=0.;
1.224     brouard  5517: 
                   5518: /* Treating live states */
1.214     brouard  5519:   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
1.224     brouard  5520:     mi=0;  /* First valid wave */
1.227     brouard  5521:     mli=0; /* Last valid wave */
1.309     brouard  5522:     m=firstpass;  /* Loop on waves */
                   5523:     while(s[m][i] <= nlstate){  /* a live state or unknown state  */
1.227     brouard  5524:       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
                   5525:        mli=m-1;/* mw[++mi][i]=m-1; */
                   5526:       }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
1.309     brouard  5527:        mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
1.227     brouard  5528:        mli=m;
1.224     brouard  5529:       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
                   5530:       if(m < lastpass){ /* m < lastpass, standard case */
1.227     brouard  5531:        m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216     brouard  5532:       }
1.309     brouard  5533:       else{ /* m = lastpass, eventual special issue with warning */
1.224     brouard  5534: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227     brouard  5535:        break;
1.224     brouard  5536: #else
1.317     brouard  5537:        if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
1.227     brouard  5538:          if(firsthree == 0){
1.302     brouard  5539:            printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
1.227     brouard  5540:            firsthree=1;
1.317     brouard  5541:          }else if(firsthree >=1 && firsthree < 10){
                   5542:            fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
                   5543:            firsthree++;
                   5544:          }else if(firsthree == 10){
                   5545:            printf("Information, too many Information flags: no more reported to log either\n");
                   5546:            fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
                   5547:            firsthree++;
                   5548:          }else{
                   5549:            firsthree++;
1.227     brouard  5550:          }
1.309     brouard  5551:          mw[++mi][i]=m; /* Valid transition with unknown status */
1.227     brouard  5552:          mli=m;
                   5553:        }
                   5554:        if(s[m][i]==-2){ /* Vital status is really unknown */
                   5555:          nbwarn++;
1.309     brouard  5556:          if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
1.227     brouard  5557:            printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                   5558:            fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                   5559:          }
                   5560:          break;
                   5561:        }
                   5562:        break;
1.224     brouard  5563: #endif
1.227     brouard  5564:       }/* End m >= lastpass */
1.126     brouard  5565:     }/* end while */
1.224     brouard  5566: 
1.227     brouard  5567:     /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
1.216     brouard  5568:     /* After last pass */
1.224     brouard  5569: /* Treating death states */
1.214     brouard  5570:     if (s[m][i] > nlstate){  /* In a death state */
1.227     brouard  5571:       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
                   5572:       /* } */
1.126     brouard  5573:       mi++;    /* Death is another wave */
                   5574:       /* if(mi==0)  never been interviewed correctly before death */
1.227     brouard  5575:       /* Only death is a correct wave */
1.126     brouard  5576:       mw[mi][i]=m;
1.257     brouard  5577:     } /* else not in a death state */
1.224     brouard  5578: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257     brouard  5579:     else if ((int) andc[i] != 9999) {  /* Date of death is known */
1.218     brouard  5580:       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.309     brouard  5581:        if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
1.227     brouard  5582:          nbwarn++;
                   5583:          if(firstfiv==0){
1.309     brouard  5584:            printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227     brouard  5585:            firstfiv=1;
                   5586:          }else{
1.309     brouard  5587:            fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227     brouard  5588:          }
1.309     brouard  5589:            s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
                   5590:        }else{ /* Month of Death occured afer last wave month, potential bias */
1.227     brouard  5591:          nberr++;
                   5592:          if(firstwo==0){
1.309     brouard  5593:            printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227     brouard  5594:            firstwo=1;
                   5595:          }
1.309     brouard  5596:          fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227     brouard  5597:        }
1.257     brouard  5598:       }else{ /* if date of interview is unknown */
1.227     brouard  5599:        /* death is known but not confirmed by death status at any wave */
                   5600:        if(firstfour==0){
1.309     brouard  5601:          printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227     brouard  5602:          firstfour=1;
                   5603:        }
1.309     brouard  5604:        fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d  with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.214     brouard  5605:       }
1.224     brouard  5606:     } /* end if date of death is known */
                   5607: #endif
1.309     brouard  5608:     wav[i]=mi; /* mi should be the last effective wave (or mli),  */
                   5609:     /* wav[i]=mw[mi][i];   */
1.126     brouard  5610:     if(mi==0){
                   5611:       nbwarn++;
                   5612:       if(first==0){
1.227     brouard  5613:        printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                   5614:        first=1;
1.126     brouard  5615:       }
                   5616:       if(first==1){
1.227     brouard  5617:        fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126     brouard  5618:       }
                   5619:     } /* end mi==0 */
                   5620:   } /* End individuals */
1.214     brouard  5621:   /* wav and mw are no more changed */
1.223     brouard  5622:        
1.317     brouard  5623:   printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
                   5624:   fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);
                   5625: 
                   5626: 
1.126     brouard  5627:   for(i=1; i<=imx; i++){
                   5628:     for(mi=1; mi<wav[i];mi++){
                   5629:       if (stepm <=0)
1.227     brouard  5630:        dh[mi][i]=1;
1.126     brouard  5631:       else{
1.260     brouard  5632:        if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227     brouard  5633:          if (agedc[i] < 2*AGESUP) {
                   5634:            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   5635:            if(j==0) j=1;  /* Survives at least one month after exam */
                   5636:            else if(j<0){
                   5637:              nberr++;
                   5638:              printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   5639:              j=1; /* Temporary Dangerous patch */
                   5640:              printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                   5641:              fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   5642:              fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                   5643:            }
                   5644:            k=k+1;
                   5645:            if (j >= jmax){
                   5646:              jmax=j;
                   5647:              ijmax=i;
                   5648:            }
                   5649:            if (j <= jmin){
                   5650:              jmin=j;
                   5651:              ijmin=i;
                   5652:            }
                   5653:            sum=sum+j;
                   5654:            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   5655:            /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                   5656:          }
                   5657:        }
                   5658:        else{
                   5659:          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126     brouard  5660: /*       if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
1.223     brouard  5661:                                        
1.227     brouard  5662:          k=k+1;
                   5663:          if (j >= jmax) {
                   5664:            jmax=j;
                   5665:            ijmax=i;
                   5666:          }
                   5667:          else if (j <= jmin){
                   5668:            jmin=j;
                   5669:            ijmin=i;
                   5670:          }
                   5671:          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                   5672:          /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                   5673:          if(j<0){
                   5674:            nberr++;
                   5675:            printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   5676:            fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   5677:          }
                   5678:          sum=sum+j;
                   5679:        }
                   5680:        jk= j/stepm;
                   5681:        jl= j -jk*stepm;
                   5682:        ju= j -(jk+1)*stepm;
                   5683:        if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                   5684:          if(jl==0){
                   5685:            dh[mi][i]=jk;
                   5686:            bh[mi][i]=0;
                   5687:          }else{ /* We want a negative bias in order to only have interpolation ie
                   5688:                  * to avoid the price of an extra matrix product in likelihood */
                   5689:            dh[mi][i]=jk+1;
                   5690:            bh[mi][i]=ju;
                   5691:          }
                   5692:        }else{
                   5693:          if(jl <= -ju){
                   5694:            dh[mi][i]=jk;
                   5695:            bh[mi][i]=jl;       /* bias is positive if real duration
                   5696:                                 * is higher than the multiple of stepm and negative otherwise.
                   5697:                                 */
                   5698:          }
                   5699:          else{
                   5700:            dh[mi][i]=jk+1;
                   5701:            bh[mi][i]=ju;
                   5702:          }
                   5703:          if(dh[mi][i]==0){
                   5704:            dh[mi][i]=1; /* At least one step */
                   5705:            bh[mi][i]=ju; /* At least one step */
                   5706:            /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
                   5707:          }
                   5708:        } /* end if mle */
1.126     brouard  5709:       }
                   5710:     } /* end wave */
                   5711:   }
                   5712:   jmean=sum/k;
                   5713:   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
1.141     brouard  5714:   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.227     brouard  5715: }
1.126     brouard  5716: 
                   5717: /*********** Tricode ****************************/
1.220     brouard  5718:  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242     brouard  5719:  {
                   5720:    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
                   5721:    /*    Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
                   5722:     * Boring subroutine which should only output nbcode[Tvar[j]][k]
                   5723:     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
                   5724:     * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
                   5725:     */
1.130     brouard  5726: 
1.242     brouard  5727:    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
                   5728:    int modmaxcovj=0; /* Modality max of covariates j */
                   5729:    int cptcode=0; /* Modality max of covariates j */
                   5730:    int modmincovj=0; /* Modality min of covariates j */
1.145     brouard  5731: 
                   5732: 
1.242     brouard  5733:    /* cptcoveff=0;  */
                   5734:    /* *cptcov=0; */
1.126     brouard  5735:  
1.242     brouard  5736:    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285     brouard  5737:    for (k=1; k <= maxncov; k++)
                   5738:      for(j=1; j<=2; j++)
                   5739:        nbcode[k][j]=0; /* Valgrind */
1.126     brouard  5740: 
1.242     brouard  5741:    /* Loop on covariates without age and products and no quantitative variable */
                   5742:    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
                   5743:      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
                   5744:      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
                   5745:        switch(Fixed[k]) {
                   5746:        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
1.311     brouard  5747:         modmaxcovj=0;
                   5748:         modmincovj=0;
1.242     brouard  5749:         for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
                   5750:           ij=(int)(covar[Tvar[k]][i]);
                   5751:           /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                   5752:            * If product of Vn*Vm, still boolean *:
                   5753:            * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                   5754:            * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
                   5755:           /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                   5756:              modality of the nth covariate of individual i. */
                   5757:           if (ij > modmaxcovj)
                   5758:             modmaxcovj=ij; 
                   5759:           else if (ij < modmincovj) 
                   5760:             modmincovj=ij; 
1.287     brouard  5761:           if (ij <0 || ij >1 ){
1.311     brouard  5762:             printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
                   5763:             fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
                   5764:             fflush(ficlog);
                   5765:             exit(1);
1.287     brouard  5766:           }
                   5767:           if ((ij < -1) || (ij > NCOVMAX)){
1.242     brouard  5768:             printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                   5769:             exit(1);
                   5770:           }else
                   5771:             Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
                   5772:           /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
                   5773:           /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                   5774:           /* getting the maximum value of the modality of the covariate
                   5775:              (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                   5776:              female ies 1, then modmaxcovj=1.
                   5777:           */
                   5778:         } /* end for loop on individuals i */
                   5779:         printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                   5780:         fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                   5781:         cptcode=modmaxcovj;
                   5782:         /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
                   5783:         /*for (i=0; i<=cptcode; i++) {*/
                   5784:         for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
                   5785:           printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
                   5786:           fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
                   5787:           if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
                   5788:             if( j != -1){
                   5789:               ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
                   5790:                                  covariate for which somebody answered excluding 
                   5791:                                  undefined. Usually 2: 0 and 1. */
                   5792:             }
                   5793:             ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
                   5794:                                     covariate for which somebody answered including 
                   5795:                                     undefined. Usually 3: -1, 0 and 1. */
                   5796:           }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
                   5797:                 * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
                   5798:         } /* Ndum[-1] number of undefined modalities */
1.231     brouard  5799:                        
1.242     brouard  5800:         /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
                   5801:         /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
                   5802:         /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
                   5803:         /* modmincovj=3; modmaxcovj = 7; */
                   5804:         /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
                   5805:         /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
                   5806:         /*              defining two dummy variables: variables V1_1 and V1_2.*/
                   5807:         /* nbcode[Tvar[j]][ij]=k; */
                   5808:         /* nbcode[Tvar[j]][1]=0; */
                   5809:         /* nbcode[Tvar[j]][2]=1; */
                   5810:         /* nbcode[Tvar[j]][3]=2; */
                   5811:         /* To be continued (not working yet). */
                   5812:         ij=0; /* ij is similar to i but can jump over null modalities */
1.287     brouard  5813: 
                   5814:         /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
                   5815:         /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
                   5816:         /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
                   5817:          * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
                   5818:         /*, could be restored in the future */
                   5819:         for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
1.242     brouard  5820:           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
                   5821:             break;
                   5822:           }
                   5823:           ij++;
1.287     brouard  5824:           nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
1.242     brouard  5825:           cptcode = ij; /* New max modality for covar j */
                   5826:         } /* end of loop on modality i=-1 to 1 or more */
                   5827:         break;
                   5828:        case 1: /* Testing on varying covariate, could be simple and
                   5829:                * should look at waves or product of fixed *
                   5830:                * varying. No time to test -1, assuming 0 and 1 only */
                   5831:         ij=0;
                   5832:         for(i=0; i<=1;i++){
                   5833:           nbcode[Tvar[k]][++ij]=i;
                   5834:         }
                   5835:         break;
                   5836:        default:
                   5837:         break;
                   5838:        } /* end switch */
                   5839:      } /* end dummy test */
1.311     brouard  5840:      if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
                   5841:        for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
                   5842:         if(isnan(covar[Tvar[k]][i])){
                   5843:           printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
                   5844:           fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
                   5845:           fflush(ficlog);
                   5846:           exit(1);
                   5847:          }
                   5848:        }
                   5849:      }
1.287     brouard  5850:    } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
1.242     brouard  5851:   
                   5852:    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
                   5853:    /* Look at fixed dummy (single or product) covariates to check empty modalities */
                   5854:    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
                   5855:      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
                   5856:      ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ 
                   5857:      Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
                   5858:      /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
                   5859:    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
                   5860:   
                   5861:    ij=0;
                   5862:    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
                   5863:    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
                   5864:      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
                   5865:      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
                   5866:      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
                   5867:        /* If product not in single variable we don't print results */
                   5868:        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
                   5869:        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
                   5870:        Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
                   5871:        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
                   5872:        TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
                   5873:        if(Fixed[k]!=0)
                   5874:         anyvaryingduminmodel=1;
                   5875:        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
                   5876:        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
                   5877:        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
                   5878:        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
                   5879:        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
                   5880:        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
                   5881:      } 
                   5882:    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
                   5883:    /* ij--; */
                   5884:    /* cptcoveff=ij; /\*Number of total covariates*\/ */
                   5885:    *cptcov=ij; /*Number of total real effective covariates: effective
                   5886:                * because they can be excluded from the model and real
                   5887:                * if in the model but excluded because missing values, but how to get k from ij?*/
                   5888:    for(j=ij+1; j<= cptcovt; j++){
                   5889:      Tvaraff[j]=0;
                   5890:      Tmodelind[j]=0;
                   5891:    }
                   5892:    for(j=ntveff+1; j<= cptcovt; j++){
                   5893:      TmodelInvind[j]=0;
                   5894:    }
                   5895:    /* To be sorted */
                   5896:    ;
                   5897:  }
1.126     brouard  5898: 
1.145     brouard  5899: 
1.126     brouard  5900: /*********** Health Expectancies ****************/
                   5901: 
1.235     brouard  5902:  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
1.126     brouard  5903: 
                   5904: {
                   5905:   /* Health expectancies, no variances */
1.164     brouard  5906:   int i, j, nhstepm, hstepm, h, nstepm;
1.126     brouard  5907:   int nhstepma, nstepma; /* Decreasing with age */
                   5908:   double age, agelim, hf;
                   5909:   double ***p3mat;
                   5910:   double eip;
                   5911: 
1.238     brouard  5912:   /* pstamp(ficreseij); */
1.126     brouard  5913:   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
                   5914:   fprintf(ficreseij,"# Age");
                   5915:   for(i=1; i<=nlstate;i++){
                   5916:     for(j=1; j<=nlstate;j++){
                   5917:       fprintf(ficreseij," e%1d%1d ",i,j);
                   5918:     }
                   5919:     fprintf(ficreseij," e%1d. ",i);
                   5920:   }
                   5921:   fprintf(ficreseij,"\n");
                   5922: 
                   5923:   
                   5924:   if(estepm < stepm){
                   5925:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   5926:   }
                   5927:   else  hstepm=estepm;   
                   5928:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   5929:    * This is mainly to measure the difference between two models: for example
                   5930:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   5931:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   5932:    * progression in between and thus overestimating or underestimating according
                   5933:    * to the curvature of the survival function. If, for the same date, we 
                   5934:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   5935:    * to compare the new estimate of Life expectancy with the same linear 
                   5936:    * hypothesis. A more precise result, taking into account a more precise
                   5937:    * curvature will be obtained if estepm is as small as stepm. */
                   5938: 
                   5939:   /* For example we decided to compute the life expectancy with the smallest unit */
                   5940:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   5941:      nhstepm is the number of hstepm from age to agelim 
                   5942:      nstepm is the number of stepm from age to agelin. 
1.270     brouard  5943:      Look at hpijx to understand the reason which relies in memory size consideration
1.126     brouard  5944:      and note for a fixed period like estepm months */
                   5945:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   5946:      survival function given by stepm (the optimization length). Unfortunately it
                   5947:      means that if the survival funtion is printed only each two years of age and if
                   5948:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   5949:      results. So we changed our mind and took the option of the best precision.
                   5950:   */
                   5951:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   5952: 
                   5953:   agelim=AGESUP;
                   5954:   /* If stepm=6 months */
                   5955:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   5956:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   5957:     
                   5958: /* nhstepm age range expressed in number of stepm */
                   5959:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   5960:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   5961:   /* if (stepm >= YEARM) hstepm=1;*/
                   5962:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   5963:   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5964: 
                   5965:   for (age=bage; age<=fage; age ++){ 
                   5966:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   5967:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   5968:     /* if (stepm >= YEARM) hstepm=1;*/
                   5969:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   5970: 
                   5971:     /* If stepm=6 months */
                   5972:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   5973:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   5974:     
1.235     brouard  5975:     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
1.126     brouard  5976:     
                   5977:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   5978:     
                   5979:     printf("%d|",(int)age);fflush(stdout);
                   5980:     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   5981:     
                   5982:     /* Computing expectancies */
                   5983:     for(i=1; i<=nlstate;i++)
                   5984:       for(j=1; j<=nlstate;j++)
                   5985:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   5986:          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                   5987:          
                   5988:          /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                   5989: 
                   5990:        }
                   5991: 
                   5992:     fprintf(ficreseij,"%3.0f",age );
                   5993:     for(i=1; i<=nlstate;i++){
                   5994:       eip=0;
                   5995:       for(j=1; j<=nlstate;j++){
                   5996:        eip +=eij[i][j][(int)age];
                   5997:        fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                   5998:       }
                   5999:       fprintf(ficreseij,"%9.4f", eip );
                   6000:     }
                   6001:     fprintf(ficreseij,"\n");
                   6002:     
                   6003:   }
                   6004:   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   6005:   printf("\n");
                   6006:   fprintf(ficlog,"\n");
                   6007:   
                   6008: }
                   6009: 
1.235     brouard  6010:  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
1.126     brouard  6011: 
                   6012: {
                   6013:   /* Covariances of health expectancies eij and of total life expectancies according
1.222     brouard  6014:      to initial status i, ei. .
1.126     brouard  6015:   */
                   6016:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
                   6017:   int nhstepma, nstepma; /* Decreasing with age */
                   6018:   double age, agelim, hf;
                   6019:   double ***p3matp, ***p3matm, ***varhe;
                   6020:   double **dnewm,**doldm;
                   6021:   double *xp, *xm;
                   6022:   double **gp, **gm;
                   6023:   double ***gradg, ***trgradg;
                   6024:   int theta;
                   6025: 
                   6026:   double eip, vip;
                   6027: 
                   6028:   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                   6029:   xp=vector(1,npar);
                   6030:   xm=vector(1,npar);
                   6031:   dnewm=matrix(1,nlstate*nlstate,1,npar);
                   6032:   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
                   6033:   
                   6034:   pstamp(ficresstdeij);
                   6035:   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
                   6036:   fprintf(ficresstdeij,"# Age");
                   6037:   for(i=1; i<=nlstate;i++){
                   6038:     for(j=1; j<=nlstate;j++)
                   6039:       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
                   6040:     fprintf(ficresstdeij," e%1d. ",i);
                   6041:   }
                   6042:   fprintf(ficresstdeij,"\n");
                   6043: 
                   6044:   pstamp(ficrescveij);
                   6045:   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
                   6046:   fprintf(ficrescveij,"# Age");
                   6047:   for(i=1; i<=nlstate;i++)
                   6048:     for(j=1; j<=nlstate;j++){
                   6049:       cptj= (j-1)*nlstate+i;
                   6050:       for(i2=1; i2<=nlstate;i2++)
                   6051:        for(j2=1; j2<=nlstate;j2++){
                   6052:          cptj2= (j2-1)*nlstate+i2;
                   6053:          if(cptj2 <= cptj)
                   6054:            fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
                   6055:        }
                   6056:     }
                   6057:   fprintf(ficrescveij,"\n");
                   6058:   
                   6059:   if(estepm < stepm){
                   6060:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   6061:   }
                   6062:   else  hstepm=estepm;   
                   6063:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   6064:    * This is mainly to measure the difference between two models: for example
                   6065:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   6066:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   6067:    * progression in between and thus overestimating or underestimating according
                   6068:    * to the curvature of the survival function. If, for the same date, we 
                   6069:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   6070:    * to compare the new estimate of Life expectancy with the same linear 
                   6071:    * hypothesis. A more precise result, taking into account a more precise
                   6072:    * curvature will be obtained if estepm is as small as stepm. */
                   6073: 
                   6074:   /* For example we decided to compute the life expectancy with the smallest unit */
                   6075:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   6076:      nhstepm is the number of hstepm from age to agelim 
                   6077:      nstepm is the number of stepm from age to agelin. 
                   6078:      Look at hpijx to understand the reason of that which relies in memory size
                   6079:      and note for a fixed period like estepm months */
                   6080:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   6081:      survival function given by stepm (the optimization length). Unfortunately it
                   6082:      means that if the survival funtion is printed only each two years of age and if
                   6083:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   6084:      results. So we changed our mind and took the option of the best precision.
                   6085:   */
                   6086:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   6087: 
                   6088:   /* If stepm=6 months */
                   6089:   /* nhstepm age range expressed in number of stepm */
                   6090:   agelim=AGESUP;
                   6091:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                   6092:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   6093:   /* if (stepm >= YEARM) hstepm=1;*/
                   6094:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   6095:   
                   6096:   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   6097:   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   6098:   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                   6099:   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                   6100:   gp=matrix(0,nhstepm,1,nlstate*nlstate);
                   6101:   gm=matrix(0,nhstepm,1,nlstate*nlstate);
                   6102: 
                   6103:   for (age=bage; age<=fage; age ++){ 
                   6104:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   6105:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   6106:     /* if (stepm >= YEARM) hstepm=1;*/
                   6107:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218     brouard  6108:                
1.126     brouard  6109:     /* If stepm=6 months */
                   6110:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   6111:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   6112:     
                   6113:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
1.218     brouard  6114:                
1.126     brouard  6115:     /* Computing  Variances of health expectancies */
                   6116:     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
                   6117:        decrease memory allocation */
                   6118:     for(theta=1; theta <=npar; theta++){
                   6119:       for(i=1; i<=npar; i++){ 
1.222     brouard  6120:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   6121:        xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126     brouard  6122:       }
1.235     brouard  6123:       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);  
                   6124:       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);  
1.218     brouard  6125:                        
1.126     brouard  6126:       for(j=1; j<= nlstate; j++){
1.222     brouard  6127:        for(i=1; i<=nlstate; i++){
                   6128:          for(h=0; h<=nhstepm-1; h++){
                   6129:            gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                   6130:            gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                   6131:          }
                   6132:        }
1.126     brouard  6133:       }
1.218     brouard  6134:                        
1.126     brouard  6135:       for(ij=1; ij<= nlstate*nlstate; ij++)
1.222     brouard  6136:        for(h=0; h<=nhstepm-1; h++){
                   6137:          gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
                   6138:        }
1.126     brouard  6139:     }/* End theta */
                   6140:     
                   6141:     
                   6142:     for(h=0; h<=nhstepm-1; h++)
                   6143:       for(j=1; j<=nlstate*nlstate;j++)
1.222     brouard  6144:        for(theta=1; theta <=npar; theta++)
                   6145:          trgradg[h][j][theta]=gradg[h][theta][j];
1.126     brouard  6146:     
1.218     brouard  6147:                
1.222     brouard  6148:     for(ij=1;ij<=nlstate*nlstate;ij++)
1.126     brouard  6149:       for(ji=1;ji<=nlstate*nlstate;ji++)
1.222     brouard  6150:        varhe[ij][ji][(int)age] =0.;
1.218     brouard  6151:                
1.222     brouard  6152:     printf("%d|",(int)age);fflush(stdout);
                   6153:     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   6154:     for(h=0;h<=nhstepm-1;h++){
1.126     brouard  6155:       for(k=0;k<=nhstepm-1;k++){
1.222     brouard  6156:        matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   6157:        matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                   6158:        for(ij=1;ij<=nlstate*nlstate;ij++)
                   6159:          for(ji=1;ji<=nlstate*nlstate;ji++)
                   6160:            varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126     brouard  6161:       }
                   6162:     }
1.320     brouard  6163:     /* if((int)age ==50){ */
                   6164:     /*   printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
                   6165:     /* } */
1.126     brouard  6166:     /* Computing expectancies */
1.235     brouard  6167:     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);  
1.126     brouard  6168:     for(i=1; i<=nlstate;i++)
                   6169:       for(j=1; j<=nlstate;j++)
1.222     brouard  6170:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   6171:          eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218     brouard  6172:                                        
1.222     brouard  6173:          /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
1.218     brouard  6174:                                        
1.222     brouard  6175:        }
1.269     brouard  6176: 
                   6177:     /* Standard deviation of expectancies ij */                
1.126     brouard  6178:     fprintf(ficresstdeij,"%3.0f",age );
                   6179:     for(i=1; i<=nlstate;i++){
                   6180:       eip=0.;
                   6181:       vip=0.;
                   6182:       for(j=1; j<=nlstate;j++){
1.222     brouard  6183:        eip += eij[i][j][(int)age];
                   6184:        for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                   6185:          vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                   6186:        fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
1.126     brouard  6187:       }
                   6188:       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
                   6189:     }
                   6190:     fprintf(ficresstdeij,"\n");
1.218     brouard  6191:                
1.269     brouard  6192:     /* Variance of expectancies ij */          
1.126     brouard  6193:     fprintf(ficrescveij,"%3.0f",age );
                   6194:     for(i=1; i<=nlstate;i++)
                   6195:       for(j=1; j<=nlstate;j++){
1.222     brouard  6196:        cptj= (j-1)*nlstate+i;
                   6197:        for(i2=1; i2<=nlstate;i2++)
                   6198:          for(j2=1; j2<=nlstate;j2++){
                   6199:            cptj2= (j2-1)*nlstate+i2;
                   6200:            if(cptj2 <= cptj)
                   6201:              fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                   6202:          }
1.126     brouard  6203:       }
                   6204:     fprintf(ficrescveij,"\n");
1.218     brouard  6205:                
1.126     brouard  6206:   }
                   6207:   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   6208:   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   6209:   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   6210:   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                   6211:   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   6212:   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   6213:   printf("\n");
                   6214:   fprintf(ficlog,"\n");
1.218     brouard  6215:        
1.126     brouard  6216:   free_vector(xm,1,npar);
                   6217:   free_vector(xp,1,npar);
                   6218:   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   6219:   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   6220:   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                   6221: }
1.218     brouard  6222:  
1.126     brouard  6223: /************ Variance ******************/
1.235     brouard  6224:  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
1.218     brouard  6225:  {
1.279     brouard  6226:    /** Variance of health expectancies 
                   6227:     *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
                   6228:     * double **newm;
                   6229:     * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav) 
                   6230:     */
1.218     brouard  6231:   
                   6232:    /* int movingaverage(); */
                   6233:    double **dnewm,**doldm;
                   6234:    double **dnewmp,**doldmp;
                   6235:    int i, j, nhstepm, hstepm, h, nstepm ;
1.288     brouard  6236:    int first=0;
1.218     brouard  6237:    int k;
                   6238:    double *xp;
1.279     brouard  6239:    double **gp, **gm;  /**< for var eij */
                   6240:    double ***gradg, ***trgradg; /**< for var eij */
                   6241:    double **gradgp, **trgradgp; /**< for var p point j */
                   6242:    double *gpp, *gmp; /**< for var p point j */
                   6243:    double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218     brouard  6244:    double ***p3mat;
                   6245:    double age,agelim, hf;
                   6246:    /* double ***mobaverage; */
                   6247:    int theta;
                   6248:    char digit[4];
                   6249:    char digitp[25];
                   6250: 
                   6251:    char fileresprobmorprev[FILENAMELENGTH];
                   6252: 
                   6253:    if(popbased==1){
                   6254:      if(mobilav!=0)
                   6255:        strcpy(digitp,"-POPULBASED-MOBILAV_");
                   6256:      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
                   6257:    }
                   6258:    else 
                   6259:      strcpy(digitp,"-STABLBASED_");
1.126     brouard  6260: 
1.218     brouard  6261:    /* if (mobilav!=0) { */
                   6262:    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   6263:    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
                   6264:    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
                   6265:    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
                   6266:    /*   } */
                   6267:    /* } */
                   6268: 
                   6269:    strcpy(fileresprobmorprev,"PRMORPREV-"); 
                   6270:    sprintf(digit,"%-d",ij);
                   6271:    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   6272:    strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   6273:    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   6274:    strcat(fileresprobmorprev,fileresu);
                   6275:    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   6276:      printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   6277:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   6278:    }
                   6279:    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   6280:    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   6281:    pstamp(ficresprobmorprev);
                   6282:    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
1.238     brouard  6283:    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
                   6284:    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   6285:      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   6286:    }
                   6287:    for(j=1;j<=cptcoveff;j++) 
                   6288:      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
                   6289:    fprintf(ficresprobmorprev,"\n");
                   6290: 
1.218     brouard  6291:    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   6292:    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   6293:      fprintf(ficresprobmorprev," p.%-d SE",j);
                   6294:      for(i=1; i<=nlstate;i++)
                   6295:        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   6296:    }  
                   6297:    fprintf(ficresprobmorprev,"\n");
                   6298:   
                   6299:    fprintf(ficgp,"\n# Routine varevsij");
                   6300:    fprintf(ficgp,"\nunset title \n");
                   6301:    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
                   6302:    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
                   6303:    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
1.279     brouard  6304: 
1.218     brouard  6305:    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   6306:    pstamp(ficresvij);
                   6307:    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
                   6308:    if(popbased==1)
                   6309:      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
                   6310:    else
                   6311:      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
                   6312:    fprintf(ficresvij,"# Age");
                   6313:    for(i=1; i<=nlstate;i++)
                   6314:      for(j=1; j<=nlstate;j++)
                   6315:        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
                   6316:    fprintf(ficresvij,"\n");
                   6317: 
                   6318:    xp=vector(1,npar);
                   6319:    dnewm=matrix(1,nlstate,1,npar);
                   6320:    doldm=matrix(1,nlstate,1,nlstate);
                   6321:    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   6322:    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   6323: 
                   6324:    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                   6325:    gpp=vector(nlstate+1,nlstate+ndeath);
                   6326:    gmp=vector(nlstate+1,nlstate+ndeath);
                   6327:    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126     brouard  6328:   
1.218     brouard  6329:    if(estepm < stepm){
                   6330:      printf ("Problem %d lower than %d\n",estepm, stepm);
                   6331:    }
                   6332:    else  hstepm=estepm;   
                   6333:    /* For example we decided to compute the life expectancy with the smallest unit */
                   6334:    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   6335:       nhstepm is the number of hstepm from age to agelim 
                   6336:       nstepm is the number of stepm from age to agelim. 
                   6337:       Look at function hpijx to understand why because of memory size limitations, 
                   6338:       we decided (b) to get a life expectancy respecting the most precise curvature of the
                   6339:       survival function given by stepm (the optimization length). Unfortunately it
                   6340:       means that if the survival funtion is printed every two years of age and if
                   6341:       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   6342:       results. So we changed our mind and took the option of the best precision.
                   6343:    */
                   6344:    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   6345:    agelim = AGESUP;
                   6346:    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   6347:      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   6348:      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   6349:      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   6350:      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                   6351:      gp=matrix(0,nhstepm,1,nlstate);
                   6352:      gm=matrix(0,nhstepm,1,nlstate);
                   6353:                
                   6354:                
                   6355:      for(theta=1; theta <=npar; theta++){
                   6356:        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                   6357:         xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   6358:        }
1.279     brouard  6359:        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
                   6360:        * returns into prlim .
1.288     brouard  6361:        */
1.242     brouard  6362:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279     brouard  6363: 
                   6364:        /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218     brouard  6365:        if (popbased==1) {
                   6366:         if(mobilav ==0){
                   6367:           for(i=1; i<=nlstate;i++)
                   6368:             prlim[i][i]=probs[(int)age][i][ij];
                   6369:         }else{ /* mobilav */ 
                   6370:           for(i=1; i<=nlstate;i++)
                   6371:             prlim[i][i]=mobaverage[(int)age][i][ij];
                   6372:         }
                   6373:        }
1.295     brouard  6374:        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279     brouard  6375:        */                      
                   6376:        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
1.292     brouard  6377:        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
1.279     brouard  6378:        * at horizon h in state j including mortality.
                   6379:        */
1.218     brouard  6380:        for(j=1; j<= nlstate; j++){
                   6381:         for(h=0; h<=nhstepm; h++){
                   6382:           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                   6383:             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   6384:         }
                   6385:        }
1.279     brouard  6386:        /* Next for computing shifted+ probability of death (h=1 means
1.218     brouard  6387:          computed over hstepm matrices product = hstepm*stepm months) 
1.279     brouard  6388:          as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218     brouard  6389:        */
                   6390:        for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   6391:         for(i=1,gpp[j]=0.; i<= nlstate; i++)
                   6392:           gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279     brouard  6393:        }
                   6394:        
                   6395:        /* Again with minus shift */
1.218     brouard  6396:                        
                   6397:        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                   6398:         xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288     brouard  6399: 
1.242     brouard  6400:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218     brouard  6401:                        
                   6402:        if (popbased==1) {
                   6403:         if(mobilav ==0){
                   6404:           for(i=1; i<=nlstate;i++)
                   6405:             prlim[i][i]=probs[(int)age][i][ij];
                   6406:         }else{ /* mobilav */ 
                   6407:           for(i=1; i<=nlstate;i++)
                   6408:             prlim[i][i]=mobaverage[(int)age][i][ij];
                   6409:         }
                   6410:        }
                   6411:                        
1.235     brouard  6412:        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  
1.218     brouard  6413:                        
                   6414:        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
                   6415:         for(h=0; h<=nhstepm; h++){
                   6416:           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   6417:             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                   6418:         }
                   6419:        }
                   6420:        /* This for computing probability of death (h=1 means
                   6421:          computed over hstepm matrices product = hstepm*stepm months) 
                   6422:          as a weighted average of prlim.
                   6423:        */
                   6424:        for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   6425:         for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   6426:           gmp[j] += prlim[i][i]*p3mat[i][j][1];
                   6427:        }    
1.279     brouard  6428:        /* end shifting computations */
                   6429: 
                   6430:        /**< Computing gradient matrix at horizon h 
                   6431:        */
1.218     brouard  6432:        for(j=1; j<= nlstate; j++) /* vareij */
                   6433:         for(h=0; h<=nhstepm; h++){
                   6434:           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   6435:         }
1.279     brouard  6436:        /**< Gradient of overall mortality p.3 (or p.j) 
                   6437:        */
                   6438:        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218     brouard  6439:         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                   6440:        }
                   6441:                        
                   6442:      } /* End theta */
1.279     brouard  6443:      
                   6444:      /* We got the gradient matrix for each theta and state j */               
1.218     brouard  6445:      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   6446:                
                   6447:      for(h=0; h<=nhstepm; h++) /* veij */
                   6448:        for(j=1; j<=nlstate;j++)
                   6449:         for(theta=1; theta <=npar; theta++)
                   6450:           trgradg[h][j][theta]=gradg[h][theta][j];
                   6451:                
                   6452:      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                   6453:        for(theta=1; theta <=npar; theta++)
                   6454:         trgradgp[j][theta]=gradgp[theta][j];
1.279     brouard  6455:      /**< as well as its transposed matrix 
                   6456:       */               
1.218     brouard  6457:                
                   6458:      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   6459:      for(i=1;i<=nlstate;i++)
                   6460:        for(j=1;j<=nlstate;j++)
                   6461:         vareij[i][j][(int)age] =0.;
1.279     brouard  6462: 
                   6463:      /* Computing trgradg by matcov by gradg at age and summing over h
                   6464:       * and k (nhstepm) formula 15 of article
                   6465:       * Lievre-Brouard-Heathcote
                   6466:       */
                   6467:      
1.218     brouard  6468:      for(h=0;h<=nhstepm;h++){
                   6469:        for(k=0;k<=nhstepm;k++){
                   6470:         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                   6471:         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                   6472:         for(i=1;i<=nlstate;i++)
                   6473:           for(j=1;j<=nlstate;j++)
                   6474:             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                   6475:        }
                   6476:      }
                   6477:                
1.279     brouard  6478:      /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
                   6479:       * p.j overall mortality formula 49 but computed directly because
                   6480:       * we compute the grad (wix pijx) instead of grad (pijx),even if
                   6481:       * wix is independent of theta.
                   6482:       */
1.218     brouard  6483:      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                   6484:      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                   6485:      for(j=nlstate+1;j<=nlstate+ndeath;j++)
                   6486:        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                   6487:         varppt[j][i]=doldmp[j][i];
                   6488:      /* end ppptj */
                   6489:      /*  x centered again */
                   6490:                
1.242     brouard  6491:      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218     brouard  6492:                
                   6493:      if (popbased==1) {
                   6494:        if(mobilav ==0){
                   6495:         for(i=1; i<=nlstate;i++)
                   6496:           prlim[i][i]=probs[(int)age][i][ij];
                   6497:        }else{ /* mobilav */ 
                   6498:         for(i=1; i<=nlstate;i++)
                   6499:           prlim[i][i]=mobaverage[(int)age][i][ij];
                   6500:        }
                   6501:      }
                   6502:                
                   6503:      /* This for computing probability of death (h=1 means
                   6504:        computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   6505:        as a weighted average of prlim.
                   6506:      */
1.235     brouard  6507:      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);  
1.218     brouard  6508:      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   6509:        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                   6510:         gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   6511:      }    
                   6512:      /* end probability of death */
                   6513:                
                   6514:      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   6515:      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   6516:        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                   6517:        for(i=1; i<=nlstate;i++){
                   6518:         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   6519:        }
                   6520:      } 
                   6521:      fprintf(ficresprobmorprev,"\n");
                   6522:                
                   6523:      fprintf(ficresvij,"%.0f ",age );
                   6524:      for(i=1; i<=nlstate;i++)
                   6525:        for(j=1; j<=nlstate;j++){
                   6526:         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                   6527:        }
                   6528:      fprintf(ficresvij,"\n");
                   6529:      free_matrix(gp,0,nhstepm,1,nlstate);
                   6530:      free_matrix(gm,0,nhstepm,1,nlstate);
                   6531:      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                   6532:      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                   6533:      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   6534:    } /* End age */
                   6535:    free_vector(gpp,nlstate+1,nlstate+ndeath);
                   6536:    free_vector(gmp,nlstate+1,nlstate+ndeath);
                   6537:    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                   6538:    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   6539:    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
                   6540:    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
                   6541:    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
                   6542:    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
                   6543:    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
                   6544:    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                   6545:    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   6546:    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   6547:    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
                   6548:    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
                   6549:    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
                   6550:    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
                   6551:    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
                   6552:    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
1.126     brouard  6553:     */
1.218     brouard  6554:    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
                   6555:    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126     brouard  6556: 
1.218     brouard  6557:    free_vector(xp,1,npar);
                   6558:    free_matrix(doldm,1,nlstate,1,nlstate);
                   6559:    free_matrix(dnewm,1,nlstate,1,npar);
                   6560:    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   6561:    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   6562:    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   6563:    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   6564:    fclose(ficresprobmorprev);
                   6565:    fflush(ficgp);
                   6566:    fflush(fichtm); 
                   6567:  }  /* end varevsij */
1.126     brouard  6568: 
                   6569: /************ Variance of prevlim ******************/
1.269     brouard  6570:  void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
1.126     brouard  6571: {
1.205     brouard  6572:   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126     brouard  6573:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164     brouard  6574: 
1.268     brouard  6575:   double **dnewmpar,**doldm;
1.126     brouard  6576:   int i, j, nhstepm, hstepm;
                   6577:   double *xp;
                   6578:   double *gp, *gm;
                   6579:   double **gradg, **trgradg;
1.208     brouard  6580:   double **mgm, **mgp;
1.126     brouard  6581:   double age,agelim;
                   6582:   int theta;
                   6583:   
                   6584:   pstamp(ficresvpl);
1.288     brouard  6585:   fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241     brouard  6586:   fprintf(ficresvpl,"# Age ");
                   6587:   if(nresult >=1)
                   6588:     fprintf(ficresvpl," Result# ");
1.126     brouard  6589:   for(i=1; i<=nlstate;i++)
                   6590:       fprintf(ficresvpl," %1d-%1d",i,i);
                   6591:   fprintf(ficresvpl,"\n");
                   6592: 
                   6593:   xp=vector(1,npar);
1.268     brouard  6594:   dnewmpar=matrix(1,nlstate,1,npar);
1.126     brouard  6595:   doldm=matrix(1,nlstate,1,nlstate);
                   6596:   
                   6597:   hstepm=1*YEARM; /* Every year of age */
                   6598:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                   6599:   agelim = AGESUP;
                   6600:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   6601:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   6602:     if (stepm >= YEARM) hstepm=1;
                   6603:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   6604:     gradg=matrix(1,npar,1,nlstate);
1.208     brouard  6605:     mgp=matrix(1,npar,1,nlstate);
                   6606:     mgm=matrix(1,npar,1,nlstate);
1.126     brouard  6607:     gp=vector(1,nlstate);
                   6608:     gm=vector(1,nlstate);
                   6609: 
                   6610:     for(theta=1; theta <=npar; theta++){
                   6611:       for(i=1; i<=npar; i++){ /* Computes gradient */
                   6612:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   6613:       }
1.288     brouard  6614:       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
                   6615:       /*       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
                   6616:       /* else */
                   6617:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208     brouard  6618:       for(i=1;i<=nlstate;i++){
1.126     brouard  6619:        gp[i] = prlim[i][i];
1.208     brouard  6620:        mgp[theta][i] = prlim[i][i];
                   6621:       }
1.126     brouard  6622:       for(i=1; i<=npar; i++) /* Computes gradient */
                   6623:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288     brouard  6624:       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
                   6625:       /*       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
                   6626:       /* else */
                   6627:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208     brouard  6628:       for(i=1;i<=nlstate;i++){
1.126     brouard  6629:        gm[i] = prlim[i][i];
1.208     brouard  6630:        mgm[theta][i] = prlim[i][i];
                   6631:       }
1.126     brouard  6632:       for(i=1;i<=nlstate;i++)
                   6633:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209     brouard  6634:       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126     brouard  6635:     } /* End theta */
                   6636: 
                   6637:     trgradg =matrix(1,nlstate,1,npar);
                   6638: 
                   6639:     for(j=1; j<=nlstate;j++)
                   6640:       for(theta=1; theta <=npar; theta++)
                   6641:        trgradg[j][theta]=gradg[theta][j];
1.209     brouard  6642:     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
                   6643:     /*   printf("\nmgm mgp %d ",(int)age); */
                   6644:     /*   for(j=1; j<=nlstate;j++){ */
                   6645:     /*         printf(" %d ",j); */
                   6646:     /*         for(theta=1; theta <=npar; theta++) */
                   6647:     /*           printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
                   6648:     /*         printf("\n "); */
                   6649:     /*   } */
                   6650:     /* } */
                   6651:     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
                   6652:     /*   printf("\n gradg %d ",(int)age); */
                   6653:     /*   for(j=1; j<=nlstate;j++){ */
                   6654:     /*         printf("%d ",j); */
                   6655:     /*         for(theta=1; theta <=npar; theta++) */
                   6656:     /*           printf("%d %lf ",theta,gradg[theta][j]); */
                   6657:     /*         printf("\n "); */
                   6658:     /*   } */
                   6659:     /* } */
1.126     brouard  6660: 
                   6661:     for(i=1;i<=nlstate;i++)
                   6662:       varpl[i][(int)age] =0.;
1.209     brouard  6663:     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
1.268     brouard  6664:     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   6665:     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205     brouard  6666:     }else{
1.268     brouard  6667:     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   6668:     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205     brouard  6669:     }
1.126     brouard  6670:     for(i=1;i<=nlstate;i++)
                   6671:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   6672: 
                   6673:     fprintf(ficresvpl,"%.0f ",age );
1.241     brouard  6674:     if(nresult >=1)
                   6675:       fprintf(ficresvpl,"%d ",nres );
1.288     brouard  6676:     for(i=1; i<=nlstate;i++){
1.126     brouard  6677:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288     brouard  6678:       /* for(j=1;j<=nlstate;j++) */
                   6679:       /*       fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
                   6680:     }
1.126     brouard  6681:     fprintf(ficresvpl,"\n");
                   6682:     free_vector(gp,1,nlstate);
                   6683:     free_vector(gm,1,nlstate);
1.208     brouard  6684:     free_matrix(mgm,1,npar,1,nlstate);
                   6685:     free_matrix(mgp,1,npar,1,nlstate);
1.126     brouard  6686:     free_matrix(gradg,1,npar,1,nlstate);
                   6687:     free_matrix(trgradg,1,nlstate,1,npar);
                   6688:   } /* End age */
                   6689: 
                   6690:   free_vector(xp,1,npar);
                   6691:   free_matrix(doldm,1,nlstate,1,npar);
1.268     brouard  6692:   free_matrix(dnewmpar,1,nlstate,1,nlstate);
                   6693: 
                   6694: }
                   6695: 
                   6696: 
                   6697: /************ Variance of backprevalence limit ******************/
1.269     brouard  6698:  void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
1.268     brouard  6699: {
                   6700:   /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
                   6701:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   6702: 
                   6703:   double **dnewmpar,**doldm;
                   6704:   int i, j, nhstepm, hstepm;
                   6705:   double *xp;
                   6706:   double *gp, *gm;
                   6707:   double **gradg, **trgradg;
                   6708:   double **mgm, **mgp;
                   6709:   double age,agelim;
                   6710:   int theta;
                   6711:   
                   6712:   pstamp(ficresvbl);
                   6713:   fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
                   6714:   fprintf(ficresvbl,"# Age ");
                   6715:   if(nresult >=1)
                   6716:     fprintf(ficresvbl," Result# ");
                   6717:   for(i=1; i<=nlstate;i++)
                   6718:       fprintf(ficresvbl," %1d-%1d",i,i);
                   6719:   fprintf(ficresvbl,"\n");
                   6720: 
                   6721:   xp=vector(1,npar);
                   6722:   dnewmpar=matrix(1,nlstate,1,npar);
                   6723:   doldm=matrix(1,nlstate,1,nlstate);
                   6724:   
                   6725:   hstepm=1*YEARM; /* Every year of age */
                   6726:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                   6727:   agelim = AGEINF;
                   6728:   for (age=fage; age>=bage; age --){ /* If stepm=6 months */
                   6729:     nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   6730:     if (stepm >= YEARM) hstepm=1;
                   6731:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   6732:     gradg=matrix(1,npar,1,nlstate);
                   6733:     mgp=matrix(1,npar,1,nlstate);
                   6734:     mgm=matrix(1,npar,1,nlstate);
                   6735:     gp=vector(1,nlstate);
                   6736:     gm=vector(1,nlstate);
                   6737: 
                   6738:     for(theta=1; theta <=npar; theta++){
                   6739:       for(i=1; i<=npar; i++){ /* Computes gradient */
                   6740:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   6741:       }
                   6742:       if(mobilavproj > 0 )
                   6743:        bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
                   6744:       else
                   6745:        bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
                   6746:       for(i=1;i<=nlstate;i++){
                   6747:        gp[i] = bprlim[i][i];
                   6748:        mgp[theta][i] = bprlim[i][i];
                   6749:       }
                   6750:      for(i=1; i<=npar; i++) /* Computes gradient */
                   6751:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   6752:        if(mobilavproj > 0 )
                   6753:        bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
                   6754:        else
                   6755:        bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
                   6756:       for(i=1;i<=nlstate;i++){
                   6757:        gm[i] = bprlim[i][i];
                   6758:        mgm[theta][i] = bprlim[i][i];
                   6759:       }
                   6760:       for(i=1;i<=nlstate;i++)
                   6761:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                   6762:       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
                   6763:     } /* End theta */
                   6764: 
                   6765:     trgradg =matrix(1,nlstate,1,npar);
                   6766: 
                   6767:     for(j=1; j<=nlstate;j++)
                   6768:       for(theta=1; theta <=npar; theta++)
                   6769:        trgradg[j][theta]=gradg[theta][j];
                   6770:     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
                   6771:     /*   printf("\nmgm mgp %d ",(int)age); */
                   6772:     /*   for(j=1; j<=nlstate;j++){ */
                   6773:     /*         printf(" %d ",j); */
                   6774:     /*         for(theta=1; theta <=npar; theta++) */
                   6775:     /*           printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
                   6776:     /*         printf("\n "); */
                   6777:     /*   } */
                   6778:     /* } */
                   6779:     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
                   6780:     /*   printf("\n gradg %d ",(int)age); */
                   6781:     /*   for(j=1; j<=nlstate;j++){ */
                   6782:     /*         printf("%d ",j); */
                   6783:     /*         for(theta=1; theta <=npar; theta++) */
                   6784:     /*           printf("%d %lf ",theta,gradg[theta][j]); */
                   6785:     /*         printf("\n "); */
                   6786:     /*   } */
                   6787:     /* } */
                   6788: 
                   6789:     for(i=1;i<=nlstate;i++)
                   6790:       varbpl[i][(int)age] =0.;
                   6791:     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
                   6792:     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   6793:     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
                   6794:     }else{
                   6795:     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   6796:     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
                   6797:     }
                   6798:     for(i=1;i<=nlstate;i++)
                   6799:       varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   6800: 
                   6801:     fprintf(ficresvbl,"%.0f ",age );
                   6802:     if(nresult >=1)
                   6803:       fprintf(ficresvbl,"%d ",nres );
                   6804:     for(i=1; i<=nlstate;i++)
                   6805:       fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
                   6806:     fprintf(ficresvbl,"\n");
                   6807:     free_vector(gp,1,nlstate);
                   6808:     free_vector(gm,1,nlstate);
                   6809:     free_matrix(mgm,1,npar,1,nlstate);
                   6810:     free_matrix(mgp,1,npar,1,nlstate);
                   6811:     free_matrix(gradg,1,npar,1,nlstate);
                   6812:     free_matrix(trgradg,1,nlstate,1,npar);
                   6813:   } /* End age */
                   6814: 
                   6815:   free_vector(xp,1,npar);
                   6816:   free_matrix(doldm,1,nlstate,1,npar);
                   6817:   free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126     brouard  6818: 
                   6819: }
                   6820: 
                   6821: /************ Variance of one-step probabilities  ******************/
                   6822: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
1.222     brouard  6823:  {
                   6824:    int i, j=0,  k1, l1, tj;
                   6825:    int k2, l2, j1,  z1;
                   6826:    int k=0, l;
                   6827:    int first=1, first1, first2;
1.326     brouard  6828:    int nres=0; /* New */
1.222     brouard  6829:    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                   6830:    double **dnewm,**doldm;
                   6831:    double *xp;
                   6832:    double *gp, *gm;
                   6833:    double **gradg, **trgradg;
                   6834:    double **mu;
                   6835:    double age, cov[NCOVMAX+1];
                   6836:    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   6837:    int theta;
                   6838:    char fileresprob[FILENAMELENGTH];
                   6839:    char fileresprobcov[FILENAMELENGTH];
                   6840:    char fileresprobcor[FILENAMELENGTH];
                   6841:    double ***varpij;
                   6842: 
                   6843:    strcpy(fileresprob,"PROB_"); 
                   6844:    strcat(fileresprob,fileres);
                   6845:    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                   6846:      printf("Problem with resultfile: %s\n", fileresprob);
                   6847:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   6848:    }
                   6849:    strcpy(fileresprobcov,"PROBCOV_"); 
                   6850:    strcat(fileresprobcov,fileresu);
                   6851:    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   6852:      printf("Problem with resultfile: %s\n", fileresprobcov);
                   6853:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   6854:    }
                   6855:    strcpy(fileresprobcor,"PROBCOR_"); 
                   6856:    strcat(fileresprobcor,fileresu);
                   6857:    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                   6858:      printf("Problem with resultfile: %s\n", fileresprobcor);
                   6859:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   6860:    }
                   6861:    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   6862:    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   6863:    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   6864:    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   6865:    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   6866:    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   6867:    pstamp(ficresprob);
                   6868:    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
                   6869:    fprintf(ficresprob,"# Age");
                   6870:    pstamp(ficresprobcov);
                   6871:    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
                   6872:    fprintf(ficresprobcov,"# Age");
                   6873:    pstamp(ficresprobcor);
                   6874:    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
                   6875:    fprintf(ficresprobcor,"# Age");
1.126     brouard  6876: 
                   6877: 
1.222     brouard  6878:    for(i=1; i<=nlstate;i++)
                   6879:      for(j=1; j<=(nlstate+ndeath);j++){
                   6880:        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                   6881:        fprintf(ficresprobcov," p%1d-%1d ",i,j);
                   6882:        fprintf(ficresprobcor," p%1d-%1d ",i,j);
                   6883:      }  
                   6884:    /* fprintf(ficresprob,"\n");
                   6885:       fprintf(ficresprobcov,"\n");
                   6886:       fprintf(ficresprobcor,"\n");
                   6887:    */
                   6888:    xp=vector(1,npar);
                   6889:    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   6890:    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   6891:    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                   6892:    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                   6893:    first=1;
                   6894:    fprintf(ficgp,"\n# Routine varprob");
                   6895:    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   6896:    fprintf(fichtm,"\n");
                   6897: 
1.288     brouard  6898:    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
1.222     brouard  6899:    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
                   6900:    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126     brouard  6901: and drawn. It helps understanding how is the covariance between two incidences.\
                   6902:  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222     brouard  6903:    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
1.126     brouard  6904: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
                   6905: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
                   6906: standard deviations wide on each axis. <br>\
                   6907:  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
                   6908:  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
                   6909: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
                   6910: 
1.222     brouard  6911:    cov[1]=1;
                   6912:    /* tj=cptcoveff; */
1.225     brouard  6913:    tj = (int) pow(2,cptcoveff);
1.222     brouard  6914:    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   6915:    j1=0;
1.224     brouard  6916:    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
1.326     brouard  6917:      for(nres=1;nres <=1; nres++){ /* For each resultline */
                   6918:      /* for(nres=1;nres <=nresult; nres++){ /\* For each resultline *\/ */
1.222     brouard  6919:      if  (cptcovn>0) {
                   6920:        fprintf(ficresprob, "\n#********** Variable "); 
1.225     brouard  6921:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6922:        fprintf(ficresprob, "**********\n#\n");
                   6923:        fprintf(ficresprobcov, "\n#********** Variable "); 
1.225     brouard  6924:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6925:        fprintf(ficresprobcov, "**********\n#\n");
1.220     brouard  6926:                        
1.222     brouard  6927:        fprintf(ficgp, "\n#********** Variable "); 
1.225     brouard  6928:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6929:        fprintf(ficgp, "**********\n#\n");
1.220     brouard  6930:                        
                   6931:                        
1.222     brouard  6932:        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
1.319     brouard  6933:        /* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */
                   6934:        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6935:        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220     brouard  6936:                        
1.222     brouard  6937:        fprintf(ficresprobcor, "\n#********** Variable ");    
1.225     brouard  6938:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6939:        fprintf(ficresprobcor, "**********\n#");    
                   6940:        if(invalidvarcomb[j1]){
                   6941:         fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
                   6942:         fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
                   6943:         continue;
                   6944:        }
                   6945:      }
                   6946:      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                   6947:      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   6948:      gp=vector(1,(nlstate)*(nlstate+ndeath));
                   6949:      gm=vector(1,(nlstate)*(nlstate+ndeath));
                   6950:      for (age=bage; age<=fage; age ++){ 
                   6951:        cov[2]=age;
                   6952:        if(nagesqr==1)
                   6953:         cov[3]= age*age;
1.326     brouard  6954:        /* for (k=1; k<=cptcovn;k++) { */
                   6955:        /*       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */
                   6956:        for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                   6957:         /* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */
                   6958:         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,k)];
1.222     brouard  6959:         /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                   6960:                                                                    * 1  1 1 1 1
                   6961:                                                                    * 2  2 1 1 1
                   6962:                                                                    * 3  1 2 1 1
                   6963:                                                                    */
                   6964:         /* nbcode[1][1]=0 nbcode[1][2]=1;*/
                   6965:        }
1.319     brouard  6966:        /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
                   6967:        /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
                   6968:        /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.326     brouard  6969:        for (k=1; k<=cptcovage;k++){  /* For product with age */
                   6970:         if(Dummy[Tage[k]]==2){ /* dummy with age */
                   6971:           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,k)]*cov[2];
                   6972:           /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
                   6973:         } else if(Dummy[Tage[k]]==3){ /* quantitative with age */
1.327     brouard  6974:           printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]);
                   6975:           exit(1);
                   6976:             /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; *\/ */
1.326     brouard  6977:           /* cov[++k1]=Tqresult[nres][k];  */
                   6978:         }
                   6979:         /* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
                   6980:        }
                   6981:        for (k=1; k<=cptcovprod;k++){/* For product without age */
                   6982:         if(Dummy[Tvard[k][1]==0]){
                   6983:           if(Dummy[Tvard[k][2]==0]){
                   6984:             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * nbcode[Tvard[k][2]][codtabm(j1,k)];
                   6985:             /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
                   6986:           }else{ /* Should we use the mean of the quantitative variables? */
                   6987:             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * Tqresult[nres][k];
                   6988:             /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
                   6989:           }
                   6990:         }else{
                   6991:           if(Dummy[Tvard[k][2]==0]){
                   6992:             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,k)] * Tqinvresult[nres][Tvard[k][1]];
                   6993:             /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
                   6994:           }else{
                   6995:             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
                   6996:             /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
                   6997:           }
                   6998:         }
                   6999:         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
                   7000:        }                       
                   7001: /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/                    
1.222     brouard  7002:        for(theta=1; theta <=npar; theta++){
                   7003:         for(i=1; i<=npar; i++)
                   7004:           xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220     brouard  7005:                                
1.222     brouard  7006:         pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220     brouard  7007:                                
1.222     brouard  7008:         k=0;
                   7009:         for(i=1; i<= (nlstate); i++){
                   7010:           for(j=1; j<=(nlstate+ndeath);j++){
                   7011:             k=k+1;
                   7012:             gp[k]=pmmij[i][j];
                   7013:           }
                   7014:         }
1.220     brouard  7015:                                
1.222     brouard  7016:         for(i=1; i<=npar; i++)
                   7017:           xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220     brouard  7018:                                
1.222     brouard  7019:         pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   7020:         k=0;
                   7021:         for(i=1; i<=(nlstate); i++){
                   7022:           for(j=1; j<=(nlstate+ndeath);j++){
                   7023:             k=k+1;
                   7024:             gm[k]=pmmij[i][j];
                   7025:           }
                   7026:         }
1.220     brouard  7027:                                
1.222     brouard  7028:         for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                   7029:           gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
                   7030:        }
1.126     brouard  7031: 
1.222     brouard  7032:        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   7033:         for(theta=1; theta <=npar; theta++)
                   7034:           trgradg[j][theta]=gradg[theta][j];
1.220     brouard  7035:                        
1.222     brouard  7036:        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   7037:        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220     brouard  7038:                        
1.222     brouard  7039:        pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220     brouard  7040:                        
1.222     brouard  7041:        k=0;
                   7042:        for(i=1; i<=(nlstate); i++){
                   7043:         for(j=1; j<=(nlstate+ndeath);j++){
                   7044:           k=k+1;
                   7045:           mu[k][(int) age]=pmmij[i][j];
                   7046:         }
                   7047:        }
                   7048:        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                   7049:         for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   7050:           varpij[i][j][(int)age] = doldm[i][j];
1.220     brouard  7051:                        
1.222     brouard  7052:        /*printf("\n%d ",(int)age);
                   7053:         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   7054:         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   7055:         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   7056:         }*/
1.220     brouard  7057:                        
1.222     brouard  7058:        fprintf(ficresprob,"\n%d ",(int)age);
                   7059:        fprintf(ficresprobcov,"\n%d ",(int)age);
                   7060:        fprintf(ficresprobcor,"\n%d ",(int)age);
1.220     brouard  7061:                        
1.222     brouard  7062:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   7063:         fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                   7064:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   7065:         fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                   7066:         fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                   7067:        }
                   7068:        i=0;
                   7069:        for (k=1; k<=(nlstate);k++){
                   7070:         for (l=1; l<=(nlstate+ndeath);l++){ 
                   7071:           i++;
                   7072:           fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   7073:           fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                   7074:           for (j=1; j<=i;j++){
                   7075:             /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                   7076:             fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                   7077:             fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   7078:           }
                   7079:         }
                   7080:        }/* end of loop for state */
                   7081:      } /* end of loop for age */
                   7082:      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                   7083:      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                   7084:      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   7085:      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   7086:     
                   7087:      /* Confidence intervalle of pij  */
                   7088:      /*
                   7089:        fprintf(ficgp,"\nunset parametric;unset label");
                   7090:        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                   7091:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                   7092:        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
                   7093:        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                   7094:        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                   7095:        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                   7096:      */
                   7097:                
                   7098:      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                   7099:      first1=1;first2=2;
                   7100:      for (k2=1; k2<=(nlstate);k2++){
                   7101:        for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                   7102:         if(l2==k2) continue;
                   7103:         j=(k2-1)*(nlstate+ndeath)+l2;
                   7104:         for (k1=1; k1<=(nlstate);k1++){
                   7105:           for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                   7106:             if(l1==k1) continue;
                   7107:             i=(k1-1)*(nlstate+ndeath)+l1;
                   7108:             if(i<=j) continue;
                   7109:             for (age=bage; age<=fage; age ++){ 
                   7110:               if ((int)age %5==0){
                   7111:                 v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                   7112:                 v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   7113:                 cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   7114:                 mu1=mu[i][(int) age]/stepm*YEARM ;
                   7115:                 mu2=mu[j][(int) age]/stepm*YEARM;
                   7116:                 c12=cv12/sqrt(v1*v2);
                   7117:                 /* Computing eigen value of matrix of covariance */
                   7118:                 lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   7119:                 lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   7120:                 if ((lc2 <0) || (lc1 <0) ){
                   7121:                   if(first2==1){
                   7122:                     first1=0;
                   7123:                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                   7124:                   }
                   7125:                   fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                   7126:                   /* lc1=fabs(lc1); */ /* If we want to have them positive */
                   7127:                   /* lc2=fabs(lc2); */
                   7128:                 }
1.220     brouard  7129:                                                                
1.222     brouard  7130:                 /* Eigen vectors */
1.280     brouard  7131:                 if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
                   7132:                   printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                   7133:                   fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                   7134:                   v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
                   7135:                 }else
                   7136:                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222     brouard  7137:                 /*v21=sqrt(1.-v11*v11); *//* error */
                   7138:                 v21=(lc1-v1)/cv12*v11;
                   7139:                 v12=-v21;
                   7140:                 v22=v11;
                   7141:                 tnalp=v21/v11;
                   7142:                 if(first1==1){
                   7143:                   first1=0;
                   7144:                   printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                   7145:                 }
                   7146:                 fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                   7147:                 /*printf(fignu*/
                   7148:                 /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                   7149:                 /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   7150:                 if(first==1){
                   7151:                   first=0;
                   7152:                   fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                   7153:                   fprintf(ficgp,"\nset parametric;unset label");
                   7154:                   fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                   7155:                   fprintf(ficgp,"\nset ter svg size 640, 480");
1.266     brouard  7156:                   fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220     brouard  7157:  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                          \
1.201     brouard  7158: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222     brouard  7159:                           subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
                   7160:                           subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   7161:                   fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   7162:                   fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                   7163:                   fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   7164:                   fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   7165:                   fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   7166:                   fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
1.280     brouard  7167:                           mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
                   7168:                           mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222     brouard  7169:                 }else{
                   7170:                   first=0;
                   7171:                   fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                   7172:                   fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   7173:                   fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   7174:                   fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
1.266     brouard  7175:                           mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
                   7176:                           mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222     brouard  7177:                 }/* if first */
                   7178:               } /* age mod 5 */
                   7179:             } /* end loop age */
                   7180:             fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   7181:             first=1;
                   7182:           } /*l12 */
                   7183:         } /* k12 */
                   7184:        } /*l1 */
                   7185:      }/* k1 */
1.326     brouard  7186:    } /* loop on nres */
1.222     brouard  7187:    }  /* loop on combination of covariates j1 */
                   7188:    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
                   7189:    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
                   7190:    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   7191:    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
                   7192:    free_vector(xp,1,npar);
                   7193:    fclose(ficresprob);
                   7194:    fclose(ficresprobcov);
                   7195:    fclose(ficresprobcor);
                   7196:    fflush(ficgp);
                   7197:    fflush(fichtmcov);
                   7198:  }
1.126     brouard  7199: 
                   7200: 
                   7201: /******************* Printing html file ***********/
1.201     brouard  7202: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126     brouard  7203:                  int lastpass, int stepm, int weightopt, char model[],\
                   7204:                  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296     brouard  7205:                  int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
                   7206:                  double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
                   7207:                  double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237     brouard  7208:   int jj1, k1, i1, cpt, k4, nres;
1.319     brouard  7209:   /* In fact some results are already printed in fichtm which is open */
1.126     brouard  7210:    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
                   7211:    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
                   7212: </ul>");
1.319     brouard  7213: /*    fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
                   7214: /* </ul>", model); */
1.214     brouard  7215:    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
                   7216:    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
                   7217:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
                   7218:    fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
1.213     brouard  7219:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
                   7220:    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126     brouard  7221:    fprintf(fichtm,"\
                   7222:  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201     brouard  7223:           stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126     brouard  7224:    fprintf(fichtm,"\
1.217     brouard  7225:  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
                   7226:           stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
                   7227:    fprintf(fichtm,"\
1.288     brouard  7228:  - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201     brouard  7229:           subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126     brouard  7230:    fprintf(fichtm,"\
1.288     brouard  7231:  - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217     brouard  7232:           subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
                   7233:    fprintf(fichtm,"\
1.211     brouard  7234:  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126     brouard  7235:    <a href=\"%s\">%s</a> <br>\n",
1.201     brouard  7236:           estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211     brouard  7237:    if(prevfcast==1){
                   7238:      fprintf(fichtm,"\
                   7239:  - Prevalence projections by age and states:                           \
1.201     brouard  7240:    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211     brouard  7241:    }
1.126     brouard  7242: 
                   7243: 
1.225     brouard  7244:    m=pow(2,cptcoveff);
1.222     brouard  7245:    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126     brouard  7246: 
1.317     brouard  7247:    fprintf(fichtm," \n<ul><li><b>Graphs (first order)</b></li><p>");
1.264     brouard  7248: 
                   7249:    jj1=0;
                   7250: 
                   7251:    fprintf(fichtm," \n<ul>");
                   7252:    for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   7253:    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
                   7254:      if(m != 1 && TKresult[nres]!= k1)
                   7255:        continue;
                   7256:      jj1++;
                   7257:      if (cptcovn > 0) {
                   7258:        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
                   7259:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
                   7260:         fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   7261:        }
                   7262:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7263:         fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7264:        }
                   7265:        fprintf(fichtm,"\">");
                   7266:        
                   7267:        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
                   7268:        fprintf(fichtm,"************ Results for covariates");
                   7269:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
                   7270:         fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   7271:        }
                   7272:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7273:         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7274:        }
                   7275:        if(invalidvarcomb[k1]){
                   7276:         fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
                   7277:         continue;
                   7278:        }
                   7279:        fprintf(fichtm,"</a></li>");
                   7280:      } /* cptcovn >0 */
                   7281:    }
1.317     brouard  7282:    fprintf(fichtm," \n</ul>");
1.264     brouard  7283: 
1.222     brouard  7284:    jj1=0;
1.237     brouard  7285: 
                   7286:    for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241     brouard  7287:    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253     brouard  7288:      if(m != 1 && TKresult[nres]!= k1)
1.237     brouard  7289:        continue;
1.220     brouard  7290: 
1.222     brouard  7291:      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
                   7292:      jj1++;
                   7293:      if (cptcovn > 0) {
1.264     brouard  7294:        fprintf(fichtm,"\n<p><a name=\"rescov");
                   7295:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
                   7296:         fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   7297:        }
                   7298:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7299:         fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7300:        }
                   7301:        fprintf(fichtm,"\"</a>");
                   7302:  
1.222     brouard  7303:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225     brouard  7304:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
1.237     brouard  7305:         fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   7306:         printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
                   7307:         /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
                   7308:         /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222     brouard  7309:        }
1.237     brouard  7310:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7311:        fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7312:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
                   7313:       }
                   7314:        
1.230     brouard  7315:        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.321     brouard  7316:        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
1.222     brouard  7317:        if(invalidvarcomb[k1]){
                   7318:         fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
                   7319:         printf("\nCombination (%d) ignored because no cases \n",k1); 
                   7320:         continue;
                   7321:        }
                   7322:      }
                   7323:      /* aij, bij */
1.259     brouard  7324:      fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
1.241     brouard  7325: <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
1.222     brouard  7326:      /* Pij */
1.241     brouard  7327:      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
                   7328: <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);     
1.222     brouard  7329:      /* Quasi-incidences */
                   7330:      fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.220     brouard  7331:  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211     brouard  7332:  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
1.241     brouard  7333: divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
                   7334: <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
1.222     brouard  7335:      /* Survival functions (period) in state j */
                   7336:      for(cpt=1; cpt<=nlstate;cpt++){
1.292     brouard  7337:        fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
1.241     brouard  7338: <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.222     brouard  7339:      }
                   7340:      /* State specific survival functions (period) */
                   7341:      for(cpt=1; cpt<=nlstate;cpt++){
1.292     brouard  7342:        fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
                   7343:  And probability to be observed in various states (up to %d) being in state %d at different ages.      \
1.283     brouard  7344:  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.222     brouard  7345:      }
1.288     brouard  7346:      /* Period (forward stable) prevalence in each health state */
1.222     brouard  7347:      for(cpt=1; cpt<=nlstate;cpt++){
1.264     brouard  7348:        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
                   7349: <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.222     brouard  7350:      }
1.296     brouard  7351:      if(prevbcast==1){
1.288     brouard  7352:        /* Backward prevalence in each health state */
1.222     brouard  7353:        for(cpt=1; cpt<=nlstate;cpt++){
1.264     brouard  7354:         fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
1.241     brouard  7355: <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.222     brouard  7356:        }
1.217     brouard  7357:      }
1.222     brouard  7358:      if(prevfcast==1){
1.288     brouard  7359:        /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222     brouard  7360:        for(cpt=1; cpt<=nlstate;cpt++){
1.314     brouard  7361:         fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
                   7362:         fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
                   7363:         fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
                   7364:                 subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222     brouard  7365:        }
                   7366:      }
1.296     brouard  7367:      if(prevbcast==1){
1.268     brouard  7368:       /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
                   7369:        for(cpt=1; cpt<=nlstate;cpt++){
1.273     brouard  7370:         fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
                   7371:  from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
                   7372:  account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
1.314     brouard  7373: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
                   7374:         fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
                   7375:         fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
1.268     brouard  7376:        }
                   7377:      }
1.220     brouard  7378:         
1.222     brouard  7379:      for(cpt=1; cpt<=nlstate;cpt++) {
1.314     brouard  7380:        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
                   7381:        fprintf(fichtm," (data from text file  <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
                   7382:        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
1.222     brouard  7383:      }
                   7384:      /* } /\* end i1 *\/ */
                   7385:    }/* End k1 */
                   7386:    fprintf(fichtm,"</ul>");
1.126     brouard  7387: 
1.222     brouard  7388:    fprintf(fichtm,"\
1.126     brouard  7389: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193     brouard  7390:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203     brouard  7391:  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
1.197     brouard  7392: But because parameters are usually highly correlated (a higher incidence of disability \
                   7393: and a higher incidence of recovery can give very close observed transition) it might \
                   7394: be very useful to look not only at linear confidence intervals estimated from the \
                   7395: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
                   7396: (parameters) of the logistic regression, it might be more meaningful to visualize the \
                   7397: covariance matrix of the one-step probabilities. \
                   7398: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126     brouard  7399: 
1.222     brouard  7400:    fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   7401:           subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
                   7402:    fprintf(fichtm,"\
1.126     brouard  7403:  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222     brouard  7404:           subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126     brouard  7405: 
1.222     brouard  7406:    fprintf(fichtm,"\
1.126     brouard  7407:  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222     brouard  7408:           subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
                   7409:    fprintf(fichtm,"\
1.126     brouard  7410:  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
                   7411:    <a href=\"%s\">%s</a> <br>\n</li>",
1.201     brouard  7412:           estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222     brouard  7413:    fprintf(fichtm,"\
1.126     brouard  7414:  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
                   7415:    <a href=\"%s\">%s</a> <br>\n</li>",
1.201     brouard  7416:           estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222     brouard  7417:    fprintf(fichtm,"\
1.288     brouard  7418:  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.222     brouard  7419:           estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
                   7420:    fprintf(fichtm,"\
1.128     brouard  7421:  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
1.222     brouard  7422:           estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
                   7423:    fprintf(fichtm,"\
1.288     brouard  7424:  - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222     brouard  7425:           subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126     brouard  7426: 
                   7427: /*  if(popforecast==1) fprintf(fichtm,"\n */
                   7428: /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                   7429: /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                   7430: /*     <br>",fileres,fileres,fileres,fileres); */
                   7431: /*  else  */
                   7432: /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
1.222     brouard  7433:    fflush(fichtm);
1.126     brouard  7434: 
1.225     brouard  7435:    m=pow(2,cptcoveff);
1.222     brouard  7436:    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126     brouard  7437: 
1.317     brouard  7438:    fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");
                   7439: 
                   7440:   jj1=0;
                   7441: 
                   7442:    fprintf(fichtm," \n<ul>");
                   7443:    for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   7444:    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
                   7445:      if(m != 1 && TKresult[nres]!= k1)
                   7446:        continue;
                   7447:      jj1++;
                   7448:      if (cptcovn > 0) {
                   7449:        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
                   7450:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
                   7451:         fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   7452:        }
                   7453:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7454:         fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7455:        }
                   7456:        fprintf(fichtm,"\">");
                   7457:        
                   7458:        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
                   7459:        fprintf(fichtm,"************ Results for covariates");
                   7460:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
                   7461:         fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   7462:        }
                   7463:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7464:         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7465:        }
                   7466:        if(invalidvarcomb[k1]){
                   7467:         fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
                   7468:         continue;
                   7469:        }
                   7470:        fprintf(fichtm,"</a></li>");
                   7471:      } /* cptcovn >0 */
                   7472:    }
                   7473:    fprintf(fichtm," \n</ul>");
                   7474: 
1.222     brouard  7475:    jj1=0;
1.237     brouard  7476: 
1.241     brouard  7477:    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222     brouard  7478:    for(k1=1; k1<=m;k1++){
1.253     brouard  7479:      if(m != 1 && TKresult[nres]!= k1)
1.237     brouard  7480:        continue;
1.222     brouard  7481:      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
                   7482:      jj1++;
1.126     brouard  7483:      if (cptcovn > 0) {
1.317     brouard  7484:        fprintf(fichtm,"\n<p><a name=\"rescovsecond");
                   7485:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
                   7486:         fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   7487:        }
                   7488:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7489:         fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7490:        }
                   7491:        fprintf(fichtm,"\"</a>");
                   7492:        
1.126     brouard  7493:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.317     brouard  7494:        for (cpt=1; cpt<=cptcoveff;cpt++){  /**< cptcoveff number of variables */
1.237     brouard  7495:         fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
1.317     brouard  7496:         printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
1.237     brouard  7497:         /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
1.317     brouard  7498:        }
1.237     brouard  7499:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7500:        fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7501:       }
                   7502: 
1.321     brouard  7503:        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
1.220     brouard  7504: 
1.222     brouard  7505:        if(invalidvarcomb[k1]){
                   7506:         fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
                   7507:         continue;
                   7508:        }
1.126     brouard  7509:      }
                   7510:      for(cpt=1; cpt<=nlstate;cpt++) {
1.258     brouard  7511:        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.314     brouard  7512: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
                   7513:        fprintf(fichtm," (data from text file  <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
                   7514:        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
1.126     brouard  7515:      }
                   7516:      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.314     brouard  7517: health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
1.128     brouard  7518: true period expectancies (those weighted with period prevalences are also\
                   7519:  drawn in addition to the population based expectancies computed using\
1.314     brouard  7520:  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
                   7521:      fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
                   7522:      fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
1.222     brouard  7523:      /* } /\* end i1 *\/ */
                   7524:    }/* End k1 */
1.241     brouard  7525:   }/* End nres */
1.222     brouard  7526:    fprintf(fichtm,"</ul>");
                   7527:    fflush(fichtm);
1.126     brouard  7528: }
                   7529: 
                   7530: /******************* Gnuplot file **************/
1.296     brouard  7531: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
1.126     brouard  7532: 
                   7533:   char dirfileres[132],optfileres[132];
1.264     brouard  7534:   char gplotcondition[132], gplotlabel[132];
1.237     brouard  7535:   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
1.211     brouard  7536:   int lv=0, vlv=0, kl=0;
1.130     brouard  7537:   int ng=0;
1.201     brouard  7538:   int vpopbased;
1.223     brouard  7539:   int ioffset; /* variable offset for columns */
1.270     brouard  7540:   int iyearc=1; /* variable column for year of projection  */
                   7541:   int iagec=1; /* variable column for age of projection  */
1.235     brouard  7542:   int nres=0; /* Index of resultline */
1.266     brouard  7543:   int istart=1; /* For starting graphs in projections */
1.219     brouard  7544: 
1.126     brouard  7545: /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
                   7546: /*     printf("Problem with file %s",optionfilegnuplot); */
                   7547: /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
                   7548: /*   } */
                   7549: 
                   7550:   /*#ifdef windows */
                   7551:   fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223     brouard  7552:   /*#endif */
1.225     brouard  7553:   m=pow(2,cptcoveff);
1.126     brouard  7554: 
1.274     brouard  7555:   /* diagram of the model */
                   7556:   fprintf(ficgp,"\n#Diagram of the model \n");
                   7557:   fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
                   7558:   fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
                   7559:   fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
                   7560: 
                   7561:   fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
                   7562:   fprintf(ficgp,"\n#show arrow\nunset label\n");
                   7563:   fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
                   7564:   fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
                   7565:   fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
                   7566:   fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
                   7567:   fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
                   7568: 
1.202     brouard  7569:   /* Contribution to likelihood */
                   7570:   /* Plot the probability implied in the likelihood */
1.223     brouard  7571:   fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
                   7572:   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
                   7573:   /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
                   7574:   fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204     brouard  7575: /* nice for mle=4 plot by number of matrix products.
1.202     brouard  7576:    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
                   7577: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
1.223     brouard  7578:   /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
                   7579:   fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
                   7580:   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
                   7581:   fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
                   7582:   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
                   7583:   for (i=1; i<= nlstate ; i ++) {
                   7584:     fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
                   7585:     fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
                   7586:     fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
                   7587:     for (j=2; j<= nlstate+ndeath ; j ++) {
                   7588:       fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
                   7589:     }
                   7590:     fprintf(ficgp,";\nset out; unset ylabel;\n"); 
                   7591:   }
                   7592:   /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */               
                   7593:   /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
                   7594:   /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
                   7595:   fprintf(ficgp,"\nset out;unset log\n");
                   7596:   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202     brouard  7597: 
1.126     brouard  7598:   strcpy(dirfileres,optionfilefiname);
                   7599:   strcpy(optfileres,"vpl");
1.223     brouard  7600:   /* 1eme*/
1.238     brouard  7601:   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
                   7602:     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236     brouard  7603:       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238     brouard  7604:        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253     brouard  7605:        if(m != 1 && TKresult[nres]!= k1)
1.238     brouard  7606:          continue;
                   7607:        /* We are interested in selected combination by the resultline */
1.246     brouard  7608:        /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288     brouard  7609:        fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
1.264     brouard  7610:        strcpy(gplotlabel,"(");
1.238     brouard  7611:        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
                   7612:          lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
                   7613:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7614:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7615:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7616:          vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
                   7617:          /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246     brouard  7618:          /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238     brouard  7619:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  7620:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238     brouard  7621:        }
                   7622:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246     brouard  7623:          /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238     brouard  7624:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  7625:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7626:        }
                   7627:        strcpy(gplotlabel+strlen(gplotlabel),")");
1.246     brouard  7628:        /* printf("\n#\n"); */
1.238     brouard  7629:        fprintf(ficgp,"\n#\n");
                   7630:        if(invalidvarcomb[k1]){
1.260     brouard  7631:           /*k1=k1-1;*/ /* To be checked */
1.238     brouard  7632:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   7633:          continue;
                   7634:        }
1.235     brouard  7635:       
1.241     brouard  7636:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
                   7637:        fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276     brouard  7638:        /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
1.321     brouard  7639:        fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
1.260     brouard  7640:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
                   7641:        /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
                   7642:       /* k1-1 error should be nres-1*/
1.238     brouard  7643:        for (i=1; i<= nlstate ; i ++) {
                   7644:          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   7645:          else        fprintf(ficgp," %%*lf (%%*lf)");
                   7646:        }
1.288     brouard  7647:        fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238     brouard  7648:        for (i=1; i<= nlstate ; i ++) {
                   7649:          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   7650:          else fprintf(ficgp," %%*lf (%%*lf)");
                   7651:        } 
1.260     brouard  7652:        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); 
1.238     brouard  7653:        for (i=1; i<= nlstate ; i ++) {
                   7654:          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   7655:          else fprintf(ficgp," %%*lf (%%*lf)");
                   7656:        }  
1.265     brouard  7657:        /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
                   7658:        
                   7659:        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
                   7660:         if(cptcoveff ==0){
1.271     brouard  7661:          fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
1.265     brouard  7662:        }else{
                   7663:          kl=0;
                   7664:          for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                   7665:            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                   7666:            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7667:            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7668:            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7669:            vlv= nbcode[Tvaraff[k]][lv];
                   7670:            kl++;
                   7671:            /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                   7672:            /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                   7673:            /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                   7674:            /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                   7675:            if(k==cptcoveff){
                   7676:              fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                   7677:                      2+cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
                   7678:            }else{
                   7679:              fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                   7680:              kl++;
                   7681:            }
                   7682:          } /* end covariate */
                   7683:        } /* end if no covariate */
                   7684: 
1.296     brouard  7685:        if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238     brouard  7686:          /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242     brouard  7687:          fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238     brouard  7688:          if(cptcoveff ==0){
1.245     brouard  7689:            fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
1.238     brouard  7690:          }else{
                   7691:            kl=0;
                   7692:            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                   7693:              lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                   7694:              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7695:              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7696:              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7697:              vlv= nbcode[Tvaraff[k]][lv];
1.223     brouard  7698:              kl++;
1.238     brouard  7699:              /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                   7700:              /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                   7701:              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                   7702:              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                   7703:              if(k==cptcoveff){
1.245     brouard  7704:                fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242     brouard  7705:                        2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
1.238     brouard  7706:              }else{
                   7707:                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                   7708:                kl++;
                   7709:              }
                   7710:            } /* end covariate */
                   7711:          } /* end if no covariate */
1.296     brouard  7712:          if(prevbcast == 1){
1.268     brouard  7713:            fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
                   7714:            /* k1-1 error should be nres-1*/
                   7715:            for (i=1; i<= nlstate ; i ++) {
                   7716:              if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   7717:              else        fprintf(ficgp," %%*lf (%%*lf)");
                   7718:            }
1.271     brouard  7719:            fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
1.268     brouard  7720:            for (i=1; i<= nlstate ; i ++) {
                   7721:              if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   7722:              else fprintf(ficgp," %%*lf (%%*lf)");
                   7723:            } 
1.276     brouard  7724:            fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
1.268     brouard  7725:            for (i=1; i<= nlstate ; i ++) {
                   7726:              if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   7727:              else fprintf(ficgp," %%*lf (%%*lf)");
                   7728:            } 
1.274     brouard  7729:            fprintf(ficgp,"\" t\"\" w l lt 4");
1.268     brouard  7730:          } /* end if backprojcast */
1.296     brouard  7731:        } /* end if prevbcast */
1.276     brouard  7732:        /* fprintf(ficgp,"\nset out ;unset label;\n"); */
                   7733:        fprintf(ficgp,"\nset out ;unset title;\n");
1.238     brouard  7734:       } /* nres */
1.201     brouard  7735:     } /* k1 */
                   7736:   } /* cpt */
1.235     brouard  7737: 
                   7738:   
1.126     brouard  7739:   /*2 eme*/
1.238     brouard  7740:   for (k1=1; k1<= m ; k1 ++){  
                   7741:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  7742:       if(m != 1 && TKresult[nres]!= k1)
1.238     brouard  7743:        continue;
                   7744:       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264     brouard  7745:       strcpy(gplotlabel,"(");
1.238     brouard  7746:       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
1.225     brouard  7747:        lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223     brouard  7748:        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7749:        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7750:        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7751:        vlv= nbcode[Tvaraff[k]][lv];
                   7752:        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  7753:        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211     brouard  7754:       }
1.237     brouard  7755:       /* for(k=1; k <= ncovds; k++){ */
1.236     brouard  7756:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238     brouard  7757:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236     brouard  7758:        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  7759:        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238     brouard  7760:       }
1.264     brouard  7761:       strcpy(gplotlabel+strlen(gplotlabel),")");
1.211     brouard  7762:       fprintf(ficgp,"\n#\n");
1.223     brouard  7763:       if(invalidvarcomb[k1]){
                   7764:        fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   7765:        continue;
                   7766:       }
1.219     brouard  7767:                        
1.241     brouard  7768:       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238     brouard  7769:       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264     brouard  7770:        fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
                   7771:        if(vpopbased==0){
1.238     brouard  7772:          fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264     brouard  7773:        }else
1.238     brouard  7774:          fprintf(ficgp,"\nreplot ");
                   7775:        for (i=1; i<= nlstate+1 ; i ++) {
                   7776:          k=2*i;
1.261     brouard  7777:          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
1.238     brouard  7778:          for (j=1; j<= nlstate+1 ; j ++) {
                   7779:            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   7780:            else fprintf(ficgp," %%*lf (%%*lf)");
                   7781:          }   
                   7782:          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
                   7783:          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261     brouard  7784:          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
1.238     brouard  7785:          for (j=1; j<= nlstate+1 ; j ++) {
                   7786:            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   7787:            else fprintf(ficgp," %%*lf (%%*lf)");
                   7788:          }   
                   7789:          fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261     brouard  7790:          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
1.238     brouard  7791:          for (j=1; j<= nlstate+1 ; j ++) {
                   7792:            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   7793:            else fprintf(ficgp," %%*lf (%%*lf)");
                   7794:          }   
                   7795:          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
                   7796:          else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
                   7797:        } /* state */
                   7798:       } /* vpopbased */
1.264     brouard  7799:       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
1.238     brouard  7800:     } /* end nres */
                   7801:   } /* k1 end 2 eme*/
                   7802:        
                   7803:        
                   7804:   /*3eme*/
                   7805:   for (k1=1; k1<= m ; k1 ++){
                   7806:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  7807:       if(m != 1 && TKresult[nres]!= k1)
1.238     brouard  7808:        continue;
                   7809: 
                   7810:       for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261     brouard  7811:        fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
1.264     brouard  7812:        strcpy(gplotlabel,"(");
1.238     brouard  7813:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   7814:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   7815:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7816:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7817:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7818:          vlv= nbcode[Tvaraff[k]][lv];
                   7819:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  7820:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238     brouard  7821:        }
                   7822:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7823:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  7824:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238     brouard  7825:        }       
1.264     brouard  7826:        strcpy(gplotlabel+strlen(gplotlabel),")");
1.238     brouard  7827:        fprintf(ficgp,"\n#\n");
                   7828:        if(invalidvarcomb[k1]){
                   7829:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   7830:          continue;
                   7831:        }
                   7832:                        
                   7833:        /*       k=2+nlstate*(2*cpt-2); */
                   7834:        k=2+(nlstate+1)*(cpt-1);
1.241     brouard  7835:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264     brouard  7836:        fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238     brouard  7837:        fprintf(ficgp,"set ter svg size 640, 480\n\
1.261     brouard  7838: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
1.238     brouard  7839:        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   7840:          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   7841:          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   7842:          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   7843:          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   7844:          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219     brouard  7845:                                
1.238     brouard  7846:        */
                   7847:        for (i=1; i< nlstate ; i ++) {
1.261     brouard  7848:          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
1.238     brouard  7849:          /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
1.219     brouard  7850:                                
1.238     brouard  7851:        } 
1.261     brouard  7852:        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
1.238     brouard  7853:       }
1.264     brouard  7854:       fprintf(ficgp,"\nunset label;\n");
1.238     brouard  7855:     } /* end nres */
                   7856:   } /* end kl 3eme */
1.126     brouard  7857:   
1.223     brouard  7858:   /* 4eme */
1.201     brouard  7859:   /* Survival functions (period) from state i in state j by initial state i */
1.238     brouard  7860:   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
                   7861:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  7862:       if(m != 1 && TKresult[nres]!= k1)
1.223     brouard  7863:        continue;
1.238     brouard  7864:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264     brouard  7865:        strcpy(gplotlabel,"(");
1.238     brouard  7866:        fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
                   7867:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   7868:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   7869:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7870:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7871:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7872:          vlv= nbcode[Tvaraff[k]][lv];
                   7873:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  7874:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238     brouard  7875:        }
                   7876:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7877:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  7878:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238     brouard  7879:        }       
1.264     brouard  7880:        strcpy(gplotlabel+strlen(gplotlabel),")");
1.238     brouard  7881:        fprintf(ficgp,"\n#\n");
                   7882:        if(invalidvarcomb[k1]){
                   7883:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   7884:          continue;
1.223     brouard  7885:        }
1.238     brouard  7886:       
1.241     brouard  7887:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264     brouard  7888:        fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.238     brouard  7889:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
                   7890: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                   7891:        k=3;
                   7892:        for (i=1; i<= nlstate ; i ++){
                   7893:          if(i==1){
                   7894:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                   7895:          }else{
                   7896:            fprintf(ficgp,", '' ");
                   7897:          }
                   7898:          l=(nlstate+ndeath)*(i-1)+1;
                   7899:          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
                   7900:          for (j=2; j<= nlstate+ndeath ; j ++)
                   7901:            fprintf(ficgp,"+$%d",k+l+j-1);
                   7902:          fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
                   7903:        } /* nlstate */
1.264     brouard  7904:        fprintf(ficgp,"\nset out; unset label;\n");
1.238     brouard  7905:       } /* end cpt state*/ 
                   7906:     } /* end nres */
                   7907:   } /* end covariate k1 */  
                   7908: 
1.220     brouard  7909: /* 5eme */
1.201     brouard  7910:   /* Survival functions (period) from state i in state j by final state j */
1.238     brouard  7911:   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
                   7912:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  7913:       if(m != 1 && TKresult[nres]!= k1)
1.227     brouard  7914:        continue;
1.238     brouard  7915:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
1.264     brouard  7916:        strcpy(gplotlabel,"(");
1.238     brouard  7917:        fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
                   7918:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   7919:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   7920:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7921:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7922:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7923:          vlv= nbcode[Tvaraff[k]][lv];
                   7924:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  7925:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238     brouard  7926:        }
                   7927:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7928:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  7929:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238     brouard  7930:        }       
1.264     brouard  7931:        strcpy(gplotlabel+strlen(gplotlabel),")");
1.238     brouard  7932:        fprintf(ficgp,"\n#\n");
                   7933:        if(invalidvarcomb[k1]){
                   7934:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   7935:          continue;
                   7936:        }
1.227     brouard  7937:       
1.241     brouard  7938:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264     brouard  7939:        fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.238     brouard  7940:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
                   7941: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                   7942:        k=3;
                   7943:        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
                   7944:          if(j==1)
                   7945:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                   7946:          else
                   7947:            fprintf(ficgp,", '' ");
                   7948:          l=(nlstate+ndeath)*(cpt-1) +j;
                   7949:          fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
                   7950:          /* for (i=2; i<= nlstate+ndeath ; i ++) */
                   7951:          /*   fprintf(ficgp,"+$%d",k+l+i-1); */
                   7952:          fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
                   7953:        } /* nlstate */
                   7954:        fprintf(ficgp,", '' ");
                   7955:        fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
                   7956:        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
                   7957:          l=(nlstate+ndeath)*(cpt-1) +j;
                   7958:          if(j < nlstate)
                   7959:            fprintf(ficgp,"$%d +",k+l);
                   7960:          else
                   7961:            fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
                   7962:        }
1.264     brouard  7963:        fprintf(ficgp,"\nset out; unset label;\n");
1.238     brouard  7964:       } /* end cpt state*/ 
                   7965:     } /* end covariate */  
                   7966:   } /* end nres */
1.227     brouard  7967:   
1.220     brouard  7968: /* 6eme */
1.202     brouard  7969:   /* CV preval stable (period) for each covariate */
1.237     brouard  7970:   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
                   7971:   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  7972:     if(m != 1 && TKresult[nres]!= k1)
1.237     brouard  7973:       continue;
1.255     brouard  7974:     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264     brouard  7975:       strcpy(gplotlabel,"(");      
1.288     brouard  7976:       fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225     brouard  7977:       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
1.227     brouard  7978:        lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   7979:        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   7980:        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   7981:        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   7982:        vlv= nbcode[Tvaraff[k]][lv];
                   7983:        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  7984:        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211     brouard  7985:       }
1.237     brouard  7986:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7987:        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  7988:        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237     brouard  7989:       }        
1.264     brouard  7990:       strcpy(gplotlabel+strlen(gplotlabel),")");
1.211     brouard  7991:       fprintf(ficgp,"\n#\n");
1.223     brouard  7992:       if(invalidvarcomb[k1]){
1.227     brouard  7993:        fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   7994:        continue;
1.223     brouard  7995:       }
1.227     brouard  7996:       
1.241     brouard  7997:       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264     brouard  7998:       fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.126     brouard  7999:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238     brouard  8000: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
1.211     brouard  8001:       k=3; /* Offset */
1.255     brouard  8002:       for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227     brouard  8003:        if(i==1)
                   8004:          fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                   8005:        else
                   8006:          fprintf(ficgp,", '' ");
1.255     brouard  8007:        l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227     brouard  8008:        fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
                   8009:        for (j=2; j<= nlstate ; j ++)
                   8010:          fprintf(ficgp,"+$%d",k+l+j-1);
                   8011:        fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153     brouard  8012:       } /* nlstate */
1.264     brouard  8013:       fprintf(ficgp,"\nset out; unset label;\n");
1.153     brouard  8014:     } /* end cpt state*/ 
                   8015:   } /* end covariate */  
1.227     brouard  8016:   
                   8017:   
1.220     brouard  8018: /* 7eme */
1.296     brouard  8019:   if(prevbcast == 1){
1.288     brouard  8020:     /* CV backward prevalence  for each covariate */
1.237     brouard  8021:     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
                   8022:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  8023:       if(m != 1 && TKresult[nres]!= k1)
1.237     brouard  8024:        continue;
1.268     brouard  8025:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264     brouard  8026:        strcpy(gplotlabel,"(");      
1.288     brouard  8027:        fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227     brouard  8028:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   8029:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   8030:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   8031:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
1.223     brouard  8032:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
1.227     brouard  8033:          vlv= nbcode[Tvaraff[k]][lv];
                   8034:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  8035:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227     brouard  8036:        }
1.237     brouard  8037:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   8038:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  8039:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237     brouard  8040:        }       
1.264     brouard  8041:        strcpy(gplotlabel+strlen(gplotlabel),")");
1.227     brouard  8042:        fprintf(ficgp,"\n#\n");
                   8043:        if(invalidvarcomb[k1]){
                   8044:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   8045:          continue;
                   8046:        }
                   8047:        
1.241     brouard  8048:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268     brouard  8049:        fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.227     brouard  8050:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238     brouard  8051: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
1.227     brouard  8052:        k=3; /* Offset */
1.268     brouard  8053:        for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227     brouard  8054:          if(i==1)
                   8055:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
                   8056:          else
                   8057:            fprintf(ficgp,", '' ");
                   8058:          /* l=(nlstate+ndeath)*(i-1)+1; */
1.255     brouard  8059:          l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.324     brouard  8060:          /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
                   8061:          /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
1.255     brouard  8062:          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227     brouard  8063:          /* for (j=2; j<= nlstate ; j ++) */
                   8064:          /*    fprintf(ficgp,"+$%d",k+l+j-1); */
                   8065:          /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268     brouard  8066:          fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227     brouard  8067:        } /* nlstate */
1.264     brouard  8068:        fprintf(ficgp,"\nset out; unset label;\n");
1.218     brouard  8069:       } /* end cpt state*/ 
                   8070:     } /* end covariate */  
1.296     brouard  8071:   } /* End if prevbcast */
1.218     brouard  8072:   
1.223     brouard  8073:   /* 8eme */
1.218     brouard  8074:   if(prevfcast==1){
1.288     brouard  8075:     /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218     brouard  8076:     
1.237     brouard  8077:     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
                   8078:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  8079:       if(m != 1 && TKresult[nres]!= k1)
1.237     brouard  8080:        continue;
1.211     brouard  8081:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264     brouard  8082:        strcpy(gplotlabel,"(");      
1.288     brouard  8083:        fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227     brouard  8084:        for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
                   8085:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                   8086:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   8087:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   8088:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   8089:          vlv= nbcode[Tvaraff[k]][lv];
                   8090:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264     brouard  8091:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227     brouard  8092:        }
1.237     brouard  8093:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   8094:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  8095:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237     brouard  8096:        }       
1.264     brouard  8097:        strcpy(gplotlabel+strlen(gplotlabel),")");
1.227     brouard  8098:        fprintf(ficgp,"\n#\n");
                   8099:        if(invalidvarcomb[k1]){
                   8100:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   8101:          continue;
                   8102:        }
                   8103:        
                   8104:        fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241     brouard  8105:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264     brouard  8106:        fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.227     brouard  8107:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238     brouard  8108: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
1.266     brouard  8109: 
                   8110:        /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
                   8111:        istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
                   8112:        /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
                   8113:        for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
1.227     brouard  8114:          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   8115:          /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                   8116:          /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   8117:          /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
1.266     brouard  8118:          if(i==istart){
1.227     brouard  8119:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
                   8120:          }else{
                   8121:            fprintf(ficgp,",\\\n '' ");
                   8122:          }
                   8123:          if(cptcoveff ==0){ /* No covariate */
                   8124:            ioffset=2; /* Age is in 2 */
                   8125:            /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                   8126:            /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                   8127:            /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                   8128:            /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                   8129:            fprintf(ficgp," u %d:(", ioffset); 
1.266     brouard  8130:            if(i==nlstate+1){
1.270     brouard  8131:              fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
1.266     brouard  8132:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                   8133:              fprintf(ficgp,",\\\n '' ");
                   8134:              fprintf(ficgp," u %d:(",ioffset); 
1.270     brouard  8135:              fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266     brouard  8136:                     offyear,                           \
1.268     brouard  8137:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266     brouard  8138:            }else
1.227     brouard  8139:              fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                   8140:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                   8141:          }else{ /* more than 2 covariates */
1.270     brouard  8142:            ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
                   8143:            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   8144:            /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                   8145:            iyearc=ioffset-1;
                   8146:            iagec=ioffset;
1.227     brouard  8147:            fprintf(ficgp," u %d:(",ioffset); 
                   8148:            kl=0;
                   8149:            strcpy(gplotcondition,"(");
                   8150:            for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                   8151:              lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                   8152:              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   8153:              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   8154:              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   8155:              vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                   8156:              kl++;
                   8157:              sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                   8158:              kl++;
                   8159:              if(k <cptcoveff && cptcoveff>1)
                   8160:                sprintf(gplotcondition+strlen(gplotcondition)," && ");
                   8161:            }
                   8162:            strcpy(gplotcondition+strlen(gplotcondition),")");
                   8163:            /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                   8164:            /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                   8165:            /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                   8166:            /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                   8167:            if(i==nlstate+1){
1.270     brouard  8168:              fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
                   8169:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266     brouard  8170:              fprintf(ficgp,",\\\n '' ");
1.270     brouard  8171:              fprintf(ficgp," u %d:(",iagec); 
                   8172:              fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
                   8173:                      iyearc, iagec, offyear,                           \
                   8174:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266     brouard  8175: /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
1.227     brouard  8176:            }else{
                   8177:              fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                   8178:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                   8179:            }
                   8180:          } /* end if covariate */
                   8181:        } /* nlstate */
1.264     brouard  8182:        fprintf(ficgp,"\nset out; unset label;\n");
1.223     brouard  8183:       } /* end cpt state*/
                   8184:     } /* end covariate */
                   8185:   } /* End if prevfcast */
1.227     brouard  8186:   
1.296     brouard  8187:   if(prevbcast==1){
1.268     brouard  8188:     /* Back projection from cross-sectional to stable (mixed) for each covariate */
                   8189:     
                   8190:     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
                   8191:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   8192:       if(m != 1 && TKresult[nres]!= k1)
                   8193:        continue;
                   8194:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                   8195:        strcpy(gplotlabel,"(");      
                   8196:        fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
                   8197:        for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
                   8198:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                   8199:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   8200:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   8201:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   8202:          vlv= nbcode[Tvaraff[k]][lv];
                   8203:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   8204:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
                   8205:        }
                   8206:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   8207:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   8208:          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   8209:        }       
                   8210:        strcpy(gplotlabel+strlen(gplotlabel),")");
                   8211:        fprintf(ficgp,"\n#\n");
                   8212:        if(invalidvarcomb[k1]){
                   8213:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   8214:          continue;
                   8215:        }
                   8216:        
                   8217:        fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
                   8218:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
                   8219:        fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
                   8220:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
                   8221: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                   8222: 
                   8223:        /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
                   8224:        istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
                   8225:        /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
                   8226:        for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                   8227:          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   8228:          /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                   8229:          /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   8230:          /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                   8231:          if(i==istart){
                   8232:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
                   8233:          }else{
                   8234:            fprintf(ficgp,",\\\n '' ");
                   8235:          }
                   8236:          if(cptcoveff ==0){ /* No covariate */
                   8237:            ioffset=2; /* Age is in 2 */
                   8238:            /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                   8239:            /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                   8240:            /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                   8241:            /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                   8242:            fprintf(ficgp," u %d:(", ioffset); 
                   8243:            if(i==nlstate+1){
1.270     brouard  8244:              fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268     brouard  8245:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                   8246:              fprintf(ficgp,",\\\n '' ");
                   8247:              fprintf(ficgp," u %d:(",ioffset); 
1.270     brouard  8248:              fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268     brouard  8249:                     offbyear,                          \
                   8250:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
                   8251:            }else
                   8252:              fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
                   8253:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
                   8254:          }else{ /* more than 2 covariates */
1.270     brouard  8255:            ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
                   8256:            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   8257:            /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                   8258:            iyearc=ioffset-1;
                   8259:            iagec=ioffset;
1.268     brouard  8260:            fprintf(ficgp," u %d:(",ioffset); 
                   8261:            kl=0;
                   8262:            strcpy(gplotcondition,"(");
                   8263:            for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                   8264:              lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                   8265:              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   8266:              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   8267:              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   8268:              vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                   8269:              kl++;
                   8270:              sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                   8271:              kl++;
                   8272:              if(k <cptcoveff && cptcoveff>1)
                   8273:                sprintf(gplotcondition+strlen(gplotcondition)," && ");
                   8274:            }
                   8275:            strcpy(gplotcondition+strlen(gplotcondition),")");
                   8276:            /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                   8277:            /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                   8278:            /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                   8279:            /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                   8280:            if(i==nlstate+1){
1.270     brouard  8281:              fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
                   8282:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268     brouard  8283:              fprintf(ficgp,",\\\n '' ");
1.270     brouard  8284:              fprintf(ficgp," u %d:(",iagec); 
1.268     brouard  8285:              /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270     brouard  8286:              fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
                   8287:                      iyearc,iagec,offbyear,                            \
                   8288:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268     brouard  8289: /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
                   8290:            }else{
                   8291:              /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
                   8292:              fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
                   8293:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
                   8294:            }
                   8295:          } /* end if covariate */
                   8296:        } /* nlstate */
                   8297:        fprintf(ficgp,"\nset out; unset label;\n");
                   8298:       } /* end cpt state*/
                   8299:     } /* end covariate */
1.296     brouard  8300:   } /* End if prevbcast */
1.268     brouard  8301:   
1.227     brouard  8302:   
1.238     brouard  8303:   /* 9eme writing MLE parameters */
                   8304:   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126     brouard  8305:   for(i=1,jk=1; i <=nlstate; i++){
1.187     brouard  8306:     fprintf(ficgp,"# initial state %d\n",i);
1.126     brouard  8307:     for(k=1; k <=(nlstate+ndeath); k++){
                   8308:       if (k != i) {
1.227     brouard  8309:        fprintf(ficgp,"#   current state %d\n",k);
                   8310:        for(j=1; j <=ncovmodel; j++){
                   8311:          fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
                   8312:          jk++; 
                   8313:        }
                   8314:        fprintf(ficgp,"\n");
1.126     brouard  8315:       }
                   8316:     }
1.223     brouard  8317:   }
1.187     brouard  8318:   fprintf(ficgp,"##############\n#\n");
1.227     brouard  8319:   
1.145     brouard  8320:   /*goto avoid;*/
1.238     brouard  8321:   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
                   8322:   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187     brouard  8323:   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
                   8324:   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
                   8325:   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
                   8326:   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
                   8327:   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
                   8328:   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
                   8329:   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
                   8330:   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
                   8331:   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
                   8332:   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
                   8333:   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
                   8334:   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
                   8335:   fprintf(ficgp,"#\n");
1.223     brouard  8336:   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238     brouard  8337:     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237     brouard  8338:     fprintf(ficgp,"#model=%s \n",model);
1.238     brouard  8339:     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264     brouard  8340:     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
                   8341:     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
1.237     brouard  8342:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264     brouard  8343:       if(m != 1 && TKresult[nres]!= k1)
1.237     brouard  8344:        continue;
1.264     brouard  8345:       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
                   8346:       strcpy(gplotlabel,"(");
1.276     brouard  8347:       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264     brouard  8348:       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
                   8349:        lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                   8350:        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   8351:        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   8352:        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   8353:        vlv= nbcode[Tvaraff[k]][lv];
                   8354:        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   8355:        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
                   8356:       }
1.237     brouard  8357:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   8358:        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264     brouard  8359:        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237     brouard  8360:       }        
1.264     brouard  8361:       strcpy(gplotlabel+strlen(gplotlabel),")");
1.237     brouard  8362:       fprintf(ficgp,"\n#\n");
1.264     brouard  8363:       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276     brouard  8364:       fprintf(ficgp,"\nset key outside ");
                   8365:       /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
                   8366:       fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223     brouard  8367:       fprintf(ficgp,"\nset ter svg size 640, 480 ");
                   8368:       if (ng==1){
                   8369:        fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
                   8370:        fprintf(ficgp,"\nunset log y");
                   8371:       }else if (ng==2){
                   8372:        fprintf(ficgp,"\nset ylabel \"Probability\"\n");
                   8373:        fprintf(ficgp,"\nset log y");
                   8374:       }else if (ng==3){
                   8375:        fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
                   8376:        fprintf(ficgp,"\nset log y");
                   8377:       }else
                   8378:        fprintf(ficgp,"\nunset title ");
                   8379:       fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                   8380:       i=1;
                   8381:       for(k2=1; k2<=nlstate; k2++) {
                   8382:        k3=i;
                   8383:        for(k=1; k<=(nlstate+ndeath); k++) {
                   8384:          if (k != k2){
                   8385:            switch( ng) {
                   8386:            case 1:
                   8387:              if(nagesqr==0)
                   8388:                fprintf(ficgp," p%d+p%d*x",i,i+1);
                   8389:              else /* nagesqr =1 */
                   8390:                fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                   8391:              break;
                   8392:            case 2: /* ng=2 */
                   8393:              if(nagesqr==0)
                   8394:                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                   8395:              else /* nagesqr =1 */
                   8396:                fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                   8397:              break;
                   8398:            case 3:
                   8399:              if(nagesqr==0)
                   8400:                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                   8401:              else /* nagesqr =1 */
                   8402:                fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                   8403:              break;
                   8404:            }
                   8405:            ij=1;/* To be checked else nbcode[0][0] wrong */
1.237     brouard  8406:            ijp=1; /* product no age */
                   8407:            /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
                   8408:            for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223     brouard  8409:              /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268     brouard  8410:              if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
1.325     brouard  8411:                if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */
1.268     brouard  8412:                  if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
1.325     brouard  8413:                    if(DummyV[j]==0){/* Bug valgrind */
1.268     brouard  8414:                      fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                   8415:                    }else{ /* quantitative */
                   8416:                      fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                   8417:                      /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   8418:                    }
                   8419:                    ij++;
1.237     brouard  8420:                  }
1.268     brouard  8421:                } 
                   8422:              }else if(cptcovprod >0){
                   8423:                if(j==Tprod[ijp]) { /* */ 
                   8424:                  /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                   8425:                  if(ijp <=cptcovprod) { /* Product */
                   8426:                    if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                   8427:                      if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                   8428:                        /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                   8429:                        fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                   8430:                      }else{ /* Vn is dummy and Vm is quanti */
                   8431:                        /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                   8432:                        fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                   8433:                      }
                   8434:                    }else{ /* Vn*Vm Vn is quanti */
                   8435:                      if(DummyV[Tvard[ijp][2]]==0){
                   8436:                        fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                   8437:                      }else{ /* Both quanti */
                   8438:                        fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                   8439:                      }
1.237     brouard  8440:                    }
1.268     brouard  8441:                    ijp++;
1.237     brouard  8442:                  }
1.268     brouard  8443:                } /* end Tprod */
1.237     brouard  8444:              } else{  /* simple covariate */
1.264     brouard  8445:                /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237     brouard  8446:                if(Dummy[j]==0){
                   8447:                  fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
                   8448:                }else{ /* quantitative */
                   8449:                  fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264     brouard  8450:                  /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223     brouard  8451:                }
1.237     brouard  8452:              } /* end simple */
                   8453:            } /* end j */
1.223     brouard  8454:          }else{
                   8455:            i=i-ncovmodel;
                   8456:            if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                   8457:              fprintf(ficgp," (1.");
                   8458:          }
1.227     brouard  8459:          
1.223     brouard  8460:          if(ng != 1){
                   8461:            fprintf(ficgp,")/(1");
1.227     brouard  8462:            
1.264     brouard  8463:            for(cpt=1; cpt <=nlstate; cpt++){ 
1.223     brouard  8464:              if(nagesqr==0)
1.264     brouard  8465:                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223     brouard  8466:              else /* nagesqr =1 */
1.264     brouard  8467:                fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
1.217     brouard  8468:               
1.223     brouard  8469:              ij=1;
                   8470:              for(j=3; j <=ncovmodel-nagesqr; j++){
1.268     brouard  8471:                 if(cptcovage >0){ 
                   8472:                   if((j-2)==Tage[ij]) { /* Bug valgrind */
                   8473:                     if(ij <=cptcovage) { /* Bug valgrind */
                   8474:                       fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
                   8475:                       /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   8476:                       ij++;
                   8477:                     }
                   8478:                   }
                   8479:                 }else
                   8480:                   fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
1.223     brouard  8481:              }
                   8482:              fprintf(ficgp,")");
                   8483:            }
                   8484:            fprintf(ficgp,")");
                   8485:            if(ng ==2)
1.276     brouard  8486:              fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
1.223     brouard  8487:            else /* ng= 3 */
1.276     brouard  8488:              fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
1.223     brouard  8489:          }else{ /* end ng <> 1 */
                   8490:            if( k !=k2) /* logit p11 is hard to draw */
1.276     brouard  8491:              fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
1.223     brouard  8492:          }
                   8493:          if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
                   8494:            fprintf(ficgp,",");
                   8495:          if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
                   8496:            fprintf(ficgp,",");
                   8497:          i=i+ncovmodel;
                   8498:        } /* end k */
                   8499:       } /* end k2 */
1.276     brouard  8500:       /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
                   8501:       fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264     brouard  8502:     } /* end k1 */
1.223     brouard  8503:   } /* end ng */
                   8504:   /* avoid: */
                   8505:   fflush(ficgp); 
1.126     brouard  8506: }  /* end gnuplot */
                   8507: 
                   8508: 
                   8509: /*************** Moving average **************/
1.219     brouard  8510: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222     brouard  8511:  int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218     brouard  8512:    
1.222     brouard  8513:    int i, cpt, cptcod;
                   8514:    int modcovmax =1;
                   8515:    int mobilavrange, mob;
                   8516:    int iage=0;
1.288     brouard  8517:    int firstA1=0, firstA2=0;
1.222     brouard  8518: 
1.266     brouard  8519:    double sum=0., sumr=0.;
1.222     brouard  8520:    double age;
1.266     brouard  8521:    double *sumnewp, *sumnewm, *sumnewmr;
                   8522:    double *agemingood, *agemaxgood; 
                   8523:    double *agemingoodr, *agemaxgoodr; 
1.222     brouard  8524:   
                   8525:   
1.278     brouard  8526:    /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
                   8527:    /*             a covariate has 2 modalities, should be equal to ncovcombmax   */
1.222     brouard  8528: 
                   8529:    sumnewp = vector(1,ncovcombmax);
                   8530:    sumnewm = vector(1,ncovcombmax);
1.266     brouard  8531:    sumnewmr = vector(1,ncovcombmax);
1.222     brouard  8532:    agemingood = vector(1,ncovcombmax); 
1.266     brouard  8533:    agemingoodr = vector(1,ncovcombmax);        
1.222     brouard  8534:    agemaxgood = vector(1,ncovcombmax);
1.266     brouard  8535:    agemaxgoodr = vector(1,ncovcombmax);
1.222     brouard  8536: 
                   8537:    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266     brouard  8538:      sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222     brouard  8539:      sumnewp[cptcod]=0.;
1.266     brouard  8540:      agemingood[cptcod]=0, agemingoodr[cptcod]=0;
                   8541:      agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222     brouard  8542:    }
                   8543:    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
                   8544:   
1.266     brouard  8545:    if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
                   8546:      if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222     brouard  8547:      else mobilavrange=mobilav;
                   8548:      for (age=bage; age<=fage; age++)
                   8549:        for (i=1; i<=nlstate;i++)
                   8550:         for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
                   8551:           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   8552:      /* We keep the original values on the extreme ages bage, fage and for 
                   8553:        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
                   8554:        we use a 5 terms etc. until the borders are no more concerned. 
                   8555:      */ 
                   8556:      for (mob=3;mob <=mobilavrange;mob=mob+2){
                   8557:        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266     brouard  8558:         for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                   8559:           sumnewm[cptcod]=0.;
                   8560:           for (i=1; i<=nlstate;i++){
1.222     brouard  8561:             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                   8562:             for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   8563:               mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   8564:               mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                   8565:             }
                   8566:             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266     brouard  8567:             sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                   8568:           } /* end i */
                   8569:           if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
                   8570:         } /* end cptcod */
1.222     brouard  8571:        }/* end age */
                   8572:      }/* end mob */
1.266     brouard  8573:    }else{
                   8574:      printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222     brouard  8575:      return -1;
1.266     brouard  8576:    }
                   8577: 
                   8578:    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222     brouard  8579:      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
                   8580:      if(invalidvarcomb[cptcod]){
                   8581:        printf("\nCombination (%d) ignored because no cases \n",cptcod); 
                   8582:        continue;
                   8583:      }
1.219     brouard  8584: 
1.266     brouard  8585:      for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
                   8586:        sumnewm[cptcod]=0.;
                   8587:        sumnewmr[cptcod]=0.;
                   8588:        for (i=1; i<=nlstate;i++){
                   8589:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                   8590:         sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
                   8591:        }
                   8592:        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
                   8593:         agemingoodr[cptcod]=age;
                   8594:        }
                   8595:        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
                   8596:           agemingood[cptcod]=age;
                   8597:        }
                   8598:      } /* age */
                   8599:      for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222     brouard  8600:        sumnewm[cptcod]=0.;
1.266     brouard  8601:        sumnewmr[cptcod]=0.;
1.222     brouard  8602:        for (i=1; i<=nlstate;i++){
                   8603:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266     brouard  8604:         sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
                   8605:        }
                   8606:        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
                   8607:         agemaxgoodr[cptcod]=age;
1.222     brouard  8608:        }
                   8609:        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266     brouard  8610:         agemaxgood[cptcod]=age;
                   8611:        }
                   8612:      } /* age */
                   8613:      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
                   8614:      /* but they will change */
1.288     brouard  8615:      firstA1=0;firstA2=0;
1.266     brouard  8616:      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
                   8617:        sumnewm[cptcod]=0.;
                   8618:        sumnewmr[cptcod]=0.;
                   8619:        for (i=1; i<=nlstate;i++){
                   8620:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                   8621:         sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
                   8622:        }
                   8623:        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
                   8624:         if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
                   8625:           agemaxgoodr[cptcod]=age;  /* age min */
                   8626:           for (i=1; i<=nlstate;i++)
                   8627:             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   8628:         }else{ /* bad we change the value with the values of good ages */
                   8629:           for (i=1; i<=nlstate;i++){
                   8630:             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
                   8631:           } /* i */
                   8632:         } /* end bad */
                   8633:        }else{
                   8634:         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
                   8635:           agemaxgood[cptcod]=age;
                   8636:         }else{ /* bad we change the value with the values of good ages */
                   8637:           for (i=1; i<=nlstate;i++){
                   8638:             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                   8639:           } /* i */
                   8640:         } /* end bad */
                   8641:        }/* end else */
                   8642:        sum=0.;sumr=0.;
                   8643:        for (i=1; i<=nlstate;i++){
                   8644:         sum+=mobaverage[(int)age][i][cptcod];
                   8645:         sumr+=probs[(int)age][i][cptcod];
                   8646:        }
                   8647:        if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288     brouard  8648:         if(!firstA1){
                   8649:           firstA1=1;
                   8650:           printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
                   8651:         }
                   8652:         fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
1.266     brouard  8653:        } /* end bad */
                   8654:        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
                   8655:        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288     brouard  8656:         if(!firstA2){
                   8657:           firstA2=1;
                   8658:           printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
                   8659:         }
                   8660:         fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
1.222     brouard  8661:        } /* end bad */
                   8662:      }/* age */
1.266     brouard  8663: 
                   8664:      for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222     brouard  8665:        sumnewm[cptcod]=0.;
1.266     brouard  8666:        sumnewmr[cptcod]=0.;
1.222     brouard  8667:        for (i=1; i<=nlstate;i++){
                   8668:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266     brouard  8669:         sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
                   8670:        } 
                   8671:        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
                   8672:         if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
                   8673:           agemingoodr[cptcod]=age;
                   8674:           for (i=1; i<=nlstate;i++)
                   8675:             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   8676:         }else{ /* bad we change the value with the values of good ages */
                   8677:           for (i=1; i<=nlstate;i++){
                   8678:             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
                   8679:           } /* i */
                   8680:         } /* end bad */
                   8681:        }else{
                   8682:         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
                   8683:           agemingood[cptcod]=age;
                   8684:         }else{ /* bad */
                   8685:           for (i=1; i<=nlstate;i++){
                   8686:             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
                   8687:           } /* i */
                   8688:         } /* end bad */
                   8689:        }/* end else */
                   8690:        sum=0.;sumr=0.;
                   8691:        for (i=1; i<=nlstate;i++){
                   8692:         sum+=mobaverage[(int)age][i][cptcod];
                   8693:         sumr+=mobaverage[(int)age][i][cptcod];
1.222     brouard  8694:        }
1.266     brouard  8695:        if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268     brouard  8696:         printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
1.266     brouard  8697:        } /* end bad */
                   8698:        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
                   8699:        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268     brouard  8700:         printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
1.222     brouard  8701:        } /* end bad */
                   8702:      }/* age */
1.266     brouard  8703: 
1.222     brouard  8704:                
                   8705:      for (age=bage; age<=fage; age++){
1.235     brouard  8706:        /* printf("%d %d ", cptcod, (int)age); */
1.222     brouard  8707:        sumnewp[cptcod]=0.;
                   8708:        sumnewm[cptcod]=0.;
                   8709:        for (i=1; i<=nlstate;i++){
                   8710:         sumnewp[cptcod]+=probs[(int)age][i][cptcod];
                   8711:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                   8712:         /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
                   8713:        }
                   8714:        /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
                   8715:      }
                   8716:      /* printf("\n"); */
                   8717:      /* } */
1.266     brouard  8718: 
1.222     brouard  8719:      /* brutal averaging */
1.266     brouard  8720:      /* for (i=1; i<=nlstate;i++){ */
                   8721:      /*   for (age=1; age<=bage; age++){ */
                   8722:      /*         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
                   8723:      /*         /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
                   8724:      /*   }     */
                   8725:      /*   for (age=fage; age<=AGESUP; age++){ */
                   8726:      /*         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
                   8727:      /*         /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
                   8728:      /*   } */
                   8729:      /* } /\* end i status *\/ */
                   8730:      /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
                   8731:      /*   for (age=1; age<=AGESUP; age++){ */
                   8732:      /*         /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
                   8733:      /*         mobaverage[(int)age][i][cptcod]=0.; */
                   8734:      /*   } */
                   8735:      /* } */
1.222     brouard  8736:    }/* end cptcod */
1.266     brouard  8737:    free_vector(agemaxgoodr,1, ncovcombmax);
                   8738:    free_vector(agemaxgood,1, ncovcombmax);
                   8739:    free_vector(agemingood,1, ncovcombmax);
                   8740:    free_vector(agemingoodr,1, ncovcombmax);
                   8741:    free_vector(sumnewmr,1, ncovcombmax);
1.222     brouard  8742:    free_vector(sumnewm,1, ncovcombmax);
                   8743:    free_vector(sumnewp,1, ncovcombmax);
                   8744:    return 0;
                   8745:  }/* End movingaverage */
1.218     brouard  8746:  
1.126     brouard  8747: 
1.296     brouard  8748:  
1.126     brouard  8749: /************** Forecasting ******************/
1.296     brouard  8750: /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
                   8751: void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
                   8752:   /* dateintemean, mean date of interviews
                   8753:      dateprojd, year, month, day of starting projection 
                   8754:      dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126     brouard  8755:      agemin, agemax range of age
                   8756:      dateprev1 dateprev2 range of dates during which prevalence is computed
                   8757:   */
1.296     brouard  8758:   /* double anprojd, mprojd, jprojd; */
                   8759:   /* double anprojf, mprojf, jprojf; */
1.267     brouard  8760:   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126     brouard  8761:   double agec; /* generic age */
1.296     brouard  8762:   double agelim, ppij, yp,yp1,yp2;
1.126     brouard  8763:   double *popeffectif,*popcount;
                   8764:   double ***p3mat;
1.218     brouard  8765:   /* double ***mobaverage; */
1.126     brouard  8766:   char fileresf[FILENAMELENGTH];
                   8767: 
                   8768:   agelim=AGESUP;
1.211     brouard  8769:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   8770:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   8771:      We still use firstpass and lastpass as another selection.
                   8772:   */
1.214     brouard  8773:   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
                   8774:   /*         firstpass, lastpass,  stepm,  weightopt, model); */
1.126     brouard  8775:  
1.201     brouard  8776:   strcpy(fileresf,"F_"); 
                   8777:   strcat(fileresf,fileresu);
1.126     brouard  8778:   if((ficresf=fopen(fileresf,"w"))==NULL) {
                   8779:     printf("Problem with forecast resultfile: %s\n", fileresf);
                   8780:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
                   8781:   }
1.235     brouard  8782:   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
                   8783:   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126     brouard  8784: 
1.225     brouard  8785:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126     brouard  8786: 
                   8787: 
                   8788:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   8789:   if (stepm<=12) stepsize=1;
                   8790:   if(estepm < stepm){
                   8791:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   8792:   }
1.270     brouard  8793:   else{
                   8794:     hstepm=estepm;   
                   8795:   }
                   8796:   if(estepm > stepm){ /* Yes every two year */
                   8797:     stepsize=2;
                   8798:   }
1.296     brouard  8799:   hstepm=hstepm/stepm;
1.126     brouard  8800: 
1.296     brouard  8801:   
                   8802:   /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                   8803:   /*                              fractional in yp1 *\/ */
                   8804:   /* aintmean=yp; */
                   8805:   /* yp2=modf((yp1*12),&yp); */
                   8806:   /* mintmean=yp; */
                   8807:   /* yp1=modf((yp2*30.5),&yp); */
                   8808:   /* jintmean=yp; */
                   8809:   /* if(jintmean==0) jintmean=1; */
                   8810:   /* if(mintmean==0) mintmean=1; */
1.126     brouard  8811: 
1.296     brouard  8812: 
                   8813:   /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
                   8814:   /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
                   8815:   /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227     brouard  8816:   i1=pow(2,cptcoveff);
1.126     brouard  8817:   if (cptcovn < 1){i1=1;}
                   8818:   
1.296     brouard  8819:   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); 
1.126     brouard  8820:   
                   8821:   fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227     brouard  8822:   
1.126     brouard  8823: /*           if (h==(int)(YEARM*yearp)){ */
1.235     brouard  8824:   for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   8825:   for(k=1; k<=i1;k++){
1.253     brouard  8826:     if(i1 != 1 && TKresult[nres]!= k)
1.235     brouard  8827:       continue;
1.227     brouard  8828:     if(invalidvarcomb[k]){
                   8829:       printf("\nCombination (%d) projection ignored because no cases \n",k); 
                   8830:       continue;
                   8831:     }
                   8832:     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
                   8833:     for(j=1;j<=cptcoveff;j++) {
                   8834:       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   8835:     }
1.235     brouard  8836:     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238     brouard  8837:       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235     brouard  8838:     }
1.227     brouard  8839:     fprintf(ficresf," yearproj age");
                   8840:     for(j=1; j<=nlstate+ndeath;j++){ 
                   8841:       for(i=1; i<=nlstate;i++)               
                   8842:        fprintf(ficresf," p%d%d",i,j);
                   8843:       fprintf(ficresf," wp.%d",j);
                   8844:     }
1.296     brouard  8845:     for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227     brouard  8846:       fprintf(ficresf,"\n");
1.296     brouard  8847:       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);   
1.270     brouard  8848:       /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
                   8849:       for (agec=fage; agec>=(bage); agec--){ 
1.227     brouard  8850:        nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                   8851:        nhstepm = nhstepm/hstepm; 
                   8852:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   8853:        oldm=oldms;savm=savms;
1.268     brouard  8854:        /* We compute pii at age agec over nhstepm);*/
1.235     brouard  8855:        hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268     brouard  8856:        /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227     brouard  8857:        for (h=0; h<=nhstepm; h++){
                   8858:          if (h*hstepm/YEARM*stepm ==yearp) {
1.268     brouard  8859:            break;
                   8860:          }
                   8861:        }
                   8862:        fprintf(ficresf,"\n");
                   8863:        for(j=1;j<=cptcoveff;j++) 
                   8864:          fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296     brouard  8865:        fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268     brouard  8866:        
                   8867:        for(j=1; j<=nlstate+ndeath;j++) {
                   8868:          ppij=0.;
                   8869:          for(i=1; i<=nlstate;i++) {
1.278     brouard  8870:            if (mobilav>=1)
                   8871:             ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
                   8872:            else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
                   8873:                ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
                   8874:            }
1.268     brouard  8875:            fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   8876:          } /* end i */
                   8877:          fprintf(ficresf," %.3f", ppij);
                   8878:        }/* end j */
1.227     brouard  8879:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   8880:       } /* end agec */
1.266     brouard  8881:       /* diffyear=(int) anproj1+yearp-ageminpar-1; */
                   8882:       /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227     brouard  8883:     } /* end yearp */
                   8884:   } /* end  k */
1.219     brouard  8885:        
1.126     brouard  8886:   fclose(ficresf);
1.215     brouard  8887:   printf("End of Computing forecasting \n");
                   8888:   fprintf(ficlog,"End of Computing forecasting\n");
                   8889: 
1.126     brouard  8890: }
                   8891: 
1.269     brouard  8892: /************** Back Forecasting ******************/
1.296     brouard  8893:  /* void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
                   8894:  void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
                   8895:   /* back1, year, month, day of starting backprojection
1.267     brouard  8896:      agemin, agemax range of age
                   8897:      dateprev1 dateprev2 range of dates during which prevalence is computed
1.269     brouard  8898:      anback2 year of end of backprojection (same day and month as back1).
                   8899:      prevacurrent and prev are prevalences.
1.267     brouard  8900:   */
                   8901:   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
                   8902:   double agec; /* generic age */
1.302     brouard  8903:   double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267     brouard  8904:   double *popeffectif,*popcount;
                   8905:   double ***p3mat;
                   8906:   /* double ***mobaverage; */
                   8907:   char fileresfb[FILENAMELENGTH];
                   8908:  
1.268     brouard  8909:   agelim=AGEINF;
1.267     brouard  8910:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   8911:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   8912:      We still use firstpass and lastpass as another selection.
                   8913:   */
                   8914:   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
                   8915:   /*         firstpass, lastpass,  stepm,  weightopt, model); */
                   8916: 
                   8917:   /*Do we need to compute prevalence again?*/
                   8918: 
                   8919:   /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
                   8920:   
                   8921:   strcpy(fileresfb,"FB_");
                   8922:   strcat(fileresfb,fileresu);
                   8923:   if((ficresfb=fopen(fileresfb,"w"))==NULL) {
                   8924:     printf("Problem with back forecast resultfile: %s\n", fileresfb);
                   8925:     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
                   8926:   }
                   8927:   printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
                   8928:   fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
                   8929:   
                   8930:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   8931:   
                   8932:    
                   8933:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   8934:   if (stepm<=12) stepsize=1;
                   8935:   if(estepm < stepm){
                   8936:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   8937:   }
1.270     brouard  8938:   else{
                   8939:     hstepm=estepm;   
                   8940:   }
                   8941:   if(estepm >= stepm){ /* Yes every two year */
                   8942:     stepsize=2;
                   8943:   }
1.267     brouard  8944:   
                   8945:   hstepm=hstepm/stepm;
1.296     brouard  8946:   /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                   8947:   /*                              fractional in yp1 *\/ */
                   8948:   /* aintmean=yp; */
                   8949:   /* yp2=modf((yp1*12),&yp); */
                   8950:   /* mintmean=yp; */
                   8951:   /* yp1=modf((yp2*30.5),&yp); */
                   8952:   /* jintmean=yp; */
                   8953:   /* if(jintmean==0) jintmean=1; */
                   8954:   /* if(mintmean==0) jintmean=1; */
1.267     brouard  8955:   
                   8956:   i1=pow(2,cptcoveff);
                   8957:   if (cptcovn < 1){i1=1;}
                   8958:   
1.296     brouard  8959:   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
                   8960:   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267     brouard  8961:   
                   8962:   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
                   8963:   
                   8964:   for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   8965:   for(k=1; k<=i1;k++){
                   8966:     if(i1 != 1 && TKresult[nres]!= k)
                   8967:       continue;
                   8968:     if(invalidvarcomb[k]){
                   8969:       printf("\nCombination (%d) projection ignored because no cases \n",k); 
                   8970:       continue;
                   8971:     }
1.268     brouard  8972:     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267     brouard  8973:     for(j=1;j<=cptcoveff;j++) {
                   8974:       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   8975:     }
                   8976:     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   8977:       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   8978:     }
                   8979:     fprintf(ficresfb," yearbproj age");
                   8980:     for(j=1; j<=nlstate+ndeath;j++){
                   8981:       for(i=1; i<=nlstate;i++)
1.268     brouard  8982:        fprintf(ficresfb," b%d%d",i,j);
                   8983:       fprintf(ficresfb," b.%d",j);
1.267     brouard  8984:     }
1.296     brouard  8985:     for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267     brouard  8986:       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
                   8987:       fprintf(ficresfb,"\n");
1.296     brouard  8988:       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273     brouard  8989:       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270     brouard  8990:       /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
                   8991:       for (agec=bage; agec<=fage; agec++){  /* testing */
1.268     brouard  8992:        /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271     brouard  8993:        nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267     brouard  8994:        nhstepm = nhstepm/hstepm;
                   8995:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   8996:        oldm=oldms;savm=savms;
1.268     brouard  8997:        /* computes hbxij at age agec over 1 to nhstepm */
1.271     brouard  8998:        /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267     brouard  8999:        hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268     brouard  9000:        /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
                   9001:        /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
                   9002:        /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267     brouard  9003:        for (h=0; h<=nhstepm; h++){
1.268     brouard  9004:          if (h*hstepm/YEARM*stepm ==-yearp) {
                   9005:            break;
                   9006:          }
                   9007:        }
                   9008:        fprintf(ficresfb,"\n");
                   9009:        for(j=1;j<=cptcoveff;j++)
                   9010:          fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296     brouard  9011:        fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268     brouard  9012:        for(i=1; i<=nlstate+ndeath;i++) {
                   9013:          ppij=0.;ppi=0.;
                   9014:          for(j=1; j<=nlstate;j++) {
                   9015:            /* if (mobilav==1) */
1.269     brouard  9016:            ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
                   9017:            ppi=ppi+prevacurrent[(int)agec][j][k];
                   9018:            /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
                   9019:            /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267     brouard  9020:              /* else { */
                   9021:              /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
                   9022:              /* } */
1.268     brouard  9023:            fprintf(ficresfb," %.3f", p3mat[i][j][h]);
                   9024:          } /* end j */
                   9025:          if(ppi <0.99){
                   9026:            printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
                   9027:            fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
                   9028:          }
                   9029:          fprintf(ficresfb," %.3f", ppij);
                   9030:        }/* end j */
1.267     brouard  9031:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   9032:       } /* end agec */
                   9033:     } /* end yearp */
                   9034:   } /* end k */
1.217     brouard  9035:   
1.267     brouard  9036:   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217     brouard  9037:   
1.267     brouard  9038:   fclose(ficresfb);
                   9039:   printf("End of Computing Back forecasting \n");
                   9040:   fprintf(ficlog,"End of Computing Back forecasting\n");
1.218     brouard  9041:        
1.267     brouard  9042: }
1.217     brouard  9043: 
1.269     brouard  9044: /* Variance of prevalence limit: varprlim */
                   9045:  void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
1.288     brouard  9046:     /*------- Variance of forward period (stable) prevalence------*/   
1.269     brouard  9047:  
                   9048:    char fileresvpl[FILENAMELENGTH];  
                   9049:    FILE *ficresvpl;
                   9050:    double **oldm, **savm;
                   9051:    double **varpl; /* Variances of prevalence limits by age */   
                   9052:    int i1, k, nres, j ;
                   9053:    
                   9054:     strcpy(fileresvpl,"VPL_");
                   9055:     strcat(fileresvpl,fileresu);
                   9056:     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288     brouard  9057:       printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
1.269     brouard  9058:       exit(0);
                   9059:     }
1.288     brouard  9060:     printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
                   9061:     fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269     brouard  9062:     
                   9063:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   9064:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   9065:     
                   9066:     i1=pow(2,cptcoveff);
                   9067:     if (cptcovn < 1){i1=1;}
                   9068: 
                   9069:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   9070:     for(k=1; k<=i1;k++){
                   9071:       if(i1 != 1 && TKresult[nres]!= k)
                   9072:        continue;
                   9073:       fprintf(ficresvpl,"\n#****** ");
                   9074:       printf("\n#****** ");
                   9075:       fprintf(ficlog,"\n#****** ");
                   9076:       for(j=1;j<=cptcoveff;j++) {
                   9077:        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9078:        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9079:        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9080:       }
                   9081:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   9082:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9083:        fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9084:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9085:       }        
                   9086:       fprintf(ficresvpl,"******\n");
                   9087:       printf("******\n");
                   9088:       fprintf(ficlog,"******\n");
                   9089:       
                   9090:       varpl=matrix(1,nlstate,(int) bage, (int) fage);
                   9091:       oldm=oldms;savm=savms;
                   9092:       varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
                   9093:       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
                   9094:       /*}*/
                   9095:     }
                   9096:     
                   9097:     fclose(ficresvpl);
1.288     brouard  9098:     printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
                   9099:     fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269     brouard  9100: 
                   9101:  }
                   9102: /* Variance of back prevalence: varbprlim */
                   9103:  void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
                   9104:       /*------- Variance of back (stable) prevalence------*/
                   9105: 
                   9106:    char fileresvbl[FILENAMELENGTH];  
                   9107:    FILE  *ficresvbl;
                   9108: 
                   9109:    double **oldm, **savm;
                   9110:    double **varbpl; /* Variances of back prevalence limits by age */   
                   9111:    int i1, k, nres, j ;
                   9112: 
                   9113:    strcpy(fileresvbl,"VBL_");
                   9114:    strcat(fileresvbl,fileresu);
                   9115:    if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
                   9116:      printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
                   9117:      exit(0);
                   9118:    }
                   9119:    printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
                   9120:    fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
                   9121:    
                   9122:    
                   9123:    i1=pow(2,cptcoveff);
                   9124:    if (cptcovn < 1){i1=1;}
                   9125:    
                   9126:    for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   9127:      for(k=1; k<=i1;k++){
                   9128:        if(i1 != 1 && TKresult[nres]!= k)
                   9129:         continue;
                   9130:        fprintf(ficresvbl,"\n#****** ");
                   9131:        printf("\n#****** ");
                   9132:        fprintf(ficlog,"\n#****** ");
                   9133:        for(j=1;j<=cptcoveff;j++) {
                   9134:         fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9135:         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9136:         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9137:        }
                   9138:        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   9139:         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9140:         fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9141:         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9142:        }
                   9143:        fprintf(ficresvbl,"******\n");
                   9144:        printf("******\n");
                   9145:        fprintf(ficlog,"******\n");
                   9146:        
                   9147:        varbpl=matrix(1,nlstate,(int) bage, (int) fage);
                   9148:        oldm=oldms;savm=savms;
                   9149:        
                   9150:        varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
                   9151:        free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
                   9152:        /*}*/
                   9153:      }
                   9154:    
                   9155:    fclose(ficresvbl);
                   9156:    printf("done variance-covariance of back prevalence\n");fflush(stdout);
                   9157:    fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
                   9158: 
                   9159:  } /* End of varbprlim */
                   9160: 
1.126     brouard  9161: /************** Forecasting *****not tested NB*************/
1.227     brouard  9162: /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
1.126     brouard  9163:   
1.227     brouard  9164: /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
                   9165: /*   int *popage; */
                   9166: /*   double calagedatem, agelim, kk1, kk2; */
                   9167: /*   double *popeffectif,*popcount; */
                   9168: /*   double ***p3mat,***tabpop,***tabpopprev; */
                   9169: /*   /\* double ***mobaverage; *\/ */
                   9170: /*   char filerespop[FILENAMELENGTH]; */
1.126     brouard  9171: 
1.227     brouard  9172: /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   9173: /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   9174: /*   agelim=AGESUP; */
                   9175: /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126     brouard  9176:   
1.227     brouard  9177: /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126     brouard  9178:   
                   9179:   
1.227     brouard  9180: /*   strcpy(filerespop,"POP_");  */
                   9181: /*   strcat(filerespop,fileresu); */
                   9182: /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
                   9183: /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
                   9184: /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
                   9185: /*   } */
                   9186: /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
                   9187: /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126     brouard  9188: 
1.227     brouard  9189: /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126     brouard  9190: 
1.227     brouard  9191: /*   /\* if (mobilav!=0) { *\/ */
                   9192: /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
                   9193: /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
                   9194: /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
                   9195: /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
                   9196: /*   /\*   } *\/ */
                   9197: /*   /\* } *\/ */
1.126     brouard  9198: 
1.227     brouard  9199: /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
                   9200: /*   if (stepm<=12) stepsize=1; */
1.126     brouard  9201:   
1.227     brouard  9202: /*   agelim=AGESUP; */
1.126     brouard  9203:   
1.227     brouard  9204: /*   hstepm=1; */
                   9205: /*   hstepm=hstepm/stepm;  */
1.218     brouard  9206:        
1.227     brouard  9207: /*   if (popforecast==1) { */
                   9208: /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
                   9209: /*       printf("Problem with population file : %s\n",popfile);exit(0); */
                   9210: /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
                   9211: /*     }  */
                   9212: /*     popage=ivector(0,AGESUP); */
                   9213: /*     popeffectif=vector(0,AGESUP); */
                   9214: /*     popcount=vector(0,AGESUP); */
1.126     brouard  9215:     
1.227     brouard  9216: /*     i=1;    */
                   9217: /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218     brouard  9218:     
1.227     brouard  9219: /*     imx=i; */
                   9220: /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
                   9221: /*   } */
1.218     brouard  9222:   
1.227     brouard  9223: /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
                   9224: /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
                   9225: /*       k=k+1; */
                   9226: /*       fprintf(ficrespop,"\n#******"); */
                   9227: /*       for(j=1;j<=cptcoveff;j++) { */
                   9228: /*     fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
                   9229: /*       } */
                   9230: /*       fprintf(ficrespop,"******\n"); */
                   9231: /*       fprintf(ficrespop,"# Age"); */
                   9232: /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
                   9233: /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
1.126     brouard  9234:       
1.227     brouard  9235: /*       for (cpt=0; cpt<=0;cpt++) {  */
                   9236: /*     fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
1.126     brouard  9237:        
1.227     brouard  9238: /*     for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
                   9239: /*       nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
                   9240: /*       nhstepm = nhstepm/hstepm;  */
1.126     brouard  9241:          
1.227     brouard  9242: /*       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   9243: /*       oldm=oldms;savm=savms; */
                   9244: /*       hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
1.218     brouard  9245:          
1.227     brouard  9246: /*       for (h=0; h<=nhstepm; h++){ */
                   9247: /*         if (h==(int) (calagedatem+YEARM*cpt)) { */
                   9248: /*           fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
                   9249: /*         }  */
                   9250: /*         for(j=1; j<=nlstate+ndeath;j++) { */
                   9251: /*           kk1=0.;kk2=0; */
                   9252: /*           for(i=1; i<=nlstate;i++) {               */
                   9253: /*             if (mobilav==1)  */
                   9254: /*               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
                   9255: /*             else { */
                   9256: /*               kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
                   9257: /*             } */
                   9258: /*           } */
                   9259: /*           if (h==(int)(calagedatem+12*cpt)){ */
                   9260: /*             tabpop[(int)(agedeb)][j][cptcod]=kk1; */
                   9261: /*             /\*fprintf(ficrespop," %.3f", kk1); */
                   9262: /*               if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
                   9263: /*           } */
                   9264: /*         } */
                   9265: /*         for(i=1; i<=nlstate;i++){ */
                   9266: /*           kk1=0.; */
                   9267: /*           for(j=1; j<=nlstate;j++){ */
                   9268: /*             kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
                   9269: /*           } */
                   9270: /*           tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
                   9271: /*         } */
1.218     brouard  9272:            
1.227     brouard  9273: /*         if (h==(int)(calagedatem+12*cpt)) */
                   9274: /*           for(j=1; j<=nlstate;j++)  */
                   9275: /*             fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
                   9276: /*       } */
                   9277: /*       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   9278: /*     } */
                   9279: /*       } */
1.218     brouard  9280:       
1.227     brouard  9281: /*       /\******\/ */
1.218     brouard  9282:       
1.227     brouard  9283: /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
                   9284: /*     fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
                   9285: /*     for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
                   9286: /*       nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
                   9287: /*       nhstepm = nhstepm/hstepm;  */
1.126     brouard  9288:          
1.227     brouard  9289: /*       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   9290: /*       oldm=oldms;savm=savms; */
                   9291: /*       hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
                   9292: /*       for (h=0; h<=nhstepm; h++){ */
                   9293: /*         if (h==(int) (calagedatem+YEARM*cpt)) { */
                   9294: /*           fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
                   9295: /*         }  */
                   9296: /*         for(j=1; j<=nlstate+ndeath;j++) { */
                   9297: /*           kk1=0.;kk2=0; */
                   9298: /*           for(i=1; i<=nlstate;i++) {               */
                   9299: /*             kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
                   9300: /*           } */
                   9301: /*           if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
                   9302: /*         } */
                   9303: /*       } */
                   9304: /*       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   9305: /*     } */
                   9306: /*       } */
                   9307: /*     }  */
                   9308: /*   } */
1.218     brouard  9309:   
1.227     brouard  9310: /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218     brouard  9311:   
1.227     brouard  9312: /*   if (popforecast==1) { */
                   9313: /*     free_ivector(popage,0,AGESUP); */
                   9314: /*     free_vector(popeffectif,0,AGESUP); */
                   9315: /*     free_vector(popcount,0,AGESUP); */
                   9316: /*   } */
                   9317: /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   9318: /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   9319: /*   fclose(ficrespop); */
                   9320: /* } /\* End of popforecast *\/ */
1.218     brouard  9321:  
1.126     brouard  9322: int fileappend(FILE *fichier, char *optionfich)
                   9323: {
                   9324:   if((fichier=fopen(optionfich,"a"))==NULL) {
                   9325:     printf("Problem with file: %s\n", optionfich);
                   9326:     fprintf(ficlog,"Problem with file: %s\n", optionfich);
                   9327:     return (0);
                   9328:   }
                   9329:   fflush(fichier);
                   9330:   return (1);
                   9331: }
                   9332: 
                   9333: 
                   9334: /**************** function prwizard **********************/
                   9335: void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
                   9336: {
                   9337: 
                   9338:   /* Wizard to print covariance matrix template */
                   9339: 
1.164     brouard  9340:   char ca[32], cb[32];
                   9341:   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126     brouard  9342:   int numlinepar;
                   9343: 
                   9344:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   9345:   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   9346:   for(i=1; i <=nlstate; i++){
                   9347:     jj=0;
                   9348:     for(j=1; j <=nlstate+ndeath; j++){
                   9349:       if(j==i) continue;
                   9350:       jj++;
                   9351:       /*ca[0]= k+'a'-1;ca[1]='\0';*/
                   9352:       printf("%1d%1d",i,j);
                   9353:       fprintf(ficparo,"%1d%1d",i,j);
                   9354:       for(k=1; k<=ncovmodel;k++){
                   9355:        /*        printf(" %lf",param[i][j][k]); */
                   9356:        /*        fprintf(ficparo," %lf",param[i][j][k]); */
                   9357:        printf(" 0.");
                   9358:        fprintf(ficparo," 0.");
                   9359:       }
                   9360:       printf("\n");
                   9361:       fprintf(ficparo,"\n");
                   9362:     }
                   9363:   }
                   9364:   printf("# Scales (for hessian or gradient estimation)\n");
                   9365:   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
                   9366:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
                   9367:   for(i=1; i <=nlstate; i++){
                   9368:     jj=0;
                   9369:     for(j=1; j <=nlstate+ndeath; j++){
                   9370:       if(j==i) continue;
                   9371:       jj++;
                   9372:       fprintf(ficparo,"%1d%1d",i,j);
                   9373:       printf("%1d%1d",i,j);
                   9374:       fflush(stdout);
                   9375:       for(k=1; k<=ncovmodel;k++){
                   9376:        /*      printf(" %le",delti3[i][j][k]); */
                   9377:        /*      fprintf(ficparo," %le",delti3[i][j][k]); */
                   9378:        printf(" 0.");
                   9379:        fprintf(ficparo," 0.");
                   9380:       }
                   9381:       numlinepar++;
                   9382:       printf("\n");
                   9383:       fprintf(ficparo,"\n");
                   9384:     }
                   9385:   }
                   9386:   printf("# Covariance matrix\n");
                   9387: /* # 121 Var(a12)\n\ */
                   9388: /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   9389: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   9390: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   9391: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   9392: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   9393: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   9394: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   9395:   fflush(stdout);
                   9396:   fprintf(ficparo,"# Covariance matrix\n");
                   9397:   /* # 121 Var(a12)\n\ */
                   9398:   /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   9399:   /* #   ...\n\ */
                   9400:   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
                   9401:   
                   9402:   for(itimes=1;itimes<=2;itimes++){
                   9403:     jj=0;
                   9404:     for(i=1; i <=nlstate; i++){
                   9405:       for(j=1; j <=nlstate+ndeath; j++){
                   9406:        if(j==i) continue;
                   9407:        for(k=1; k<=ncovmodel;k++){
                   9408:          jj++;
                   9409:          ca[0]= k+'a'-1;ca[1]='\0';
                   9410:          if(itimes==1){
                   9411:            printf("#%1d%1d%d",i,j,k);
                   9412:            fprintf(ficparo,"#%1d%1d%d",i,j,k);
                   9413:          }else{
                   9414:            printf("%1d%1d%d",i,j,k);
                   9415:            fprintf(ficparo,"%1d%1d%d",i,j,k);
                   9416:            /*  printf(" %.5le",matcov[i][j]); */
                   9417:          }
                   9418:          ll=0;
                   9419:          for(li=1;li <=nlstate; li++){
                   9420:            for(lj=1;lj <=nlstate+ndeath; lj++){
                   9421:              if(lj==li) continue;
                   9422:              for(lk=1;lk<=ncovmodel;lk++){
                   9423:                ll++;
                   9424:                if(ll<=jj){
                   9425:                  cb[0]= lk +'a'-1;cb[1]='\0';
                   9426:                  if(ll<jj){
                   9427:                    if(itimes==1){
                   9428:                      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   9429:                      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   9430:                    }else{
                   9431:                      printf(" 0.");
                   9432:                      fprintf(ficparo," 0.");
                   9433:                    }
                   9434:                  }else{
                   9435:                    if(itimes==1){
                   9436:                      printf(" Var(%s%1d%1d)",ca,i,j);
                   9437:                      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                   9438:                    }else{
                   9439:                      printf(" 0.");
                   9440:                      fprintf(ficparo," 0.");
                   9441:                    }
                   9442:                  }
                   9443:                }
                   9444:              } /* end lk */
                   9445:            } /* end lj */
                   9446:          } /* end li */
                   9447:          printf("\n");
                   9448:          fprintf(ficparo,"\n");
                   9449:          numlinepar++;
                   9450:        } /* end k*/
                   9451:       } /*end j */
                   9452:     } /* end i */
                   9453:   } /* end itimes */
                   9454: 
                   9455: } /* end of prwizard */
                   9456: /******************* Gompertz Likelihood ******************************/
                   9457: double gompertz(double x[])
                   9458: { 
1.302     brouard  9459:   double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126     brouard  9460:   int i,n=0; /* n is the size of the sample */
                   9461: 
1.220     brouard  9462:   for (i=1;i<=imx ; i++) {
1.126     brouard  9463:     sump=sump+weight[i];
                   9464:     /*    sump=sump+1;*/
                   9465:     num=num+1;
                   9466:   }
1.302     brouard  9467:   L=0.0;
                   9468:   /* agegomp=AGEGOMP; */
1.126     brouard  9469:   /* for (i=0; i<=imx; i++) 
                   9470:      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
                   9471: 
1.302     brouard  9472:   for (i=1;i<=imx ; i++) {
                   9473:     /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
                   9474:        mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
                   9475:      * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month) 
                   9476:      *   and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
                   9477:      * +
                   9478:      * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
                   9479:      */
                   9480:      if (wav[i] > 1 || agedc[i] < AGESUP) {
                   9481:        if (cens[i] == 1){
                   9482:         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
                   9483:        } else if (cens[i] == 0){
1.126     brouard  9484:        A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302     brouard  9485:          +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
                   9486:       } else
                   9487:         printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126     brouard  9488:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302     brouard  9489:        L=L+A*weight[i];
1.126     brouard  9490:        /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
1.302     brouard  9491:      }
                   9492:   }
1.126     brouard  9493: 
1.302     brouard  9494:   /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126     brouard  9495:  
                   9496:   return -2*L*num/sump;
                   9497: }
                   9498: 
1.136     brouard  9499: #ifdef GSL
                   9500: /******************* Gompertz_f Likelihood ******************************/
                   9501: double gompertz_f(const gsl_vector *v, void *params)
                   9502: { 
1.302     brouard  9503:   double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136     brouard  9504:   double *x= (double *) v->data;
                   9505:   int i,n=0; /* n is the size of the sample */
                   9506: 
                   9507:   for (i=0;i<=imx-1 ; i++) {
                   9508:     sump=sump+weight[i];
                   9509:     /*    sump=sump+1;*/
                   9510:     num=num+1;
                   9511:   }
                   9512:  
                   9513:  
                   9514:   /* for (i=0; i<=imx; i++) 
                   9515:      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
                   9516:   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
                   9517:   for (i=1;i<=imx ; i++)
                   9518:     {
                   9519:       if (cens[i] == 1 && wav[i]>1)
                   9520:        A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
                   9521:       
                   9522:       if (cens[i] == 0 && wav[i]>1)
                   9523:        A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                   9524:             +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
                   9525:       
                   9526:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
                   9527:       if (wav[i] > 1 ) { /* ??? */
                   9528:        LL=LL+A*weight[i];
                   9529:        /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
                   9530:       }
                   9531:     }
                   9532: 
                   9533:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
                   9534:   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
                   9535:  
                   9536:   return -2*LL*num/sump;
                   9537: }
                   9538: #endif
                   9539: 
1.126     brouard  9540: /******************* Printing html file ***********/
1.201     brouard  9541: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126     brouard  9542:                  int lastpass, int stepm, int weightopt, char model[],\
                   9543:                  int imx,  double p[],double **matcov,double agemortsup){
                   9544:   int i,k;
                   9545: 
                   9546:   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
                   9547:   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
                   9548:   for (i=1;i<=2;i++) 
                   9549:     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.199     brouard  9550:   fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126     brouard  9551:   fprintf(fichtm,"</ul>");
                   9552: 
                   9553: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
                   9554: 
                   9555:  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
                   9556: 
                   9557:  for (k=agegomp;k<(agemortsup-2);k++) 
                   9558:    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
                   9559: 
                   9560:  
                   9561:   fflush(fichtm);
                   9562: }
                   9563: 
                   9564: /******************* Gnuplot file **************/
1.201     brouard  9565: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126     brouard  9566: 
                   9567:   char dirfileres[132],optfileres[132];
1.164     brouard  9568: 
1.126     brouard  9569:   int ng;
                   9570: 
                   9571: 
                   9572:   /*#ifdef windows */
                   9573:   fprintf(ficgp,"cd \"%s\" \n",pathc);
                   9574:     /*#endif */
                   9575: 
                   9576: 
                   9577:   strcpy(dirfileres,optionfilefiname);
                   9578:   strcpy(optfileres,"vpl");
1.199     brouard  9579:   fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
1.126     brouard  9580:   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
1.199     brouard  9581:   fprintf(ficgp, "set ter svg size 640, 480\n set log y\n"); 
1.145     brouard  9582:   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126     brouard  9583:   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
                   9584: 
                   9585: } 
                   9586: 
1.136     brouard  9587: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
                   9588: {
1.126     brouard  9589: 
1.136     brouard  9590:   /*-------- data file ----------*/
                   9591:   FILE *fic;
                   9592:   char dummy[]="                         ";
1.240     brouard  9593:   int i=0, j=0, n=0, iv=0, v;
1.223     brouard  9594:   int lstra;
1.136     brouard  9595:   int linei, month, year,iout;
1.302     brouard  9596:   int noffset=0; /* This is the offset if BOM data file */
1.136     brouard  9597:   char line[MAXLINE], linetmp[MAXLINE];
1.164     brouard  9598:   char stra[MAXLINE], strb[MAXLINE];
1.136     brouard  9599:   char *stratrunc;
1.223     brouard  9600: 
1.240     brouard  9601:   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
                   9602:   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.328   ! brouard  9603:   for(v=1;v<NCOVMAX;v++){
        !          9604:     DummyV[v]=0;
        !          9605:     FixedV[v]=0;
        !          9606:   }
1.126     brouard  9607: 
1.240     brouard  9608:   for(v=1; v <=ncovcol;v++){
                   9609:     DummyV[v]=0;
                   9610:     FixedV[v]=0;
                   9611:   }
                   9612:   for(v=ncovcol+1; v <=ncovcol+nqv;v++){
                   9613:     DummyV[v]=1;
                   9614:     FixedV[v]=0;
                   9615:   }
                   9616:   for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
                   9617:     DummyV[v]=0;
                   9618:     FixedV[v]=1;
                   9619:   }
                   9620:   for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
                   9621:     DummyV[v]=1;
                   9622:     FixedV[v]=1;
                   9623:   }
                   9624:   for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
                   9625:     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
                   9626:     fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
                   9627:   }
1.126     brouard  9628: 
1.136     brouard  9629:   if((fic=fopen(datafile,"r"))==NULL)    {
1.218     brouard  9630:     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
                   9631:     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136     brouard  9632:   }
1.126     brouard  9633: 
1.302     brouard  9634:     /* Is it a BOM UTF-8 Windows file? */
                   9635:   /* First data line */
                   9636:   linei=0;
                   9637:   while(fgets(line, MAXLINE, fic)) {
                   9638:     noffset=0;
                   9639:     if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
                   9640:     {
                   9641:       noffset=noffset+3;
                   9642:       printf("# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
                   9643:       fprintf(ficlog,"# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
                   9644:       fflush(ficlog); return 1;
                   9645:     }
                   9646:     /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
                   9647:     else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
                   9648:     {
                   9649:       noffset=noffset+2;
1.304     brouard  9650:       printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
                   9651:       fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
1.302     brouard  9652:       fflush(ficlog); return 1;
                   9653:     }
                   9654:     else if( line[0] == 0 && line[1] == 0)
                   9655:     {
                   9656:       if( line[2] == (char)0xFE && line[3] == (char)0xFF){
                   9657:        noffset=noffset+4;
1.304     brouard  9658:        printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
                   9659:        fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
1.302     brouard  9660:        fflush(ficlog); return 1;
                   9661:       }
                   9662:     } else{
                   9663:       ;/*printf(" Not a BOM file\n");*/
                   9664:     }
                   9665:         /* If line starts with a # it is a comment */
                   9666:     if (line[noffset] == '#') {
                   9667:       linei=linei+1;
                   9668:       break;
                   9669:     }else{
                   9670:       break;
                   9671:     }
                   9672:   }
                   9673:   fclose(fic);
                   9674:   if((fic=fopen(datafile,"r"))==NULL)    {
                   9675:     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
                   9676:     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
                   9677:   }
                   9678:   /* Not a Bom file */
                   9679:   
1.136     brouard  9680:   i=1;
                   9681:   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
                   9682:     linei=linei+1;
                   9683:     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
                   9684:       if(line[j] == '\t')
                   9685:        line[j] = ' ';
                   9686:     }
                   9687:     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
                   9688:       ;
                   9689:     };
                   9690:     line[j+1]=0;  /* Trims blanks at end of line */
                   9691:     if(line[0]=='#'){
                   9692:       fprintf(ficlog,"Comment line\n%s\n",line);
                   9693:       printf("Comment line\n%s\n",line);
                   9694:       continue;
                   9695:     }
                   9696:     trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164     brouard  9697:     strcpy(line, linetmp);
1.223     brouard  9698:     
                   9699:     /* Loops on waves */
                   9700:     for (j=maxwav;j>=1;j--){
                   9701:       for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
1.238     brouard  9702:        cutv(stra, strb, line, ' '); 
                   9703:        if(strb[0]=='.') { /* Missing value */
                   9704:          lval=-1;
                   9705:          cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
                   9706:          cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
                   9707:          if(isalpha(strb[1])) { /* .m or .d Really Missing value */
                   9708:            printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
                   9709:            fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
                   9710:            return 1;
                   9711:          }
                   9712:        }else{
                   9713:          errno=0;
                   9714:          /* what_kind_of_number(strb); */
                   9715:          dval=strtod(strb,&endptr); 
                   9716:          /* if( strb[0]=='\0' || (*endptr != '\0')){ */
                   9717:          /* if(strb != endptr && *endptr == '\0') */
                   9718:          /*    dval=dlval; */
                   9719:          /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                   9720:          if( strb[0]=='\0' || (*endptr != '\0')){
                   9721:            printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
                   9722:            fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
                   9723:            return 1;
                   9724:          }
                   9725:          cotqvar[j][iv][i]=dval; 
                   9726:          cotvar[j][ntv+iv][i]=dval; 
                   9727:        }
                   9728:        strcpy(line,stra);
1.223     brouard  9729:       }/* end loop ntqv */
1.225     brouard  9730:       
1.223     brouard  9731:       for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
1.238     brouard  9732:        cutv(stra, strb, line, ' '); 
                   9733:        if(strb[0]=='.') { /* Missing value */
                   9734:          lval=-1;
                   9735:        }else{
                   9736:          errno=0;
                   9737:          lval=strtol(strb,&endptr,10); 
                   9738:          /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                   9739:          if( strb[0]=='\0' || (*endptr != '\0')){
                   9740:            printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
                   9741:            fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
                   9742:            return 1;
                   9743:          }
                   9744:        }
                   9745:        if(lval <-1 || lval >1){
                   9746:          printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.319     brouard  9747:  Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
1.223     brouard  9748:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238     brouard  9749:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   9750:  build V1=0 V2=0 for the reference value (1),\n                                \
                   9751:         V1=1 V2=0 for (2) \n                                           \
1.223     brouard  9752:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238     brouard  9753:  output of IMaCh is often meaningless.\n                               \
1.319     brouard  9754:  Exiting.\n",lval,linei, i,line,iv,j);
1.238     brouard  9755:          fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.319     brouard  9756:  Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
1.223     brouard  9757:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238     brouard  9758:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   9759:  build V1=0 V2=0 for the reference value (1),\n                                \
                   9760:         V1=1 V2=0 for (2) \n                                           \
1.223     brouard  9761:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238     brouard  9762:  output of IMaCh is often meaningless.\n                               \
1.319     brouard  9763:  Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
1.238     brouard  9764:          return 1;
                   9765:        }
                   9766:        cotvar[j][iv][i]=(double)(lval);
                   9767:        strcpy(line,stra);
1.223     brouard  9768:       }/* end loop ntv */
1.225     brouard  9769:       
1.223     brouard  9770:       /* Statuses  at wave */
1.137     brouard  9771:       cutv(stra, strb, line, ' '); 
1.223     brouard  9772:       if(strb[0]=='.') { /* Missing value */
1.238     brouard  9773:        lval=-1;
1.136     brouard  9774:       }else{
1.238     brouard  9775:        errno=0;
                   9776:        lval=strtol(strb,&endptr,10); 
                   9777:        /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                   9778:        if( strb[0]=='\0' || (*endptr != '\0')){
                   9779:          printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
                   9780:          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
                   9781:          return 1;
                   9782:        }
1.136     brouard  9783:       }
1.225     brouard  9784:       
1.136     brouard  9785:       s[j][i]=lval;
1.225     brouard  9786:       
1.223     brouard  9787:       /* Date of Interview */
1.136     brouard  9788:       strcpy(line,stra);
                   9789:       cutv(stra, strb,line,' ');
1.169     brouard  9790:       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  9791:       }
1.169     brouard  9792:       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225     brouard  9793:        month=99;
                   9794:        year=9999;
1.136     brouard  9795:       }else{
1.225     brouard  9796:        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
                   9797:        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
                   9798:        return 1;
1.136     brouard  9799:       }
                   9800:       anint[j][i]= (double) year; 
1.302     brouard  9801:       mint[j][i]= (double)month;
                   9802:       /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
                   9803:       /*       printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
                   9804:       /*       fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
                   9805:       /* } */
1.136     brouard  9806:       strcpy(line,stra);
1.223     brouard  9807:     } /* End loop on waves */
1.225     brouard  9808:     
1.223     brouard  9809:     /* Date of death */
1.136     brouard  9810:     cutv(stra, strb,line,' '); 
1.169     brouard  9811:     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  9812:     }
1.169     brouard  9813:     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136     brouard  9814:       month=99;
                   9815:       year=9999;
                   9816:     }else{
1.141     brouard  9817:       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
1.225     brouard  9818:       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
                   9819:       return 1;
1.136     brouard  9820:     }
                   9821:     andc[i]=(double) year; 
                   9822:     moisdc[i]=(double) month; 
                   9823:     strcpy(line,stra);
                   9824:     
1.223     brouard  9825:     /* Date of birth */
1.136     brouard  9826:     cutv(stra, strb,line,' '); 
1.169     brouard  9827:     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  9828:     }
1.169     brouard  9829:     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136     brouard  9830:       month=99;
                   9831:       year=9999;
                   9832:     }else{
1.141     brouard  9833:       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
                   9834:       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225     brouard  9835:       return 1;
1.136     brouard  9836:     }
                   9837:     if (year==9999) {
1.141     brouard  9838:       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
                   9839:       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225     brouard  9840:       return 1;
                   9841:       
1.136     brouard  9842:     }
                   9843:     annais[i]=(double)(year);
1.302     brouard  9844:     moisnais[i]=(double)(month);
                   9845:     for (j=1;j<=maxwav;j++){
                   9846:       if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
                   9847:        printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
                   9848:        fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
                   9849:       }
                   9850:     }
                   9851: 
1.136     brouard  9852:     strcpy(line,stra);
1.225     brouard  9853:     
1.223     brouard  9854:     /* Sample weight */
1.136     brouard  9855:     cutv(stra, strb,line,' '); 
                   9856:     errno=0;
                   9857:     dval=strtod(strb,&endptr); 
                   9858:     if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  9859:       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
                   9860:       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
1.136     brouard  9861:       fflush(ficlog);
                   9862:       return 1;
                   9863:     }
                   9864:     weight[i]=dval; 
                   9865:     strcpy(line,stra);
1.225     brouard  9866:     
1.223     brouard  9867:     for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
                   9868:       cutv(stra, strb, line, ' '); 
                   9869:       if(strb[0]=='.') { /* Missing value */
1.225     brouard  9870:        lval=-1;
1.311     brouard  9871:        coqvar[iv][i]=NAN; 
                   9872:        covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */ 
1.223     brouard  9873:       }else{
1.225     brouard  9874:        errno=0;
                   9875:        /* what_kind_of_number(strb); */
                   9876:        dval=strtod(strb,&endptr);
                   9877:        /* if(strb != endptr && *endptr == '\0') */
                   9878:        /*   dval=dlval; */
                   9879:        /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                   9880:        if( strb[0]=='\0' || (*endptr != '\0')){
                   9881:          printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
                   9882:          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
                   9883:          return 1;
                   9884:        }
                   9885:        coqvar[iv][i]=dval; 
1.226     brouard  9886:        covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ 
1.223     brouard  9887:       }
                   9888:       strcpy(line,stra);
                   9889:     }/* end loop nqv */
1.136     brouard  9890:     
1.223     brouard  9891:     /* Covariate values */
1.136     brouard  9892:     for (j=ncovcol;j>=1;j--){
                   9893:       cutv(stra, strb,line,' '); 
1.223     brouard  9894:       if(strb[0]=='.') { /* Missing covariate value */
1.225     brouard  9895:        lval=-1;
1.136     brouard  9896:       }else{
1.225     brouard  9897:        errno=0;
                   9898:        lval=strtol(strb,&endptr,10); 
                   9899:        if( strb[0]=='\0' || (*endptr != '\0')){
                   9900:          printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
                   9901:          fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
                   9902:          return 1;
                   9903:        }
1.136     brouard  9904:       }
                   9905:       if(lval <-1 || lval >1){
1.225     brouard  9906:        printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  9907:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   9908:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225     brouard  9909:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   9910:  build V1=0 V2=0 for the reference value (1),\n                                \
                   9911:         V1=1 V2=0 for (2) \n                                           \
1.136     brouard  9912:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225     brouard  9913:  output of IMaCh is often meaningless.\n                               \
1.136     brouard  9914:  Exiting.\n",lval,linei, i,line,j);
1.225     brouard  9915:        fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  9916:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   9917:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225     brouard  9918:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   9919:  build V1=0 V2=0 for the reference value (1),\n                                \
                   9920:         V1=1 V2=0 for (2) \n                                           \
1.136     brouard  9921:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225     brouard  9922:  output of IMaCh is often meaningless.\n                               \
1.136     brouard  9923:  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225     brouard  9924:        return 1;
1.136     brouard  9925:       }
                   9926:       covar[j][i]=(double)(lval);
                   9927:       strcpy(line,stra);
                   9928:     }  
                   9929:     lstra=strlen(stra);
1.225     brouard  9930:     
1.136     brouard  9931:     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
                   9932:       stratrunc = &(stra[lstra-9]);
                   9933:       num[i]=atol(stratrunc);
                   9934:     }
                   9935:     else
                   9936:       num[i]=atol(stra);
                   9937:     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
                   9938:       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
                   9939:     
                   9940:     i=i+1;
                   9941:   } /* End loop reading  data */
1.225     brouard  9942:   
1.136     brouard  9943:   *imax=i-1; /* Number of individuals */
                   9944:   fclose(fic);
1.225     brouard  9945:   
1.136     brouard  9946:   return (0);
1.164     brouard  9947:   /* endread: */
1.225     brouard  9948:   printf("Exiting readdata: ");
                   9949:   fclose(fic);
                   9950:   return (1);
1.223     brouard  9951: }
1.126     brouard  9952: 
1.234     brouard  9953: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230     brouard  9954:   char *p1 = *stri, *p2 = *stri;
1.235     brouard  9955:   while (*p2 == ' ')
1.234     brouard  9956:     p2++; 
                   9957:   /* while ((*p1++ = *p2++) !=0) */
                   9958:   /*   ; */
                   9959:   /* do */
                   9960:   /*   while (*p2 == ' ') */
                   9961:   /*     p2++; */
                   9962:   /* while (*p1++ == *p2++); */
                   9963:   *stri=p2; 
1.145     brouard  9964: }
                   9965: 
1.235     brouard  9966: int decoderesult ( char resultline[], int nres)
1.230     brouard  9967: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
                   9968: {
1.235     brouard  9969:   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230     brouard  9970:   char resultsav[MAXLINE];
1.234     brouard  9971:   int resultmodel[MAXLINE];
                   9972:   int modelresult[MAXLINE];
1.230     brouard  9973:   char stra[80], strb[80], strc[80], strd[80],stre[80];
                   9974: 
1.234     brouard  9975:   removefirstspace(&resultline);
1.230     brouard  9976: 
                   9977:   if (strstr(resultline,"v") !=0){
                   9978:     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
                   9979:     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
                   9980:     return 1;
                   9981:   }
                   9982:   trimbb(resultsav, resultline);
                   9983:   if (strlen(resultsav) >1){
                   9984:     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
                   9985:   }
1.253     brouard  9986:   if(j == 0){ /* Resultline but no = */
                   9987:     TKresult[nres]=0; /* Combination for the nresult and the model */
                   9988:     return (0);
                   9989:   }
1.234     brouard  9990:   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
1.318     brouard  9991:     printf("ERROR: the number of variables in this result line, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
1.310     brouard  9992:     fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
1.234     brouard  9993:   }
                   9994:   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
                   9995:     if(nbocc(resultsav,'=') >1){
1.318     brouard  9996:       cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
                   9997:       cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */
1.234     brouard  9998:     }else
                   9999:       cutl(strc,strd,resultsav,'=');
1.318     brouard  10000:     Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
1.234     brouard  10001:     
1.230     brouard  10002:     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
1.318     brouard  10003:     Tvarsel[k]=atoi(strc);  /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
1.230     brouard  10004:     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
                   10005:     /* cptcovsel++;     */
                   10006:     if (nbocc(stra,'=') >0)
                   10007:       strcpy(resultsav,stra); /* and analyzes it */
                   10008:   }
1.235     brouard  10009:   /* Checking for missing or useless values in comparison of current model needs */
1.318     brouard  10010:   for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   10011:     if(Typevar[k1]==0){ /* Single covariate in model *//*0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
1.234     brouard  10012:       match=0;
1.318     brouard  10013:       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
                   10014:        if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
1.236     brouard  10015:          modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
1.318     brouard  10016:          match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
1.234     brouard  10017:          break;
                   10018:        }
                   10019:       }
                   10020:       if(match == 0){
1.310     brouard  10021:        printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
                   10022:        fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
                   10023:        return 1;
1.234     brouard  10024:       }
                   10025:     }
                   10026:   }
1.235     brouard  10027:   /* Checking for missing or useless values in comparison of current model needs */
1.318     brouard  10028:   for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
1.234     brouard  10029:     match=0;
1.318     brouard  10030:     for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.235     brouard  10031:       if(Typevar[k1]==0){ /* Single */
1.237     brouard  10032:        if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
1.318     brouard  10033:          resultmodel[k1]=k2;  /* k2th variable of the model corresponds to k1 variable of the model. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
1.234     brouard  10034:          ++match;
                   10035:        }
                   10036:       }
                   10037:     }
                   10038:     if(match == 0){
                   10039:       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
1.310     brouard  10040:       fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
                   10041:       return 1;
1.234     brouard  10042:     }else if(match > 1){
                   10043:       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
1.310     brouard  10044:       fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
                   10045:       return 1;
1.234     brouard  10046:     }
                   10047:   }
1.235     brouard  10048:       
1.234     brouard  10049:   /* We need to deduce which combination number is chosen and save quantitative values */
1.235     brouard  10050:   /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   10051:   /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
                   10052:   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
                   10053:   /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
                   10054:   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
                   10055:   /*    1 0 0 0 */
                   10056:   /*    2 1 0 0 */
                   10057:   /*    3 0 1 0 */ 
                   10058:   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
                   10059:   /*    5 0 0 1 */
                   10060:   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
                   10061:   /*    7 0 1 1 */
                   10062:   /*    8 1 1 1 */
1.237     brouard  10063:   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
                   10064:   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
                   10065:   /* V5*age V5 known which value for nres?  */
                   10066:   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
1.318     brouard  10067:   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop on model line */
1.235     brouard  10068:     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237     brouard  10069:       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235     brouard  10070:       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
                   10071:       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
1.237     brouard  10072:       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
                   10073:       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
                   10074:       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235     brouard  10075:       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
                   10076:       k4++;;
                   10077:     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
1.318     brouard  10078:       k3q= resultmodel[k1]; /* resultmodel[1(V5)] = 25.1=k3q */
                   10079:       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
1.237     brouard  10080:       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
                   10081:       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
                   10082:       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235     brouard  10083:       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
                   10084:       k4q++;;
                   10085:     }
                   10086:   }
1.234     brouard  10087:   
1.235     brouard  10088:   TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230     brouard  10089:   return (0);
                   10090: }
1.235     brouard  10091: 
1.230     brouard  10092: int decodemodel( char model[], int lastobs)
                   10093:  /**< This routine decodes the model and returns:
1.224     brouard  10094:        * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
                   10095:        * - nagesqr = 1 if age*age in the model, otherwise 0.
                   10096:        * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
                   10097:        * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
                   10098:        * - cptcovage number of covariates with age*products =2
                   10099:        * - cptcovs number of simple covariates
                   10100:        * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
                   10101:        *     which is a new column after the 9 (ncovcol) variables. 
1.319     brouard  10102:        * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
1.224     brouard  10103:        * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
                   10104:        *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
                   10105:        * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
                   10106:        */
1.319     brouard  10107: /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
1.136     brouard  10108: {
1.238     brouard  10109:   int i, j, k, ks, v;
1.227     brouard  10110:   int  j1, k1, k2, k3, k4;
1.136     brouard  10111:   char modelsav[80];
1.145     brouard  10112:   char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187     brouard  10113:   char *strpt;
1.136     brouard  10114: 
1.145     brouard  10115:   /*removespace(model);*/
1.136     brouard  10116:   if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145     brouard  10117:     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137     brouard  10118:     if (strstr(model,"AGE") !=0){
1.192     brouard  10119:       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
                   10120:       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136     brouard  10121:       return 1;
                   10122:     }
1.141     brouard  10123:     if (strstr(model,"v") !=0){
                   10124:       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
                   10125:       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
                   10126:       return 1;
                   10127:     }
1.187     brouard  10128:     strcpy(modelsav,model); 
                   10129:     if ((strpt=strstr(model,"age*age")) !=0){
                   10130:       printf(" strpt=%s, model=%s\n",strpt, model);
                   10131:       if(strpt != model){
1.234     brouard  10132:        printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192     brouard  10133:  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187     brouard  10134:  corresponding column of parameters.\n",model);
1.234     brouard  10135:        fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192     brouard  10136:  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187     brouard  10137:  corresponding column of parameters.\n",model); fflush(ficlog);
1.234     brouard  10138:        return 1;
1.225     brouard  10139:       }
1.187     brouard  10140:       nagesqr=1;
                   10141:       if (strstr(model,"+age*age") !=0)
1.234     brouard  10142:        substrchaine(modelsav, model, "+age*age");
1.187     brouard  10143:       else if (strstr(model,"age*age+") !=0)
1.234     brouard  10144:        substrchaine(modelsav, model, "age*age+");
1.187     brouard  10145:       else 
1.234     brouard  10146:        substrchaine(modelsav, model, "age*age");
1.187     brouard  10147:     }else
                   10148:       nagesqr=0;
                   10149:     if (strlen(modelsav) >1){
                   10150:       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
                   10151:       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224     brouard  10152:       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
1.187     brouard  10153:       cptcovt= j+1; /* Number of total covariates in the model, not including
1.225     brouard  10154:                     * cst, age and age*age 
                   10155:                     * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
                   10156:       /* including age products which are counted in cptcovage.
                   10157:        * but the covariates which are products must be treated 
                   10158:        * separately: ncovn=4- 2=2 (V1+V3). */
1.187     brouard  10159:       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
                   10160:       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
1.225     brouard  10161:       
                   10162:       
1.187     brouard  10163:       /*   Design
                   10164:        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
                   10165:        *  <          ncovcol=8                >
                   10166:        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
                   10167:        *   k=  1    2      3       4     5       6      7        8
                   10168:        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
                   10169:        *  covar[k,i], value of kth covariate if not including age for individual i:
1.224     brouard  10170:        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
                   10171:        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187     brouard  10172:        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
                   10173:        *  Tage[++cptcovage]=k
                   10174:        *       if products, new covar are created after ncovcol with k1
                   10175:        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
                   10176:        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
                   10177:        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
                   10178:        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
                   10179:        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
                   10180:        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
                   10181:        *  <          ncovcol=8                >
                   10182:        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
                   10183:        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
                   10184:        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
1.319     brouard  10185:        * p Tvar[1]@12={2,   1,     3,      3,  11,     10,     8,       8,   7,   8,   5,  6}
1.187     brouard  10186:        * p Tprod[1]@2={                         6, 5}
                   10187:        *p Tvard[1][1]@4= {7, 8, 5, 6}
                   10188:        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
                   10189:        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1.319     brouard  10190:        *How to reorganize? Tvars(orted)
1.187     brouard  10191:        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
                   10192:        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
                   10193:        *       {2,   1,     4,      8,    5,      6,     3,       7}
                   10194:        * Struct []
                   10195:        */
1.225     brouard  10196:       
1.187     brouard  10197:       /* This loop fills the array Tvar from the string 'model'.*/
                   10198:       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
                   10199:       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
                   10200:       /*       k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
                   10201:       /*       k=3 V4 Tvar[k=3]= 4 (from V4) */
                   10202:       /*       k=2 V1 Tvar[k=2]= 1 (from V1) */
                   10203:       /*       k=1 Tvar[1]=2 (from V2) */
                   10204:       /*       k=5 Tvar[5] */
                   10205:       /* for (k=1; k<=cptcovn;k++) { */
1.198     brouard  10206:       /*       cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187     brouard  10207:       /*       } */
1.198     brouard  10208:       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187     brouard  10209:       /*
                   10210:        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227     brouard  10211:       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
                   10212:         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
                   10213:       }
1.187     brouard  10214:       cptcovage=0;
1.319     brouard  10215:       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
                   10216:        cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
                   10217:                                         modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
                   10218:        if (nbocc(modelsav,'+')==0)
                   10219:          strcpy(strb,modelsav); /* and analyzes it */
1.234     brouard  10220:        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
                   10221:        /*scanf("%d",i);*/
1.319     brouard  10222:        if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */
                   10223:          cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
1.234     brouard  10224:          if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
                   10225:            /* covar is not filled and then is empty */
                   10226:            cptcovprod--;
                   10227:            cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
1.319     brouard  10228:            Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
1.234     brouard  10229:            Typevar[k]=1;  /* 1 for age product */
1.319     brouard  10230:            cptcovage++; /* Counts the number of covariates which include age as a product */
                   10231:            Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
1.234     brouard  10232:            /*printf("stre=%s ", stre);*/
                   10233:          } else if (strcmp(strd,"age")==0) { /* or age*Vn */
                   10234:            cptcovprod--;
                   10235:            cutl(stre,strb,strc,'V');
                   10236:            Tvar[k]=atoi(stre);
                   10237:            Typevar[k]=1;  /* 1 for age product */
                   10238:            cptcovage++;
                   10239:            Tage[cptcovage]=k;
                   10240:          } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
                   10241:            /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
                   10242:            cptcovn++;
                   10243:            cptcovprodnoage++;k1++;
                   10244:            cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
                   10245:            Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                   10246:                                                because this model-covariate is a construction we invent a new column
                   10247:                                                which is after existing variables ncovcol+nqv+ntv+nqtv + k1
1.319     brouard  10248:                                                If already ncovcol=4 and model=V2 + V1 +V1*V4 +age*V3 +V3*V2
                   10249:                                                thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
                   10250:                                                Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */
1.234     brouard  10251:            Typevar[k]=2;  /* 2 for double fixed dummy covariates */
                   10252:            cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
                   10253:            Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
1.319     brouard  10254:            Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
1.234     brouard  10255:            Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
                   10256:            Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
                   10257:            k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
                   10258:            /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
                   10259:            /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225     brouard  10260:             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234     brouard  10261:            /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
                   10262:            for (i=1; i<=lastobs;i++){
                   10263:              /* Computes the new covariate which is a product of
                   10264:                 covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                   10265:              covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
                   10266:            }
                   10267:          } /* End age is not in the model */
                   10268:        } /* End if model includes a product */
1.319     brouard  10269:        else { /* not a product */
1.234     brouard  10270:          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
                   10271:          /*  scanf("%d",i);*/
                   10272:          cutl(strd,strc,strb,'V');
                   10273:          ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
                   10274:          cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
                   10275:          Tvar[k]=atoi(strd);
                   10276:          Typevar[k]=0;  /* 0 for simple covariates */
                   10277:        }
                   10278:        strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
1.223     brouard  10279:                                /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225     brouard  10280:                                  scanf("%d",i);*/
1.187     brouard  10281:       } /* end of loop + on total covariates */
                   10282:     } /* end if strlen(modelsave == 0) age*age might exist */
                   10283:   } /* end if strlen(model == 0) */
1.136     brouard  10284:   
                   10285:   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
                   10286:     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225     brouard  10287:   
1.136     brouard  10288:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225     brouard  10289:      printf("cptcovprod=%d ", cptcovprod);
                   10290:      fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
                   10291:      scanf("%d ",i);*/
                   10292: 
                   10293: 
1.230     brouard  10294: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
                   10295:    of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226     brouard  10296: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
                   10297:    model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
                   10298:    k =           1    2   3     4       5       6      7      8        9
                   10299:    Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
1.319     brouard  10300:    Typevar[k]=   0    0   0     2       1       0      2      1        0
1.227     brouard  10301:    Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
                   10302:    Dummy[k]      1    0   0     0       3       1      1      2        3
                   10303:          Tmodelind[combination of covar]=k;
1.225     brouard  10304: */  
                   10305: /* Dispatching between quantitative and time varying covariates */
1.226     brouard  10306:   /* If Tvar[k] >ncovcol it is a product */
1.225     brouard  10307:   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
1.226     brouard  10308:        /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.318     brouard  10309:   printf("Model=1+age+%s\n\
1.227     brouard  10310: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
                   10311: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
                   10312: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
1.318     brouard  10313:   fprintf(ficlog,"Model=1+age+%s\n\
1.227     brouard  10314: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
                   10315: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
                   10316: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
1.285     brouard  10317:   for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234     brouard  10318:   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
                   10319:     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227     brouard  10320:       Fixed[k]= 0;
                   10321:       Dummy[k]= 0;
1.225     brouard  10322:       ncoveff++;
1.232     brouard  10323:       ncovf++;
1.234     brouard  10324:       nsd++;
                   10325:       modell[k].maintype= FTYPE;
                   10326:       TvarsD[nsd]=Tvar[k];
                   10327:       TvarsDind[nsd]=k;
                   10328:       TvarF[ncovf]=Tvar[k];
                   10329:       TvarFind[ncovf]=k;
                   10330:       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   10331:       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   10332:     }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
                   10333:       Fixed[k]= 0;
                   10334:       Dummy[k]= 0;
                   10335:       ncoveff++;
                   10336:       ncovf++;
                   10337:       modell[k].maintype= FTYPE;
                   10338:       TvarF[ncovf]=Tvar[k];
                   10339:       TvarFind[ncovf]=k;
1.230     brouard  10340:       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231     brouard  10341:       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240     brouard  10342:     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
1.227     brouard  10343:       Fixed[k]= 0;
                   10344:       Dummy[k]= 1;
1.230     brouard  10345:       nqfveff++;
1.234     brouard  10346:       modell[k].maintype= FTYPE;
                   10347:       modell[k].subtype= FQ;
                   10348:       nsq++;
                   10349:       TvarsQ[nsq]=Tvar[k];
                   10350:       TvarsQind[nsq]=k;
1.232     brouard  10351:       ncovf++;
1.234     brouard  10352:       TvarF[ncovf]=Tvar[k];
                   10353:       TvarFind[ncovf]=k;
1.231     brouard  10354:       TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.230     brouard  10355:       TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.242     brouard  10356:     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227     brouard  10357:       Fixed[k]= 1;
                   10358:       Dummy[k]= 0;
1.225     brouard  10359:       ntveff++; /* Only simple time varying dummy variable */
1.234     brouard  10360:       modell[k].maintype= VTYPE;
                   10361:       modell[k].subtype= VD;
                   10362:       nsd++;
                   10363:       TvarsD[nsd]=Tvar[k];
                   10364:       TvarsDind[nsd]=k;
                   10365:       ncovv++; /* Only simple time varying variables */
                   10366:       TvarV[ncovv]=Tvar[k];
1.242     brouard  10367:       TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
1.231     brouard  10368:       TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
                   10369:       TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
1.228     brouard  10370:       printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
                   10371:       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231     brouard  10372:     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234     brouard  10373:       Fixed[k]= 1;
                   10374:       Dummy[k]= 1;
                   10375:       nqtveff++;
                   10376:       modell[k].maintype= VTYPE;
                   10377:       modell[k].subtype= VQ;
                   10378:       ncovv++; /* Only simple time varying variables */
                   10379:       nsq++;
1.319     brouard  10380:       TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
1.234     brouard  10381:       TvarsQind[nsq]=k;
                   10382:       TvarV[ncovv]=Tvar[k];
1.242     brouard  10383:       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
1.231     brouard  10384:       TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
                   10385:       TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
1.234     brouard  10386:       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
                   10387:       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
                   10388:       printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
1.228     brouard  10389:       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227     brouard  10390:     }else if (Typevar[k] == 1) {  /* product with age */
1.234     brouard  10391:       ncova++;
                   10392:       TvarA[ncova]=Tvar[k];
                   10393:       TvarAind[ncova]=k;
1.231     brouard  10394:       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240     brouard  10395:        Fixed[k]= 2;
                   10396:        Dummy[k]= 2;
                   10397:        modell[k].maintype= ATYPE;
                   10398:        modell[k].subtype= APFD;
                   10399:        /* ncoveff++; */
1.227     brouard  10400:       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240     brouard  10401:        Fixed[k]= 2;
                   10402:        Dummy[k]= 3;
                   10403:        modell[k].maintype= ATYPE;
                   10404:        modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
                   10405:        /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
1.227     brouard  10406:       }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240     brouard  10407:        Fixed[k]= 3;
                   10408:        Dummy[k]= 2;
                   10409:        modell[k].maintype= ATYPE;
                   10410:        modell[k].subtype= APVD;                /*      Product age * varying dummy */
                   10411:        /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227     brouard  10412:       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240     brouard  10413:        Fixed[k]= 3;
                   10414:        Dummy[k]= 3;
                   10415:        modell[k].maintype= ATYPE;
                   10416:        modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
                   10417:        /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227     brouard  10418:       }
                   10419:     }else if (Typevar[k] == 2) {  /* product without age */
                   10420:       k1=Tposprod[k];
                   10421:       if(Tvard[k1][1] <=ncovcol){
1.240     brouard  10422:        if(Tvard[k1][2] <=ncovcol){
                   10423:          Fixed[k]= 1;
                   10424:          Dummy[k]= 0;
                   10425:          modell[k].maintype= FTYPE;
                   10426:          modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
                   10427:          ncovf++; /* Fixed variables without age */
                   10428:          TvarF[ncovf]=Tvar[k];
                   10429:          TvarFind[ncovf]=k;
                   10430:        }else if(Tvard[k1][2] <=ncovcol+nqv){
                   10431:          Fixed[k]= 0;  /* or 2 ?*/
                   10432:          Dummy[k]= 1;
                   10433:          modell[k].maintype= FTYPE;
                   10434:          modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
                   10435:          ncovf++; /* Varying variables without age */
                   10436:          TvarF[ncovf]=Tvar[k];
                   10437:          TvarFind[ncovf]=k;
                   10438:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   10439:          Fixed[k]= 1;
                   10440:          Dummy[k]= 0;
                   10441:          modell[k].maintype= VTYPE;
                   10442:          modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
                   10443:          ncovv++; /* Varying variables without age */
                   10444:          TvarV[ncovv]=Tvar[k];
                   10445:          TvarVind[ncovv]=k;
                   10446:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   10447:          Fixed[k]= 1;
                   10448:          Dummy[k]= 1;
                   10449:          modell[k].maintype= VTYPE;
                   10450:          modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
                   10451:          ncovv++; /* Varying variables without age */
                   10452:          TvarV[ncovv]=Tvar[k];
                   10453:          TvarVind[ncovv]=k;
                   10454:        }
1.227     brouard  10455:       }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240     brouard  10456:        if(Tvard[k1][2] <=ncovcol){
                   10457:          Fixed[k]= 0;  /* or 2 ?*/
                   10458:          Dummy[k]= 1;
                   10459:          modell[k].maintype= FTYPE;
                   10460:          modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
                   10461:          ncovf++; /* Fixed variables without age */
                   10462:          TvarF[ncovf]=Tvar[k];
                   10463:          TvarFind[ncovf]=k;
                   10464:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   10465:          Fixed[k]= 1;
                   10466:          Dummy[k]= 1;
                   10467:          modell[k].maintype= VTYPE;
                   10468:          modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
                   10469:          ncovv++; /* Varying variables without age */
                   10470:          TvarV[ncovv]=Tvar[k];
                   10471:          TvarVind[ncovv]=k;
                   10472:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   10473:          Fixed[k]= 1;
                   10474:          Dummy[k]= 1;
                   10475:          modell[k].maintype= VTYPE;
                   10476:          modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
                   10477:          ncovv++; /* Varying variables without age */
                   10478:          TvarV[ncovv]=Tvar[k];
                   10479:          TvarVind[ncovv]=k;
                   10480:          ncovv++; /* Varying variables without age */
                   10481:          TvarV[ncovv]=Tvar[k];
                   10482:          TvarVind[ncovv]=k;
                   10483:        }
1.227     brouard  10484:       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240     brouard  10485:        if(Tvard[k1][2] <=ncovcol){
                   10486:          Fixed[k]= 1;
                   10487:          Dummy[k]= 1;
                   10488:          modell[k].maintype= VTYPE;
                   10489:          modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
                   10490:          ncovv++; /* Varying variables without age */
                   10491:          TvarV[ncovv]=Tvar[k];
                   10492:          TvarVind[ncovv]=k;
                   10493:        }else if(Tvard[k1][2] <=ncovcol+nqv){
                   10494:          Fixed[k]= 1;
                   10495:          Dummy[k]= 1;
                   10496:          modell[k].maintype= VTYPE;
                   10497:          modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
                   10498:          ncovv++; /* Varying variables without age */
                   10499:          TvarV[ncovv]=Tvar[k];
                   10500:          TvarVind[ncovv]=k;
                   10501:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   10502:          Fixed[k]= 1;
                   10503:          Dummy[k]= 0;
                   10504:          modell[k].maintype= VTYPE;
                   10505:          modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
                   10506:          ncovv++; /* Varying variables without age */
                   10507:          TvarV[ncovv]=Tvar[k];
                   10508:          TvarVind[ncovv]=k;
                   10509:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   10510:          Fixed[k]= 1;
                   10511:          Dummy[k]= 1;
                   10512:          modell[k].maintype= VTYPE;
                   10513:          modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
                   10514:          ncovv++; /* Varying variables without age */
                   10515:          TvarV[ncovv]=Tvar[k];
                   10516:          TvarVind[ncovv]=k;
                   10517:        }
1.227     brouard  10518:       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240     brouard  10519:        if(Tvard[k1][2] <=ncovcol){
                   10520:          Fixed[k]= 1;
                   10521:          Dummy[k]= 1;
                   10522:          modell[k].maintype= VTYPE;
                   10523:          modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
                   10524:          ncovv++; /* Varying variables without age */
                   10525:          TvarV[ncovv]=Tvar[k];
                   10526:          TvarVind[ncovv]=k;
                   10527:        }else if(Tvard[k1][2] <=ncovcol+nqv){
                   10528:          Fixed[k]= 1;
                   10529:          Dummy[k]= 1;
                   10530:          modell[k].maintype= VTYPE;
                   10531:          modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
                   10532:          ncovv++; /* Varying variables without age */
                   10533:          TvarV[ncovv]=Tvar[k];
                   10534:          TvarVind[ncovv]=k;
                   10535:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   10536:          Fixed[k]= 1;
                   10537:          Dummy[k]= 1;
                   10538:          modell[k].maintype= VTYPE;
                   10539:          modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
                   10540:          ncovv++; /* Varying variables without age */
                   10541:          TvarV[ncovv]=Tvar[k];
                   10542:          TvarVind[ncovv]=k;
                   10543:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   10544:          Fixed[k]= 1;
                   10545:          Dummy[k]= 1;
                   10546:          modell[k].maintype= VTYPE;
                   10547:          modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
                   10548:          ncovv++; /* Varying variables without age */
                   10549:          TvarV[ncovv]=Tvar[k];
                   10550:          TvarVind[ncovv]=k;
                   10551:        }
1.227     brouard  10552:       }else{
1.240     brouard  10553:        printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
                   10554:        fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
                   10555:       } /*end k1*/
1.225     brouard  10556:     }else{
1.226     brouard  10557:       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
                   10558:       fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
1.225     brouard  10559:     }
1.227     brouard  10560:     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
1.231     brouard  10561:     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227     brouard  10562:     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
                   10563:   }
                   10564:   /* Searching for doublons in the model */
                   10565:   for(k1=1; k1<= cptcovt;k1++){
                   10566:     for(k2=1; k2 <k1;k2++){
1.285     brouard  10567:       /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
                   10568:       if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234     brouard  10569:        if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
                   10570:          if(Tvar[k1]==Tvar[k2]){
1.285     brouard  10571:            printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
                   10572:            fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
1.234     brouard  10573:            return(1);
                   10574:          }
                   10575:        }else if (Typevar[k1] ==2){
                   10576:          k3=Tposprod[k1];
                   10577:          k4=Tposprod[k2];
                   10578:          if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
                   10579:            printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
                   10580:            fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
                   10581:            return(1);
                   10582:          }
                   10583:        }
1.227     brouard  10584:       }
                   10585:     }
1.225     brouard  10586:   }
                   10587:   printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
                   10588:   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234     brouard  10589:   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
                   10590:   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137     brouard  10591:   return (0); /* with covar[new additional covariate if product] and Tage if age */ 
1.164     brouard  10592:   /*endread:*/
1.225     brouard  10593:   printf("Exiting decodemodel: ");
                   10594:   return (1);
1.136     brouard  10595: }
                   10596: 
1.169     brouard  10597: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248     brouard  10598: {/* Check ages at death */
1.136     brouard  10599:   int i, m;
1.218     brouard  10600:   int firstone=0;
                   10601:   
1.136     brouard  10602:   for (i=1; i<=imx; i++) {
                   10603:     for(m=2; (m<= maxwav); m++) {
                   10604:       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
                   10605:        anint[m][i]=9999;
1.216     brouard  10606:        if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
                   10607:          s[m][i]=-1;
1.136     brouard  10608:       }
                   10609:       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260     brouard  10610:        *nberr = *nberr + 1;
1.218     brouard  10611:        if(firstone == 0){
                   10612:          firstone=1;
1.260     brouard  10613:        printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
1.218     brouard  10614:        }
1.262     brouard  10615:        fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
1.260     brouard  10616:        s[m][i]=-1;  /* Droping the death status */
1.136     brouard  10617:       }
                   10618:       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169     brouard  10619:        (*nberr)++;
1.259     brouard  10620:        printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
1.262     brouard  10621:        fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
1.259     brouard  10622:        s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136     brouard  10623:       }
                   10624:     }
                   10625:   }
                   10626: 
                   10627:   for (i=1; i<=imx; i++)  {
                   10628:     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
                   10629:     for(m=firstpass; (m<= lastpass); m++){
1.214     brouard  10630:       if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
1.136     brouard  10631:        if (s[m][i] >= nlstate+1) {
1.169     brouard  10632:          if(agedc[i]>0){
                   10633:            if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136     brouard  10634:              agev[m][i]=agedc[i];
1.214     brouard  10635:              /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169     brouard  10636:            }else {
1.136     brouard  10637:              if ((int)andc[i]!=9999){
                   10638:                nbwarn++;
                   10639:                printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   10640:                fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   10641:                agev[m][i]=-1;
                   10642:              }
                   10643:            }
1.169     brouard  10644:          } /* agedc > 0 */
1.214     brouard  10645:        } /* end if */
1.136     brouard  10646:        else if(s[m][i] !=9){ /* Standard case, age in fractional
                   10647:                                 years but with the precision of a month */
                   10648:          agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
                   10649:          if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
                   10650:            agev[m][i]=1;
                   10651:          else if(agev[m][i] < *agemin){ 
                   10652:            *agemin=agev[m][i];
                   10653:            printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
                   10654:          }
                   10655:          else if(agev[m][i] >*agemax){
                   10656:            *agemax=agev[m][i];
1.156     brouard  10657:            /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136     brouard  10658:          }
                   10659:          /*agev[m][i]=anint[m][i]-annais[i];*/
                   10660:          /*     agev[m][i] = age[i]+2*m;*/
1.214     brouard  10661:        } /* en if 9*/
1.136     brouard  10662:        else { /* =9 */
1.214     brouard  10663:          /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136     brouard  10664:          agev[m][i]=1;
                   10665:          s[m][i]=-1;
                   10666:        }
                   10667:       }
1.214     brouard  10668:       else if(s[m][i]==0) /*= 0 Unknown */
1.136     brouard  10669:        agev[m][i]=1;
1.214     brouard  10670:       else{
                   10671:        printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
                   10672:        fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
                   10673:        agev[m][i]=0;
                   10674:       }
                   10675:     } /* End for lastpass */
                   10676:   }
1.136     brouard  10677:     
                   10678:   for (i=1; i<=imx; i++)  {
                   10679:     for(m=firstpass; (m<=lastpass); m++){
                   10680:       if (s[m][i] > (nlstate+ndeath)) {
1.169     brouard  10681:        (*nberr)++;
1.136     brouard  10682:        printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
                   10683:        fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
                   10684:        return 1;
                   10685:       }
                   10686:     }
                   10687:   }
                   10688: 
                   10689:   /*for (i=1; i<=imx; i++){
                   10690:   for (m=firstpass; (m<lastpass); m++){
                   10691:      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
                   10692: }
                   10693: 
                   10694: }*/
                   10695: 
                   10696: 
1.139     brouard  10697:   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
                   10698:   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
1.136     brouard  10699: 
                   10700:   return (0);
1.164     brouard  10701:  /* endread:*/
1.136     brouard  10702:     printf("Exiting calandcheckages: ");
                   10703:     return (1);
                   10704: }
                   10705: 
1.172     brouard  10706: #if defined(_MSC_VER)
                   10707: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
                   10708: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
                   10709: //#include "stdafx.h"
                   10710: //#include <stdio.h>
                   10711: //#include <tchar.h>
                   10712: //#include <windows.h>
                   10713: //#include <iostream>
                   10714: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
                   10715: 
                   10716: LPFN_ISWOW64PROCESS fnIsWow64Process;
                   10717: 
                   10718: BOOL IsWow64()
                   10719: {
                   10720:        BOOL bIsWow64 = FALSE;
                   10721: 
                   10722:        //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
                   10723:        //  (HANDLE, PBOOL);
                   10724: 
                   10725:        //LPFN_ISWOW64PROCESS fnIsWow64Process;
                   10726: 
                   10727:        HMODULE module = GetModuleHandle(_T("kernel32"));
                   10728:        const char funcName[] = "IsWow64Process";
                   10729:        fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   10730:                GetProcAddress(module, funcName);
                   10731: 
                   10732:        if (NULL != fnIsWow64Process)
                   10733:        {
                   10734:                if (!fnIsWow64Process(GetCurrentProcess(),
                   10735:                        &bIsWow64))
                   10736:                        //throw std::exception("Unknown error");
                   10737:                        printf("Unknown error\n");
                   10738:        }
                   10739:        return bIsWow64 != FALSE;
                   10740: }
                   10741: #endif
1.177     brouard  10742: 
1.191     brouard  10743: void syscompilerinfo(int logged)
1.292     brouard  10744: {
                   10745: #include <stdint.h>
                   10746: 
                   10747:   /* #include "syscompilerinfo.h"*/
1.185     brouard  10748:    /* command line Intel compiler 32bit windows, XP compatible:*/
                   10749:    /* /GS /W3 /Gy
                   10750:       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
                   10751:       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
                   10752:       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186     brouard  10753:       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
                   10754:    */ 
                   10755:    /* 64 bits */
1.185     brouard  10756:    /*
                   10757:      /GS /W3 /Gy
                   10758:      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
                   10759:      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
                   10760:      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
                   10761:      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
                   10762:    /* Optimization are useless and O3 is slower than O2 */
                   10763:    /*
                   10764:      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
                   10765:      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
                   10766:      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
                   10767:      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
                   10768:    */
1.186     brouard  10769:    /* Link is */ /* /OUT:"visual studio
1.185     brouard  10770:       2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
                   10771:       /PDB:"visual studio
                   10772:       2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
                   10773:       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
                   10774:       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
                   10775:       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
                   10776:       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
                   10777:       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
                   10778:       uiAccess='false'"
                   10779:       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
                   10780:       /NOLOGO /TLBID:1
                   10781:    */
1.292     brouard  10782: 
                   10783: 
1.177     brouard  10784: #if defined __INTEL_COMPILER
1.178     brouard  10785: #if defined(__GNUC__)
                   10786:        struct utsname sysInfo;  /* For Intel on Linux and OS/X */
                   10787: #endif
1.177     brouard  10788: #elif defined(__GNUC__) 
1.179     brouard  10789: #ifndef  __APPLE__
1.174     brouard  10790: #include <gnu/libc-version.h>  /* Only on gnu */
1.179     brouard  10791: #endif
1.177     brouard  10792:    struct utsname sysInfo;
1.178     brouard  10793:    int cross = CROSS;
                   10794:    if (cross){
                   10795:           printf("Cross-");
1.191     brouard  10796:           if(logged) fprintf(ficlog, "Cross-");
1.178     brouard  10797:    }
1.174     brouard  10798: #endif
                   10799: 
1.191     brouard  10800:    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169     brouard  10801: #if defined(__clang__)
1.191     brouard  10802:    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");      /* Clang/LLVM. ---------------------------------------------- */
1.169     brouard  10803: #endif
                   10804: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191     brouard  10805:    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169     brouard  10806: #endif
                   10807: #if defined(__GNUC__) || defined(__GNUG__)
1.191     brouard  10808:    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169     brouard  10809: #endif
                   10810: #if defined(__HP_cc) || defined(__HP_aCC)
1.191     brouard  10811:    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169     brouard  10812: #endif
                   10813: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191     brouard  10814:    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169     brouard  10815: #endif
                   10816: #if defined(_MSC_VER)
1.191     brouard  10817:    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169     brouard  10818: #endif
                   10819: #if defined(__PGI)
1.191     brouard  10820:    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169     brouard  10821: #endif
                   10822: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191     brouard  10823:    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167     brouard  10824: #endif
1.191     brouard  10825:    printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169     brouard  10826:    
1.167     brouard  10827: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
                   10828: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
                   10829:     // Windows (x64 and x86)
1.191     brouard  10830:    printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167     brouard  10831: #elif __unix__ // all unices, not all compilers
                   10832:     // Unix
1.191     brouard  10833:    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167     brouard  10834: #elif __linux__
                   10835:     // linux
1.191     brouard  10836:    printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167     brouard  10837: #elif __APPLE__
1.174     brouard  10838:     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191     brouard  10839:    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167     brouard  10840: #endif
                   10841: 
                   10842: /*  __MINGW32__          */
                   10843: /*  __CYGWIN__  */
                   10844: /* __MINGW64__  */
                   10845: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
                   10846: /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
                   10847: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
                   10848: /* _WIN64  // Defined for applications for Win64. */
                   10849: /* _M_X64 // Defined for compilations that target x64 processors. */
                   10850: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171     brouard  10851: 
1.167     brouard  10852: #if UINTPTR_MAX == 0xffffffff
1.191     brouard  10853:    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167     brouard  10854: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191     brouard  10855:    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167     brouard  10856: #else
1.191     brouard  10857:    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167     brouard  10858: #endif
                   10859: 
1.169     brouard  10860: #if defined(__GNUC__)
                   10861: # if defined(__GNUC_PATCHLEVEL__)
                   10862: #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                   10863:                             + __GNUC_MINOR__ * 100 \
                   10864:                             + __GNUC_PATCHLEVEL__)
                   10865: # else
                   10866: #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                   10867:                             + __GNUC_MINOR__ * 100)
                   10868: # endif
1.174     brouard  10869:    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191     brouard  10870:    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176     brouard  10871: 
                   10872:    if (uname(&sysInfo) != -1) {
                   10873:      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191     brouard  10874:         if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.176     brouard  10875:    }
                   10876:    else
                   10877:       perror("uname() error");
1.179     brouard  10878:    //#ifndef __INTEL_COMPILER 
                   10879: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174     brouard  10880:    printf("GNU libc version: %s\n", gnu_get_libc_version()); 
1.191     brouard  10881:    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177     brouard  10882: #endif
1.169     brouard  10883: #endif
1.172     brouard  10884: 
1.286     brouard  10885:    //   void main ()
1.172     brouard  10886:    //   {
1.169     brouard  10887: #if defined(_MSC_VER)
1.174     brouard  10888:    if (IsWow64()){
1.191     brouard  10889:           printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
                   10890:           if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174     brouard  10891:    }
                   10892:    else{
1.191     brouard  10893:           printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
                   10894:           if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174     brouard  10895:    }
1.172     brouard  10896:    //     printf("\nPress Enter to continue...");
                   10897:    //     getchar();
                   10898:    //   }
                   10899: 
1.169     brouard  10900: #endif
                   10901:    
1.167     brouard  10902: 
1.219     brouard  10903: }
1.136     brouard  10904: 
1.219     brouard  10905: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288     brouard  10906:   /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
1.235     brouard  10907:   int i, j, k, i1, k4=0, nres=0 ;
1.202     brouard  10908:   /* double ftolpl = 1.e-10; */
1.180     brouard  10909:   double age, agebase, agelim;
1.203     brouard  10910:   double tot;
1.180     brouard  10911: 
1.202     brouard  10912:   strcpy(filerespl,"PL_");
                   10913:   strcat(filerespl,fileresu);
                   10914:   if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288     brouard  10915:     printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
                   10916:     fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202     brouard  10917:   }
1.288     brouard  10918:   printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
                   10919:   fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202     brouard  10920:   pstamp(ficrespl);
1.288     brouard  10921:   fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202     brouard  10922:   fprintf(ficrespl,"#Age ");
                   10923:   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
                   10924:   fprintf(ficrespl,"\n");
1.180     brouard  10925:   
1.219     brouard  10926:   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180     brouard  10927: 
1.219     brouard  10928:   agebase=ageminpar;
                   10929:   agelim=agemaxpar;
1.180     brouard  10930: 
1.227     brouard  10931:   /* i1=pow(2,ncoveff); */
1.234     brouard  10932:   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219     brouard  10933:   if (cptcovn < 1){i1=1;}
1.180     brouard  10934: 
1.238     brouard  10935:   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
                   10936:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253     brouard  10937:       if(i1 != 1 && TKresult[nres]!= k)
1.238     brouard  10938:        continue;
1.235     brouard  10939: 
1.238     brouard  10940:       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   10941:       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
                   10942:       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   10943:       /* k=k+1; */
                   10944:       /* to clean */
                   10945:       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
                   10946:       fprintf(ficrespl,"#******");
                   10947:       printf("#******");
                   10948:       fprintf(ficlog,"#******");
                   10949:       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
                   10950:        fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
                   10951:        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   10952:        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   10953:       }
                   10954:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   10955:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   10956:        fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   10957:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   10958:       }
                   10959:       fprintf(ficrespl,"******\n");
                   10960:       printf("******\n");
                   10961:       fprintf(ficlog,"******\n");
                   10962:       if(invalidvarcomb[k]){
                   10963:        printf("\nCombination (%d) ignored because no case \n",k); 
                   10964:        fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
                   10965:        fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
                   10966:        continue;
                   10967:       }
1.219     brouard  10968: 
1.238     brouard  10969:       fprintf(ficrespl,"#Age ");
                   10970:       for(j=1;j<=cptcoveff;j++) {
                   10971:        fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   10972:       }
                   10973:       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
                   10974:       fprintf(ficrespl,"Total Years_to_converge\n");
1.227     brouard  10975:     
1.238     brouard  10976:       for (age=agebase; age<=agelim; age++){
                   10977:        /* for (age=agebase; age<=agebase; age++){ */
                   10978:        prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
                   10979:        fprintf(ficrespl,"%.0f ",age );
                   10980:        for(j=1;j<=cptcoveff;j++)
                   10981:          fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   10982:        tot=0.;
                   10983:        for(i=1; i<=nlstate;i++){
                   10984:          tot +=  prlim[i][i];
                   10985:          fprintf(ficrespl," %.5f", prlim[i][i]);
                   10986:        }
                   10987:        fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
                   10988:       } /* Age */
                   10989:       /* was end of cptcod */
                   10990:     } /* cptcov */
                   10991:   } /* nres */
1.219     brouard  10992:   return 0;
1.180     brouard  10993: }
                   10994: 
1.218     brouard  10995: int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
1.288     brouard  10996:        /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
1.218     brouard  10997:        
                   10998:        /* Computes the back prevalence limit  for any combination      of covariate values 
                   10999:    * at any age between ageminpar and agemaxpar
                   11000:         */
1.235     brouard  11001:   int i, j, k, i1, nres=0 ;
1.217     brouard  11002:   /* double ftolpl = 1.e-10; */
                   11003:   double age, agebase, agelim;
                   11004:   double tot;
1.218     brouard  11005:   /* double ***mobaverage; */
                   11006:   /* double     **dnewm, **doldm, **dsavm;  /\* for use *\/ */
1.217     brouard  11007: 
                   11008:   strcpy(fileresplb,"PLB_");
                   11009:   strcat(fileresplb,fileresu);
                   11010:   if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288     brouard  11011:     printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
                   11012:     fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217     brouard  11013:   }
1.288     brouard  11014:   printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
                   11015:   fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217     brouard  11016:   pstamp(ficresplb);
1.288     brouard  11017:   fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217     brouard  11018:   fprintf(ficresplb,"#Age ");
                   11019:   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
                   11020:   fprintf(ficresplb,"\n");
                   11021:   
1.218     brouard  11022:   
                   11023:   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
                   11024:   
                   11025:   agebase=ageminpar;
                   11026:   agelim=agemaxpar;
                   11027:   
                   11028:   
1.227     brouard  11029:   i1=pow(2,cptcoveff);
1.218     brouard  11030:   if (cptcovn < 1){i1=1;}
1.227     brouard  11031:   
1.238     brouard  11032:   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   11033:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253     brouard  11034:      if(i1 != 1 && TKresult[nres]!= k)
1.238     brouard  11035:        continue;
                   11036:       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
                   11037:       fprintf(ficresplb,"#******");
                   11038:       printf("#******");
                   11039:       fprintf(ficlog,"#******");
                   11040:       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
                   11041:        fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11042:        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11043:        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11044:       }
                   11045:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   11046:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11047:        fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11048:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11049:       }
                   11050:       fprintf(ficresplb,"******\n");
                   11051:       printf("******\n");
                   11052:       fprintf(ficlog,"******\n");
                   11053:       if(invalidvarcomb[k]){
                   11054:        printf("\nCombination (%d) ignored because no cases \n",k); 
                   11055:        fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
                   11056:        fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
                   11057:        continue;
                   11058:       }
1.218     brouard  11059:     
1.238     brouard  11060:       fprintf(ficresplb,"#Age ");
                   11061:       for(j=1;j<=cptcoveff;j++) {
                   11062:        fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11063:       }
                   11064:       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
                   11065:       fprintf(ficresplb,"Total Years_to_converge\n");
1.218     brouard  11066:     
                   11067:     
1.238     brouard  11068:       for (age=agebase; age<=agelim; age++){
                   11069:        /* for (age=agebase; age<=agebase; age++){ */
                   11070:        if(mobilavproj > 0){
                   11071:          /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
                   11072:          /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242     brouard  11073:          bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238     brouard  11074:        }else if (mobilavproj == 0){
                   11075:          printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
                   11076:          fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
                   11077:          exit(1);
                   11078:        }else{
                   11079:          /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242     brouard  11080:          bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266     brouard  11081:          /* printf("TOTOT\n"); */
                   11082:           /* exit(1); */
1.238     brouard  11083:        }
                   11084:        fprintf(ficresplb,"%.0f ",age );
                   11085:        for(j=1;j<=cptcoveff;j++)
                   11086:          fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11087:        tot=0.;
                   11088:        for(i=1; i<=nlstate;i++){
                   11089:          tot +=  bprlim[i][i];
                   11090:          fprintf(ficresplb," %.5f", bprlim[i][i]);
                   11091:        }
                   11092:        fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
                   11093:       } /* Age */
                   11094:       /* was end of cptcod */
1.255     brouard  11095:       /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238     brouard  11096:     } /* end of any combination */
                   11097:   } /* end of nres */  
1.218     brouard  11098:   /* hBijx(p, bage, fage); */
                   11099:   /* fclose(ficrespijb); */
                   11100:   
                   11101:   return 0;
1.217     brouard  11102: }
1.218     brouard  11103:  
1.180     brouard  11104: int hPijx(double *p, int bage, int fage){
                   11105:     /*------------- h Pij x at various ages ------------*/
                   11106: 
                   11107:   int stepsize;
                   11108:   int agelim;
                   11109:   int hstepm;
                   11110:   int nhstepm;
1.235     brouard  11111:   int h, i, i1, j, k, k4, nres=0;
1.180     brouard  11112: 
                   11113:   double agedeb;
                   11114:   double ***p3mat;
                   11115: 
1.201     brouard  11116:     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
1.180     brouard  11117:     if((ficrespij=fopen(filerespij,"w"))==NULL) {
                   11118:       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
                   11119:       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
                   11120:     }
                   11121:     printf("Computing pij: result on file '%s' \n", filerespij);
                   11122:     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
                   11123:   
                   11124:     stepsize=(int) (stepm+YEARM-1)/YEARM;
                   11125:     /*if (stepm<=24) stepsize=2;*/
                   11126: 
                   11127:     agelim=AGESUP;
                   11128:     hstepm=stepsize*YEARM; /* Every year of age */
                   11129:     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
1.218     brouard  11130:                
1.180     brouard  11131:     /* hstepm=1;   aff par mois*/
                   11132:     pstamp(ficrespij);
                   11133:     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227     brouard  11134:     i1= pow(2,cptcoveff);
1.218     brouard  11135:                /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   11136:                /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                   11137:                /*      k=k+1;  */
1.235     brouard  11138:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   11139:     for(k=1; k<=i1;k++){
1.253     brouard  11140:       if(i1 != 1 && TKresult[nres]!= k)
1.235     brouard  11141:        continue;
1.183     brouard  11142:       fprintf(ficrespij,"\n#****** ");
1.227     brouard  11143:       for(j=1;j<=cptcoveff;j++) 
1.198     brouard  11144:        fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235     brouard  11145:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   11146:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   11147:        fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   11148:       }
1.183     brouard  11149:       fprintf(ficrespij,"******\n");
                   11150:       
                   11151:       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
                   11152:        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   11153:        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   11154:        
                   11155:        /*        nhstepm=nhstepm*YEARM; aff par mois*/
1.180     brouard  11156:        
1.183     brouard  11157:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   11158:        oldm=oldms;savm=savms;
1.235     brouard  11159:        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);  
1.183     brouard  11160:        fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
                   11161:        for(i=1; i<=nlstate;i++)
                   11162:          for(j=1; j<=nlstate+ndeath;j++)
                   11163:            fprintf(ficrespij," %1d-%1d",i,j);
                   11164:        fprintf(ficrespij,"\n");
                   11165:        for (h=0; h<=nhstepm; h++){
                   11166:          /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
                   11167:          fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180     brouard  11168:          for(i=1; i<=nlstate;i++)
                   11169:            for(j=1; j<=nlstate+ndeath;j++)
1.183     brouard  11170:              fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180     brouard  11171:          fprintf(ficrespij,"\n");
                   11172:        }
1.183     brouard  11173:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   11174:        fprintf(ficrespij,"\n");
                   11175:       }
1.180     brouard  11176:       /*}*/
                   11177:     }
1.218     brouard  11178:     return 0;
1.180     brouard  11179: }
1.218     brouard  11180:  
                   11181:  int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217     brouard  11182:     /*------------- h Bij x at various ages ------------*/
                   11183: 
                   11184:   int stepsize;
1.218     brouard  11185:   /* int agelim; */
                   11186:        int ageminl;
1.217     brouard  11187:   int hstepm;
                   11188:   int nhstepm;
1.238     brouard  11189:   int h, i, i1, j, k, nres;
1.218     brouard  11190:        
1.217     brouard  11191:   double agedeb;
                   11192:   double ***p3mat;
1.218     brouard  11193:        
                   11194:   strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
                   11195:   if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
                   11196:     printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
                   11197:     fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
                   11198:   }
                   11199:   printf("Computing pij back: result on file '%s' \n", filerespijb);
                   11200:   fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
                   11201:   
                   11202:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   11203:   /*if (stepm<=24) stepsize=2;*/
1.217     brouard  11204:   
1.218     brouard  11205:   /* agelim=AGESUP; */
1.289     brouard  11206:   ageminl=AGEINF; /* was 30 */
1.218     brouard  11207:   hstepm=stepsize*YEARM; /* Every year of age */
                   11208:   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
                   11209:   
                   11210:   /* hstepm=1;   aff par mois*/
                   11211:   pstamp(ficrespijb);
1.255     brouard  11212:   fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
1.227     brouard  11213:   i1= pow(2,cptcoveff);
1.218     brouard  11214:   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   11215:   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                   11216:   /*   k=k+1;  */
1.238     brouard  11217:   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   11218:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253     brouard  11219:       if(i1 != 1 && TKresult[nres]!= k)
1.238     brouard  11220:        continue;
                   11221:       fprintf(ficrespijb,"\n#****** ");
                   11222:       for(j=1;j<=cptcoveff;j++)
                   11223:        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11224:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   11225:        fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11226:       }
                   11227:       fprintf(ficrespijb,"******\n");
1.264     brouard  11228:       if(invalidvarcomb[k]){  /* Is it necessary here? */
1.238     brouard  11229:        fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
                   11230:        continue;
                   11231:       }
                   11232:       
                   11233:       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
                   11234:       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
                   11235:        /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297     brouard  11236:        nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
                   11237:        nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238     brouard  11238:        
                   11239:        /*        nhstepm=nhstepm*YEARM; aff par mois*/
                   11240:        
1.266     brouard  11241:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
                   11242:        /* and memory limitations if stepm is small */
                   11243: 
1.238     brouard  11244:        /* oldm=oldms;savm=savms; */
                   11245:        /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
1.325     brouard  11246:        hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
1.238     brouard  11247:        /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255     brouard  11248:        fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217     brouard  11249:        for(i=1; i<=nlstate;i++)
                   11250:          for(j=1; j<=nlstate+ndeath;j++)
1.238     brouard  11251:            fprintf(ficrespijb," %1d-%1d",i,j);
1.217     brouard  11252:        fprintf(ficrespijb,"\n");
1.238     brouard  11253:        for (h=0; h<=nhstepm; h++){
                   11254:          /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
                   11255:          fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
                   11256:          /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
                   11257:          for(i=1; i<=nlstate;i++)
                   11258:            for(j=1; j<=nlstate+ndeath;j++)
1.325     brouard  11259:              fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
1.238     brouard  11260:          fprintf(ficrespijb,"\n");
                   11261:        }
                   11262:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   11263:        fprintf(ficrespijb,"\n");
                   11264:       } /* end age deb */
                   11265:     } /* end combination */
                   11266:   } /* end nres */
1.218     brouard  11267:   return 0;
                   11268:  } /*  hBijx */
1.217     brouard  11269: 
1.180     brouard  11270: 
1.136     brouard  11271: /***********************************************/
                   11272: /**************** Main Program *****************/
                   11273: /***********************************************/
                   11274: 
                   11275: int main(int argc, char *argv[])
                   11276: {
                   11277: #ifdef GSL
                   11278:   const gsl_multimin_fminimizer_type *T;
                   11279:   size_t iteri = 0, it;
                   11280:   int rval = GSL_CONTINUE;
                   11281:   int status = GSL_SUCCESS;
                   11282:   double ssval;
                   11283: #endif
                   11284:   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290     brouard  11285:   int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
                   11286:   /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209     brouard  11287:   int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164     brouard  11288:   int jj, ll, li, lj, lk;
1.136     brouard  11289:   int numlinepar=0; /* Current linenumber of parameter file */
1.197     brouard  11290:   int num_filled;
1.136     brouard  11291:   int itimes;
                   11292:   int NDIM=2;
                   11293:   int vpopbased=0;
1.235     brouard  11294:   int nres=0;
1.258     brouard  11295:   int endishere=0;
1.277     brouard  11296:   int noffset=0;
1.274     brouard  11297:   int ncurrv=0; /* Temporary variable */
                   11298:   
1.164     brouard  11299:   char ca[32], cb[32];
1.136     brouard  11300:   /*  FILE *fichtm; *//* Html File */
                   11301:   /* FILE *ficgp;*/ /*Gnuplot File */
                   11302:   struct stat info;
1.191     brouard  11303:   double agedeb=0.;
1.194     brouard  11304: 
                   11305:   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219     brouard  11306:   double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136     brouard  11307: 
1.165     brouard  11308:   double fret;
1.191     brouard  11309:   double dum=0.; /* Dummy variable */
1.136     brouard  11310:   double ***p3mat;
1.218     brouard  11311:   /* double ***mobaverage; */
1.319     brouard  11312:   double wald;
1.164     brouard  11313: 
                   11314:   char line[MAXLINE];
1.197     brouard  11315:   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
                   11316: 
1.234     brouard  11317:   char  modeltemp[MAXLINE];
1.230     brouard  11318:   char resultline[MAXLINE];
                   11319:   
1.136     brouard  11320:   char pathr[MAXLINE], pathimach[MAXLINE]; 
1.164     brouard  11321:   char *tok, *val; /* pathtot */
1.290     brouard  11322:   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195     brouard  11323:   int c,  h , cpt, c2;
1.191     brouard  11324:   int jl=0;
                   11325:   int i1, j1, jk, stepsize=0;
1.194     brouard  11326:   int count=0;
                   11327: 
1.164     brouard  11328:   int *tab; 
1.136     brouard  11329:   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296     brouard  11330:   /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
                   11331:   /* double anprojf, mprojf, jprojf; */
                   11332:   /* double jintmean,mintmean,aintmean;   */
                   11333:   int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
                   11334:   int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
                   11335:   double yrfproj= 10.0; /* Number of years of forward projections */
                   11336:   double yrbproj= 10.0; /* Number of years of backward projections */
                   11337:   int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136     brouard  11338:   int mobilav=0,popforecast=0;
1.191     brouard  11339:   int hstepm=0, nhstepm=0;
1.136     brouard  11340:   int agemortsup;
                   11341:   float  sumlpop=0.;
                   11342:   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
                   11343:   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
                   11344: 
1.191     brouard  11345:   double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136     brouard  11346:   double ftolpl=FTOL;
                   11347:   double **prlim;
1.217     brouard  11348:   double **bprlim;
1.317     brouard  11349:   double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel) 
                   11350:                     state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
1.251     brouard  11351:   double ***paramstart; /* Matrix of starting parameter values */
                   11352:   double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136     brouard  11353:   double **matcov; /* Matrix of covariance */
1.203     brouard  11354:   double **hess; /* Hessian matrix */
1.136     brouard  11355:   double ***delti3; /* Scale */
                   11356:   double *delti; /* Scale */
                   11357:   double ***eij, ***vareij;
                   11358:   double **varpl; /* Variances of prevalence limits by age */
1.269     brouard  11359: 
1.136     brouard  11360:   double *epj, vepp;
1.164     brouard  11361: 
1.273     brouard  11362:   double dateprev1, dateprev2;
1.296     brouard  11363:   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
                   11364:   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
                   11365: 
1.217     brouard  11366: 
1.136     brouard  11367:   double **ximort;
1.145     brouard  11368:   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136     brouard  11369:   int *dcwave;
                   11370: 
1.164     brouard  11371:   char z[1]="c";
1.136     brouard  11372: 
                   11373:   /*char  *strt;*/
                   11374:   char strtend[80];
1.126     brouard  11375: 
1.164     brouard  11376: 
1.126     brouard  11377: /*   setlocale (LC_ALL, ""); */
                   11378: /*   bindtextdomain (PACKAGE, LOCALEDIR); */
                   11379: /*   textdomain (PACKAGE); */
                   11380: /*   setlocale (LC_CTYPE, ""); */
                   11381: /*   setlocale (LC_MESSAGES, ""); */
                   11382: 
                   11383:   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157     brouard  11384:   rstart_time = time(NULL);  
                   11385:   /*  (void) gettimeofday(&start_time,&tzp);*/
                   11386:   start_time = *localtime(&rstart_time);
1.126     brouard  11387:   curr_time=start_time;
1.157     brouard  11388:   /*tml = *localtime(&start_time.tm_sec);*/
                   11389:   /* strcpy(strstart,asctime(&tml)); */
                   11390:   strcpy(strstart,asctime(&start_time));
1.126     brouard  11391: 
                   11392: /*  printf("Localtime (at start)=%s",strstart); */
1.157     brouard  11393: /*  tp.tm_sec = tp.tm_sec +86400; */
                   11394: /*  tm = *localtime(&start_time.tm_sec); */
1.126     brouard  11395: /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
                   11396: /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
                   11397: /*   tmg.tm_hour=tmg.tm_hour + 1; */
1.157     brouard  11398: /*   tp.tm_sec = mktime(&tmg); */
1.126     brouard  11399: /*   strt=asctime(&tmg); */
                   11400: /*   printf("Time(after) =%s",strstart);  */
                   11401: /*  (void) time (&time_value);
                   11402: *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
                   11403: *  tm = *localtime(&time_value);
                   11404: *  strstart=asctime(&tm);
                   11405: *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
                   11406: */
                   11407: 
                   11408:   nberr=0; /* Number of errors and warnings */
                   11409:   nbwarn=0;
1.184     brouard  11410: #ifdef WIN32
                   11411:   _getcwd(pathcd, size);
                   11412: #else
1.126     brouard  11413:   getcwd(pathcd, size);
1.184     brouard  11414: #endif
1.191     brouard  11415:   syscompilerinfo(0);
1.196     brouard  11416:   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126     brouard  11417:   if(argc <=1){
                   11418:     printf("\nEnter the parameter file name: ");
1.205     brouard  11419:     if(!fgets(pathr,FILENAMELENGTH,stdin)){
                   11420:       printf("ERROR Empty parameter file name\n");
                   11421:       goto end;
                   11422:     }
1.126     brouard  11423:     i=strlen(pathr);
                   11424:     if(pathr[i-1]=='\n')
                   11425:       pathr[i-1]='\0';
1.156     brouard  11426:     i=strlen(pathr);
1.205     brouard  11427:     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156     brouard  11428:       pathr[i-1]='\0';
1.205     brouard  11429:     }
                   11430:     i=strlen(pathr);
                   11431:     if( i==0 ){
                   11432:       printf("ERROR Empty parameter file name\n");
                   11433:       goto end;
                   11434:     }
                   11435:     for (tok = pathr; tok != NULL; ){
1.126     brouard  11436:       printf("Pathr |%s|\n",pathr);
                   11437:       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
                   11438:       printf("val= |%s| pathr=%s\n",val,pathr);
                   11439:       strcpy (pathtot, val);
                   11440:       if(pathr[0] == '\0') break; /* Dirty */
                   11441:     }
                   11442:   }
1.281     brouard  11443:   else if (argc<=2){
                   11444:     strcpy(pathtot,argv[1]);
                   11445:   }
1.126     brouard  11446:   else{
                   11447:     strcpy(pathtot,argv[1]);
1.281     brouard  11448:     strcpy(z,argv[2]);
                   11449:     printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126     brouard  11450:   }
                   11451:   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
                   11452:   /*cygwin_split_path(pathtot,path,optionfile);
                   11453:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
                   11454:   /* cutv(path,optionfile,pathtot,'\\');*/
                   11455: 
                   11456:   /* Split argv[0], imach program to get pathimach */
                   11457:   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
                   11458:   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   11459:   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   11460:  /*   strcpy(pathimach,argv[0]); */
                   11461:   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
                   11462:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
                   11463:   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184     brouard  11464: #ifdef WIN32
                   11465:   _chdir(path); /* Can be a relative path */
                   11466:   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
                   11467: #else
1.126     brouard  11468:   chdir(path); /* Can be a relative path */
1.184     brouard  11469:   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
                   11470: #endif
                   11471:   printf("Current directory %s!\n",pathcd);
1.126     brouard  11472:   strcpy(command,"mkdir ");
                   11473:   strcat(command,optionfilefiname);
                   11474:   if((outcmd=system(command)) != 0){
1.169     brouard  11475:     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126     brouard  11476:     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
                   11477:     /* fclose(ficlog); */
                   11478: /*     exit(1); */
                   11479:   }
                   11480: /*   if((imk=mkdir(optionfilefiname))<0){ */
                   11481: /*     perror("mkdir"); */
                   11482: /*   } */
                   11483: 
                   11484:   /*-------- arguments in the command line --------*/
                   11485: 
1.186     brouard  11486:   /* Main Log file */
1.126     brouard  11487:   strcat(filelog, optionfilefiname);
                   11488:   strcat(filelog,".log");    /* */
                   11489:   if((ficlog=fopen(filelog,"w"))==NULL)    {
                   11490:     printf("Problem with logfile %s\n",filelog);
                   11491:     goto end;
                   11492:   }
                   11493:   fprintf(ficlog,"Log filename:%s\n",filelog);
1.197     brouard  11494:   fprintf(ficlog,"Version %s %s",version,fullversion);
1.126     brouard  11495:   fprintf(ficlog,"\nEnter the parameter file name: \n");
                   11496:   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
                   11497:  path=%s \n\
                   11498:  optionfile=%s\n\
                   11499:  optionfilext=%s\n\
1.156     brouard  11500:  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126     brouard  11501: 
1.197     brouard  11502:   syscompilerinfo(1);
1.167     brouard  11503: 
1.126     brouard  11504:   printf("Local time (at start):%s",strstart);
                   11505:   fprintf(ficlog,"Local time (at start): %s",strstart);
                   11506:   fflush(ficlog);
                   11507: /*   (void) gettimeofday(&curr_time,&tzp); */
1.157     brouard  11508: /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126     brouard  11509: 
                   11510:   /* */
                   11511:   strcpy(fileres,"r");
                   11512:   strcat(fileres, optionfilefiname);
1.201     brouard  11513:   strcat(fileresu, optionfilefiname); /* Without r in front */
1.126     brouard  11514:   strcat(fileres,".txt");    /* Other files have txt extension */
1.201     brouard  11515:   strcat(fileresu,".txt");    /* Other files have txt extension */
1.126     brouard  11516: 
1.186     brouard  11517:   /* Main ---------arguments file --------*/
1.126     brouard  11518: 
                   11519:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
1.155     brouard  11520:     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
                   11521:     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126     brouard  11522:     fflush(ficlog);
1.149     brouard  11523:     /* goto end; */
                   11524:     exit(70); 
1.126     brouard  11525:   }
                   11526: 
                   11527:   strcpy(filereso,"o");
1.201     brouard  11528:   strcat(filereso,fileresu);
1.126     brouard  11529:   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
                   11530:     printf("Problem with Output resultfile: %s\n", filereso);
                   11531:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
                   11532:     fflush(ficlog);
                   11533:     goto end;
                   11534:   }
1.278     brouard  11535:       /*-------- Rewriting parameter file ----------*/
                   11536:   strcpy(rfileres,"r");    /* "Rparameterfile */
                   11537:   strcat(rfileres,optionfilefiname);    /* Parameter file first name */
                   11538:   strcat(rfileres,".");    /* */
                   11539:   strcat(rfileres,optionfilext);    /* Other files have txt extension */
                   11540:   if((ficres =fopen(rfileres,"w"))==NULL) {
                   11541:     printf("Problem writing new parameter file: %s\n", rfileres);goto end;
                   11542:     fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
                   11543:     fflush(ficlog);
                   11544:     goto end;
                   11545:   }
                   11546:   fprintf(ficres,"#IMaCh %s\n",version);
1.126     brouard  11547: 
1.278     brouard  11548:                                      
1.126     brouard  11549:   /* Reads comments: lines beginning with '#' */
                   11550:   numlinepar=0;
1.277     brouard  11551:   /* Is it a BOM UTF-8 Windows file? */
                   11552:   /* First parameter line */
1.197     brouard  11553:   while(fgets(line, MAXLINE, ficpar)) {
1.277     brouard  11554:     noffset=0;
                   11555:     if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
                   11556:     {
                   11557:       noffset=noffset+3;
                   11558:       printf("# File is an UTF8 Bom.\n"); // 0xBF
                   11559:     }
1.302     brouard  11560: /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
                   11561:     else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277     brouard  11562:     {
                   11563:       noffset=noffset+2;
                   11564:       printf("# File is an UTF16BE BOM file\n");
                   11565:     }
                   11566:     else if( line[0] == 0 && line[1] == 0)
                   11567:     {
                   11568:       if( line[2] == (char)0xFE && line[3] == (char)0xFF){
                   11569:        noffset=noffset+4;
                   11570:        printf("# File is an UTF16BE BOM file\n");
                   11571:       }
                   11572:     } else{
                   11573:       ;/*printf(" Not a BOM file\n");*/
                   11574:     }
                   11575:   
1.197     brouard  11576:     /* If line starts with a # it is a comment */
1.277     brouard  11577:     if (line[noffset] == '#') {
1.197     brouard  11578:       numlinepar++;
                   11579:       fputs(line,stdout);
                   11580:       fputs(line,ficparo);
1.278     brouard  11581:       fputs(line,ficres);
1.197     brouard  11582:       fputs(line,ficlog);
                   11583:       continue;
                   11584:     }else
                   11585:       break;
                   11586:   }
                   11587:   if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                   11588:                        title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
                   11589:     if (num_filled != 5) {
                   11590:       printf("Should be 5 parameters\n");
1.283     brouard  11591:       fprintf(ficlog,"Should be 5 parameters\n");
1.197     brouard  11592:     }
1.126     brouard  11593:     numlinepar++;
1.197     brouard  11594:     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283     brouard  11595:     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
                   11596:     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
                   11597:     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197     brouard  11598:   }
                   11599:   /* Second parameter line */
                   11600:   while(fgets(line, MAXLINE, ficpar)) {
1.283     brouard  11601:     /* while(fscanf(ficpar,"%[^\n]", line)) { */
                   11602:     /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197     brouard  11603:     if (line[0] == '#') {
                   11604:       numlinepar++;
1.283     brouard  11605:       printf("%s",line);
                   11606:       fprintf(ficres,"%s",line);
                   11607:       fprintf(ficparo,"%s",line);
                   11608:       fprintf(ficlog,"%s",line);
1.197     brouard  11609:       continue;
                   11610:     }else
                   11611:       break;
                   11612:   }
1.223     brouard  11613:   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                   11614:                        &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
                   11615:     if (num_filled != 11) {
                   11616:       printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
1.209     brouard  11617:       printf("but line=%s\n",line);
1.283     brouard  11618:       fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
                   11619:       fprintf(ficlog,"but line=%s\n",line);
1.197     brouard  11620:     }
1.286     brouard  11621:     if( lastpass > maxwav){
                   11622:       printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
                   11623:       fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
                   11624:       fflush(ficlog);
                   11625:       goto end;
                   11626:     }
                   11627:       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.283     brouard  11628:     fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.286     brouard  11629:     fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
1.283     brouard  11630:     fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.126     brouard  11631:   }
1.203     brouard  11632:   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209     brouard  11633:   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197     brouard  11634:   /* Third parameter line */
                   11635:   while(fgets(line, MAXLINE, ficpar)) {
                   11636:     /* If line starts with a # it is a comment */
                   11637:     if (line[0] == '#') {
                   11638:       numlinepar++;
1.283     brouard  11639:       printf("%s",line);
                   11640:       fprintf(ficres,"%s",line);
                   11641:       fprintf(ficparo,"%s",line);
                   11642:       fprintf(ficlog,"%s",line);
1.197     brouard  11643:       continue;
                   11644:     }else
                   11645:       break;
                   11646:   }
1.201     brouard  11647:   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279     brouard  11648:     if (num_filled != 1){
1.302     brouard  11649:       printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
                   11650:       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197     brouard  11651:       model[0]='\0';
                   11652:       goto end;
                   11653:     }
                   11654:     else{
                   11655:       if (model[0]=='+'){
                   11656:        for(i=1; i<=strlen(model);i++)
                   11657:          modeltemp[i-1]=model[i];
1.201     brouard  11658:        strcpy(model,modeltemp); 
1.197     brouard  11659:       }
                   11660:     }
1.199     brouard  11661:     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203     brouard  11662:     printf("model=1+age+%s\n",model);fflush(stdout);
1.283     brouard  11663:     fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
                   11664:     fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
                   11665:     fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197     brouard  11666:   }
                   11667:   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
                   11668:   /* numlinepar=numlinepar+3; /\* In general *\/ */
                   11669:   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
1.283     brouard  11670:   /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
                   11671:   /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
1.126     brouard  11672:   fflush(ficlog);
1.190     brouard  11673:   /* if(model[0]=='#'|| model[0]== '\0'){ */
                   11674:   if(model[0]=='#'){
1.279     brouard  11675:     printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
                   11676:  'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
                   11677:  'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");           \
1.187     brouard  11678:     if(mle != -1){
1.279     brouard  11679:       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
1.187     brouard  11680:       exit(1);
                   11681:     }
                   11682:   }
1.126     brouard  11683:   while((c=getc(ficpar))=='#' && c!= EOF){
                   11684:     ungetc(c,ficpar);
                   11685:     fgets(line, MAXLINE, ficpar);
                   11686:     numlinepar++;
1.195     brouard  11687:     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
                   11688:       z[0]=line[1];
                   11689:     }
                   11690:     /* printf("****line [1] = %c \n",line[1]); */
1.141     brouard  11691:     fputs(line, stdout);
                   11692:     //puts(line);
1.126     brouard  11693:     fputs(line,ficparo);
                   11694:     fputs(line,ficlog);
                   11695:   }
                   11696:   ungetc(c,ficpar);
                   11697: 
                   11698:    
1.290     brouard  11699:   covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
                   11700:   if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
                   11701:   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
                   11702:   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
1.136     brouard  11703:   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
                   11704:   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
                   11705:      v1+v2*age+v2*v3 makes cptcovn = 3
                   11706:   */
                   11707:   if (strlen(model)>1) 
1.187     brouard  11708:     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
1.145     brouard  11709:   else
1.187     brouard  11710:     ncovmodel=2; /* Constant and age */
1.133     brouard  11711:   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
                   11712:   npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131     brouard  11713:   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
                   11714:     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
                   11715:     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
                   11716:     fflush(stdout);
                   11717:     fclose (ficlog);
                   11718:     goto end;
                   11719:   }
1.126     brouard  11720:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   11721:   delti=delti3[1][1];
                   11722:   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
                   11723:   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247     brouard  11724: /* We could also provide initial parameters values giving by simple logistic regression 
                   11725:  * only one way, that is without matrix product. We will have nlstate maximizations */
                   11726:       /* for(i=1;i<nlstate;i++){ */
                   11727:       /*       /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
                   11728:       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
                   11729:       /* } */
1.126     brouard  11730:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191     brouard  11731:     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   11732:     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126     brouard  11733:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   11734:     fclose (ficparo);
                   11735:     fclose (ficlog);
                   11736:     goto end;
                   11737:     exit(0);
1.220     brouard  11738:   }  else if(mle==-5) { /* Main Wizard */
1.126     brouard  11739:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192     brouard  11740:     printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
                   11741:     fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126     brouard  11742:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   11743:     matcov=matrix(1,npar,1,npar);
1.203     brouard  11744:     hess=matrix(1,npar,1,npar);
1.220     brouard  11745:   }  else{ /* Begin of mle != -1 or -5 */
1.145     brouard  11746:     /* Read guessed parameters */
1.126     brouard  11747:     /* Reads comments: lines beginning with '#' */
                   11748:     while((c=getc(ficpar))=='#' && c!= EOF){
                   11749:       ungetc(c,ficpar);
                   11750:       fgets(line, MAXLINE, ficpar);
                   11751:       numlinepar++;
1.141     brouard  11752:       fputs(line,stdout);
1.126     brouard  11753:       fputs(line,ficparo);
                   11754:       fputs(line,ficlog);
                   11755:     }
                   11756:     ungetc(c,ficpar);
                   11757:     
                   11758:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251     brouard  11759:     paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126     brouard  11760:     for(i=1; i <=nlstate; i++){
1.234     brouard  11761:       j=0;
1.126     brouard  11762:       for(jj=1; jj <=nlstate+ndeath; jj++){
1.234     brouard  11763:        if(jj==i) continue;
                   11764:        j++;
1.292     brouard  11765:        while((c=getc(ficpar))=='#' && c!= EOF){
                   11766:          ungetc(c,ficpar);
                   11767:          fgets(line, MAXLINE, ficpar);
                   11768:          numlinepar++;
                   11769:          fputs(line,stdout);
                   11770:          fputs(line,ficparo);
                   11771:          fputs(line,ficlog);
                   11772:        }
                   11773:        ungetc(c,ficpar);
1.234     brouard  11774:        fscanf(ficpar,"%1d%1d",&i1,&j1);
                   11775:        if ((i1 != i) || (j1 != jj)){
                   11776:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126     brouard  11777: It might be a problem of design; if ncovcol and the model are correct\n \
                   11778: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234     brouard  11779:          exit(1);
                   11780:        }
                   11781:        fprintf(ficparo,"%1d%1d",i1,j1);
                   11782:        if(mle==1)
                   11783:          printf("%1d%1d",i,jj);
                   11784:        fprintf(ficlog,"%1d%1d",i,jj);
                   11785:        for(k=1; k<=ncovmodel;k++){
                   11786:          fscanf(ficpar," %lf",&param[i][j][k]);
                   11787:          if(mle==1){
                   11788:            printf(" %lf",param[i][j][k]);
                   11789:            fprintf(ficlog," %lf",param[i][j][k]);
                   11790:          }
                   11791:          else
                   11792:            fprintf(ficlog," %lf",param[i][j][k]);
                   11793:          fprintf(ficparo," %lf",param[i][j][k]);
                   11794:        }
                   11795:        fscanf(ficpar,"\n");
                   11796:        numlinepar++;
                   11797:        if(mle==1)
                   11798:          printf("\n");
                   11799:        fprintf(ficlog,"\n");
                   11800:        fprintf(ficparo,"\n");
1.126     brouard  11801:       }
                   11802:     }  
                   11803:     fflush(ficlog);
1.234     brouard  11804:     
1.251     brouard  11805:     /* Reads parameters values */
1.126     brouard  11806:     p=param[1][1];
1.251     brouard  11807:     pstart=paramstart[1][1];
1.126     brouard  11808:     
                   11809:     /* Reads comments: lines beginning with '#' */
                   11810:     while((c=getc(ficpar))=='#' && c!= EOF){
                   11811:       ungetc(c,ficpar);
                   11812:       fgets(line, MAXLINE, ficpar);
                   11813:       numlinepar++;
1.141     brouard  11814:       fputs(line,stdout);
1.126     brouard  11815:       fputs(line,ficparo);
                   11816:       fputs(line,ficlog);
                   11817:     }
                   11818:     ungetc(c,ficpar);
                   11819: 
                   11820:     for(i=1; i <=nlstate; i++){
                   11821:       for(j=1; j <=nlstate+ndeath-1; j++){
1.234     brouard  11822:        fscanf(ficpar,"%1d%1d",&i1,&j1);
                   11823:        if ( (i1-i) * (j1-j) != 0){
                   11824:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   11825:          exit(1);
                   11826:        }
                   11827:        printf("%1d%1d",i,j);
                   11828:        fprintf(ficparo,"%1d%1d",i1,j1);
                   11829:        fprintf(ficlog,"%1d%1d",i1,j1);
                   11830:        for(k=1; k<=ncovmodel;k++){
                   11831:          fscanf(ficpar,"%le",&delti3[i][j][k]);
                   11832:          printf(" %le",delti3[i][j][k]);
                   11833:          fprintf(ficparo," %le",delti3[i][j][k]);
                   11834:          fprintf(ficlog," %le",delti3[i][j][k]);
                   11835:        }
                   11836:        fscanf(ficpar,"\n");
                   11837:        numlinepar++;
                   11838:        printf("\n");
                   11839:        fprintf(ficparo,"\n");
                   11840:        fprintf(ficlog,"\n");
1.126     brouard  11841:       }
                   11842:     }
                   11843:     fflush(ficlog);
1.234     brouard  11844:     
1.145     brouard  11845:     /* Reads covariance matrix */
1.126     brouard  11846:     delti=delti3[1][1];
1.220     brouard  11847:                
                   11848:                
1.126     brouard  11849:     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.220     brouard  11850:                
1.126     brouard  11851:     /* Reads comments: lines beginning with '#' */
                   11852:     while((c=getc(ficpar))=='#' && c!= EOF){
                   11853:       ungetc(c,ficpar);
                   11854:       fgets(line, MAXLINE, ficpar);
                   11855:       numlinepar++;
1.141     brouard  11856:       fputs(line,stdout);
1.126     brouard  11857:       fputs(line,ficparo);
                   11858:       fputs(line,ficlog);
                   11859:     }
                   11860:     ungetc(c,ficpar);
1.220     brouard  11861:                
1.126     brouard  11862:     matcov=matrix(1,npar,1,npar);
1.203     brouard  11863:     hess=matrix(1,npar,1,npar);
1.131     brouard  11864:     for(i=1; i <=npar; i++)
                   11865:       for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220     brouard  11866:                
1.194     brouard  11867:     /* Scans npar lines */
1.126     brouard  11868:     for(i=1; i <=npar; i++){
1.226     brouard  11869:       count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194     brouard  11870:       if(count != 3){
1.226     brouard  11871:        printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194     brouard  11872: This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
                   11873: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226     brouard  11874:        fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194     brouard  11875: This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
                   11876: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226     brouard  11877:        exit(1);
1.220     brouard  11878:       }else{
1.226     brouard  11879:        if(mle==1)
                   11880:          printf("%1d%1d%d",i1,j1,jk);
                   11881:       }
                   11882:       fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
                   11883:       fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126     brouard  11884:       for(j=1; j <=i; j++){
1.226     brouard  11885:        fscanf(ficpar," %le",&matcov[i][j]);
                   11886:        if(mle==1){
                   11887:          printf(" %.5le",matcov[i][j]);
                   11888:        }
                   11889:        fprintf(ficlog," %.5le",matcov[i][j]);
                   11890:        fprintf(ficparo," %.5le",matcov[i][j]);
1.126     brouard  11891:       }
                   11892:       fscanf(ficpar,"\n");
                   11893:       numlinepar++;
                   11894:       if(mle==1)
1.220     brouard  11895:                                printf("\n");
1.126     brouard  11896:       fprintf(ficlog,"\n");
                   11897:       fprintf(ficparo,"\n");
                   11898:     }
1.194     brouard  11899:     /* End of read covariance matrix npar lines */
1.126     brouard  11900:     for(i=1; i <=npar; i++)
                   11901:       for(j=i+1;j<=npar;j++)
1.226     brouard  11902:        matcov[i][j]=matcov[j][i];
1.126     brouard  11903:     
                   11904:     if(mle==1)
                   11905:       printf("\n");
                   11906:     fprintf(ficlog,"\n");
                   11907:     
                   11908:     fflush(ficlog);
                   11909:     
                   11910:   }    /* End of mle != -3 */
1.218     brouard  11911:   
1.186     brouard  11912:   /*  Main data
                   11913:    */
1.290     brouard  11914:   nobs=lastobs-firstobs+1; /* was = lastobs;*/
                   11915:   /* num=lvector(1,n); */
                   11916:   /* moisnais=vector(1,n); */
                   11917:   /* annais=vector(1,n); */
                   11918:   /* moisdc=vector(1,n); */
                   11919:   /* andc=vector(1,n); */
                   11920:   /* weight=vector(1,n); */
                   11921:   /* agedc=vector(1,n); */
                   11922:   /* cod=ivector(1,n); */
                   11923:   /* for(i=1;i<=n;i++){ */
                   11924:   num=lvector(firstobs,lastobs);
                   11925:   moisnais=vector(firstobs,lastobs);
                   11926:   annais=vector(firstobs,lastobs);
                   11927:   moisdc=vector(firstobs,lastobs);
                   11928:   andc=vector(firstobs,lastobs);
                   11929:   weight=vector(firstobs,lastobs);
                   11930:   agedc=vector(firstobs,lastobs);
                   11931:   cod=ivector(firstobs,lastobs);
                   11932:   for(i=firstobs;i<=lastobs;i++){
1.234     brouard  11933:     num[i]=0;
                   11934:     moisnais[i]=0;
                   11935:     annais[i]=0;
                   11936:     moisdc[i]=0;
                   11937:     andc[i]=0;
                   11938:     agedc[i]=0;
                   11939:     cod[i]=0;
                   11940:     weight[i]=1.0; /* Equal weights, 1 by default */
                   11941:   }
1.290     brouard  11942:   mint=matrix(1,maxwav,firstobs,lastobs);
                   11943:   anint=matrix(1,maxwav,firstobs,lastobs);
1.325     brouard  11944:   s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
                   11945:   printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel));
1.126     brouard  11946:   tab=ivector(1,NCOVMAX);
1.144     brouard  11947:   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192     brouard  11948:   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126     brouard  11949: 
1.136     brouard  11950:   /* Reads data from file datafile */
                   11951:   if (readdata(datafile, firstobs, lastobs, &imx)==1)
                   11952:     goto end;
                   11953: 
                   11954:   /* Calculation of the number of parameters from char model */
1.234     brouard  11955:   /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
1.137     brouard  11956:        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
                   11957:        k=3 V4 Tvar[k=3]= 4 (from V4)
                   11958:        k=2 V1 Tvar[k=2]= 1 (from V1)
                   11959:        k=1 Tvar[1]=2 (from V2)
1.234     brouard  11960:   */
                   11961:   
                   11962:   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
                   11963:   TvarsDind=ivector(1,NCOVMAX); /*  */
                   11964:   TvarsD=ivector(1,NCOVMAX); /*  */
                   11965:   TvarsQind=ivector(1,NCOVMAX); /*  */
                   11966:   TvarsQ=ivector(1,NCOVMAX); /*  */
1.232     brouard  11967:   TvarF=ivector(1,NCOVMAX); /*  */
                   11968:   TvarFind=ivector(1,NCOVMAX); /*  */
                   11969:   TvarV=ivector(1,NCOVMAX); /*  */
                   11970:   TvarVind=ivector(1,NCOVMAX); /*  */
                   11971:   TvarA=ivector(1,NCOVMAX); /*  */
                   11972:   TvarAind=ivector(1,NCOVMAX); /*  */
1.231     brouard  11973:   TvarFD=ivector(1,NCOVMAX); /*  */
                   11974:   TvarFDind=ivector(1,NCOVMAX); /*  */
                   11975:   TvarFQ=ivector(1,NCOVMAX); /*  */
                   11976:   TvarFQind=ivector(1,NCOVMAX); /*  */
                   11977:   TvarVD=ivector(1,NCOVMAX); /*  */
                   11978:   TvarVDind=ivector(1,NCOVMAX); /*  */
                   11979:   TvarVQ=ivector(1,NCOVMAX); /*  */
                   11980:   TvarVQind=ivector(1,NCOVMAX); /*  */
                   11981: 
1.230     brouard  11982:   Tvalsel=vector(1,NCOVMAX); /*  */
1.233     brouard  11983:   Tvarsel=ivector(1,NCOVMAX); /*  */
1.226     brouard  11984:   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
                   11985:   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
                   11986:   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137     brouard  11987:   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
                   11988:       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
                   11989:       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
                   11990:   */
                   11991:   /* For model-covariate k tells which data-covariate to use but
                   11992:     because this model-covariate is a construction we invent a new column
                   11993:     ncovcol + k1
                   11994:     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
                   11995:     Tvar[3=V1*V4]=4+1 etc */
1.227     brouard  11996:   Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
                   11997:   Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137     brouard  11998:   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
                   11999:      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
1.227     brouard  12000:      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
1.137     brouard  12001:   */
1.145     brouard  12002:   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
                   12003:   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141     brouard  12004:                            * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                   12005:                            * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145     brouard  12006:   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137     brouard  12007:                         4 covariates (3 plus signs)
                   12008:                         Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
1.328   ! brouard  12009:                           */  
        !          12010:   for(i=1;i<NCOVMAX;i++)
        !          12011:     Tage[i]=0;
1.230     brouard  12012:   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227     brouard  12013:                                * individual dummy, fixed or varying:
                   12014:                                * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                   12015:                                * 3, 1, 0, 0, 0, 0, 0, 0},
1.230     brouard  12016:                                * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , 
                   12017:                                * V1 df, V2 qf, V3 & V4 dv, V5 qv
                   12018:                                * Tmodelind[1]@9={9,0,3,2,}*/
                   12019:   TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
                   12020:   TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228     brouard  12021:                                * individual quantitative, fixed or varying:
                   12022:                                * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                   12023:                                * 3, 1, 0, 0, 0, 0, 0, 0},
                   12024:                                * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186     brouard  12025: /* Main decodemodel */
                   12026: 
1.187     brouard  12027: 
1.223     brouard  12028:   if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
1.136     brouard  12029:     goto end;
                   12030: 
1.137     brouard  12031:   if((double)(lastobs-imx)/(double)imx > 1.10){
                   12032:     nbwarn++;
                   12033:     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
                   12034:     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
                   12035:   }
1.136     brouard  12036:     /*  if(mle==1){*/
1.137     brouard  12037:   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
                   12038:     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136     brouard  12039:   }
                   12040: 
                   12041:     /*-calculation of age at interview from date of interview and age at death -*/
                   12042:   agev=matrix(1,maxwav,1,imx);
                   12043: 
                   12044:   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
                   12045:     goto end;
                   12046: 
1.126     brouard  12047: 
1.136     brouard  12048:   agegomp=(int)agemin;
1.290     brouard  12049:   free_vector(moisnais,firstobs,lastobs);
                   12050:   free_vector(annais,firstobs,lastobs);
1.126     brouard  12051:   /* free_matrix(mint,1,maxwav,1,n);
                   12052:      free_matrix(anint,1,maxwav,1,n);*/
1.215     brouard  12053:   /* free_vector(moisdc,1,n); */
                   12054:   /* free_vector(andc,1,n); */
1.145     brouard  12055:   /* */
                   12056:   
1.126     brouard  12057:   wav=ivector(1,imx);
1.214     brouard  12058:   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
                   12059:   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
                   12060:   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
                   12061:   dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
                   12062:   bh=imatrix(1,lastpass-firstpass+2,1,imx);
                   12063:   mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126     brouard  12064:    
                   12065:   /* Concatenates waves */
1.214     brouard  12066:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   12067:      Death is a valid wave (if date is known).
                   12068:      mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
                   12069:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   12070:      and mw[mi+1][i]. dh depends on stepm.
                   12071:   */
                   12072: 
1.126     brouard  12073:   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
1.248     brouard  12074:   /* Concatenates waves */
1.145     brouard  12075:  
1.290     brouard  12076:   free_vector(moisdc,firstobs,lastobs);
                   12077:   free_vector(andc,firstobs,lastobs);
1.215     brouard  12078: 
1.126     brouard  12079:   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
                   12080:   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
                   12081:   ncodemax[1]=1;
1.145     brouard  12082:   Ndum =ivector(-1,NCOVMAX);  
1.225     brouard  12083:   cptcoveff=0;
1.220     brouard  12084:   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
                   12085:     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227     brouard  12086:   }
                   12087:   
                   12088:   ncovcombmax=pow(2,cptcoveff);
                   12089:   invalidvarcomb=ivector(1, ncovcombmax); 
                   12090:   for(i=1;i<ncovcombmax;i++)
                   12091:     invalidvarcomb[i]=0;
                   12092:   
1.211     brouard  12093:   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186     brouard  12094:      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211     brouard  12095:   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227     brouard  12096:   
1.200     brouard  12097:   /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198     brouard  12098:   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186     brouard  12099:   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211     brouard  12100:   /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, 
                   12101:    * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded 
                   12102:    * (currently 0 or 1) in the data.
                   12103:    * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of 
                   12104:    * corresponding modality (h,j).
                   12105:    */
                   12106: 
1.145     brouard  12107:   h=0;
                   12108:   /*if (cptcovn > 0) */
1.126     brouard  12109:   m=pow(2,cptcoveff);
                   12110:  
1.144     brouard  12111:          /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211     brouard  12112:           * For k=4 covariates, h goes from 1 to m=2**k
                   12113:           * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
                   12114:            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
1.186     brouard  12115:           *     h\k   1     2     3     4
1.143     brouard  12116:           *______________________________  
                   12117:           *     1 i=1 1 i=1 1 i=1 1 i=1 1
                   12118:           *     2     2     1     1     1
                   12119:           *     3 i=2 1     2     1     1
                   12120:           *     4     2     2     1     1
                   12121:           *     5 i=3 1 i=2 1     2     1
                   12122:           *     6     2     1     2     1
                   12123:           *     7 i=4 1     2     2     1
                   12124:           *     8     2     2     2     1
1.197     brouard  12125:           *     9 i=5 1 i=3 1 i=2 1     2
                   12126:           *    10     2     1     1     2
                   12127:           *    11 i=6 1     2     1     2
                   12128:           *    12     2     2     1     2
                   12129:           *    13 i=7 1 i=4 1     2     2    
                   12130:           *    14     2     1     2     2
                   12131:           *    15 i=8 1     2     2     2
                   12132:           *    16     2     2     2     2
1.143     brouard  12133:           */
1.212     brouard  12134:   /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211     brouard  12135:      /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
                   12136:      * and the value of each covariate?
                   12137:      * V1=1, V2=1, V3=2, V4=1 ?
                   12138:      * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
                   12139:      * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
                   12140:      * In order to get the real value in the data, we use nbcode
                   12141:      * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
                   12142:      * We are keeping this crazy system in order to be able (in the future?) 
                   12143:      * to have more than 2 values (0 or 1) for a covariate.
                   12144:      * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
                   12145:      * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
                   12146:      *              bbbbbbbb
                   12147:      *              76543210     
                   12148:      *   h-1        00000101 (6-1=5)
1.219     brouard  12149:      *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211     brouard  12150:      *           &
                   12151:      *     1        00000001 (1)
1.219     brouard  12152:      *              00000000        = 1 & ((h-1) >> (k-1))
                   12153:      *          +1= 00000001 =1 
1.211     brouard  12154:      *
                   12155:      * h=14, k=3 => h'=h-1=13, k'=k-1=2
                   12156:      *          h'      1101 =2^3+2^2+0x2^1+2^0
                   12157:      *    >>k'            11
                   12158:      *          &   00000001
                   12159:      *            = 00000001
                   12160:      *      +1    = 00000010=2    =  codtabm(14,3)   
                   12161:      * Reverse h=6 and m=16?
                   12162:      * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
                   12163:      * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
                   12164:      * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 
                   12165:      * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
                   12166:      * V3=decodtabm(14,3,2**4)=2
                   12167:      *          h'=13   1101 =2^3+2^2+0x2^1+2^0
                   12168:      *(h-1) >> (j-1)    0011 =13 >> 2
                   12169:      *          &1 000000001
                   12170:      *           = 000000001
                   12171:      *         +1= 000000010 =2
                   12172:      *                  2211
                   12173:      *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
                   12174:      *                  V3=2
1.220     brouard  12175:                 * codtabm and decodtabm are identical
1.211     brouard  12176:      */
                   12177: 
1.145     brouard  12178: 
                   12179:  free_ivector(Ndum,-1,NCOVMAX);
                   12180: 
                   12181: 
1.126     brouard  12182:     
1.186     brouard  12183:   /* Initialisation of ----------- gnuplot -------------*/
1.126     brouard  12184:   strcpy(optionfilegnuplot,optionfilefiname);
                   12185:   if(mle==-3)
1.201     brouard  12186:     strcat(optionfilegnuplot,"-MORT_");
1.126     brouard  12187:   strcat(optionfilegnuplot,".gp");
                   12188: 
                   12189:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
                   12190:     printf("Problem with file %s",optionfilegnuplot);
                   12191:   }
                   12192:   else{
1.204     brouard  12193:     fprintf(ficgp,"\n# IMaCh-%s\n", version); 
1.126     brouard  12194:     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
1.141     brouard  12195:     //fprintf(ficgp,"set missing 'NaNq'\n");
                   12196:     fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126     brouard  12197:   }
                   12198:   /*  fclose(ficgp);*/
1.186     brouard  12199: 
                   12200: 
                   12201:   /* Initialisation of --------- index.htm --------*/
1.126     brouard  12202: 
                   12203:   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
                   12204:   if(mle==-3)
1.201     brouard  12205:     strcat(optionfilehtm,"-MORT_");
1.126     brouard  12206:   strcat(optionfilehtm,".htm");
                   12207:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
1.131     brouard  12208:     printf("Problem with %s \n",optionfilehtm);
                   12209:     exit(0);
1.126     brouard  12210:   }
                   12211: 
                   12212:   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
                   12213:   strcat(optionfilehtmcov,"-cov.htm");
                   12214:   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
                   12215:     printf("Problem with %s \n",optionfilehtmcov), exit(0);
                   12216:   }
                   12217:   else{
                   12218:   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                   12219: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204     brouard  12220: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126     brouard  12221:          optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   12222:   }
                   12223: 
1.324     brouard  12224:   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
1.204     brouard  12225: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   12226: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126     brouard  12227: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204     brouard  12228: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126     brouard  12229: \n\
                   12230: <hr  size=\"2\" color=\"#EC5E5E\">\
                   12231:  <ul><li><h4>Parameter files</h4>\n\
                   12232:  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
                   12233:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
                   12234:  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
                   12235:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
                   12236:  - Date and time at start: %s</ul>\n",\
                   12237:          optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
                   12238:          optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
                   12239:          fileres,fileres,\
                   12240:          filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
                   12241:   fflush(fichtm);
                   12242: 
                   12243:   strcpy(pathr,path);
                   12244:   strcat(pathr,optionfilefiname);
1.184     brouard  12245: #ifdef WIN32
                   12246:   _chdir(optionfilefiname); /* Move to directory named optionfile */
                   12247: #else
1.126     brouard  12248:   chdir(optionfilefiname); /* Move to directory named optionfile */
1.184     brouard  12249: #endif
                   12250:          
1.126     brouard  12251:   
1.220     brouard  12252:   /* Calculates basic frequencies. Computes observed prevalence at single age 
                   12253:                 and for any valid combination of covariates
1.126     brouard  12254:      and prints on file fileres'p'. */
1.251     brouard  12255:   freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227     brouard  12256:              firstpass, lastpass,  stepm,  weightopt, model);
1.126     brouard  12257: 
                   12258:   fprintf(fichtm,"\n");
1.286     brouard  12259:   fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
1.274     brouard  12260:          ftol, stepm);
                   12261:   fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
                   12262:   ncurrv=1;
                   12263:   for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
                   12264:   fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); 
                   12265:   ncurrv=i;
                   12266:   for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290     brouard  12267:   fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274     brouard  12268:   ncurrv=i;
                   12269:   for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290     brouard  12270:   fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
1.274     brouard  12271:   ncurrv=i;
                   12272:   for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
                   12273:   fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
                   12274:           nlstate, ndeath, maxwav, mle, weightopt);
                   12275: 
                   12276:   fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
                   12277: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
                   12278: 
                   12279:   
1.317     brouard  12280:   fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) observations=%d <br>\n\
1.126     brouard  12281: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
                   12282: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274     brouard  12283:   imx,agemin,agemax,jmin,jmax,jmean);
1.126     brouard  12284:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268     brouard  12285:   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   12286:   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   12287:   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   12288:   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218     brouard  12289: 
1.126     brouard  12290:   /* For Powell, parameters are in a vector p[] starting at p[1]
                   12291:      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
                   12292:   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
                   12293: 
                   12294:   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186     brouard  12295:   /* For mortality only */
1.126     brouard  12296:   if (mle==-3){
1.136     brouard  12297:     ximort=matrix(1,NDIM,1,NDIM); 
1.248     brouard  12298:     for(i=1;i<=NDIM;i++)
                   12299:       for(j=1;j<=NDIM;j++)
                   12300:        ximort[i][j]=0.;
1.186     brouard  12301:     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290     brouard  12302:     cens=ivector(firstobs,lastobs);
                   12303:     ageexmed=vector(firstobs,lastobs);
                   12304:     agecens=vector(firstobs,lastobs);
                   12305:     dcwave=ivector(firstobs,lastobs);
1.223     brouard  12306:                
1.126     brouard  12307:     for (i=1; i<=imx; i++){
                   12308:       dcwave[i]=-1;
                   12309:       for (m=firstpass; m<=lastpass; m++)
1.226     brouard  12310:        if (s[m][i]>nlstate) {
                   12311:          dcwave[i]=m;
                   12312:          /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                   12313:          break;
                   12314:        }
1.126     brouard  12315:     }
1.226     brouard  12316:     
1.126     brouard  12317:     for (i=1; i<=imx; i++) {
                   12318:       if (wav[i]>0){
1.226     brouard  12319:        ageexmed[i]=agev[mw[1][i]][i];
                   12320:        j=wav[i];
                   12321:        agecens[i]=1.; 
                   12322:        
                   12323:        if (ageexmed[i]> 1 && wav[i] > 0){
                   12324:          agecens[i]=agev[mw[j][i]][i];
                   12325:          cens[i]= 1;
                   12326:        }else if (ageexmed[i]< 1) 
                   12327:          cens[i]= -1;
                   12328:        if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                   12329:          cens[i]=0 ;
1.126     brouard  12330:       }
                   12331:       else cens[i]=-1;
                   12332:     }
                   12333:     
                   12334:     for (i=1;i<=NDIM;i++) {
                   12335:       for (j=1;j<=NDIM;j++)
1.226     brouard  12336:        ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126     brouard  12337:     }
                   12338:     
1.302     brouard  12339:     p[1]=0.0268; p[NDIM]=0.083;
                   12340:     /* printf("%lf %lf", p[1], p[2]); */
1.126     brouard  12341:     
                   12342:     
1.136     brouard  12343: #ifdef GSL
                   12344:     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
1.162     brouard  12345: #else
1.126     brouard  12346:     printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.136     brouard  12347: #endif
1.201     brouard  12348:     strcpy(filerespow,"POW-MORT_"); 
                   12349:     strcat(filerespow,fileresu);
1.126     brouard  12350:     if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   12351:       printf("Problem with resultfile: %s\n", filerespow);
                   12352:       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   12353:     }
1.136     brouard  12354: #ifdef GSL
                   12355:     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162     brouard  12356: #else
1.126     brouard  12357:     fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136     brouard  12358: #endif
1.126     brouard  12359:     /*  for (i=1;i<=nlstate;i++)
                   12360:        for(j=1;j<=nlstate+ndeath;j++)
                   12361:        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   12362:     */
                   12363:     fprintf(ficrespow,"\n");
1.136     brouard  12364: #ifdef GSL
                   12365:     /* gsl starts here */ 
                   12366:     T = gsl_multimin_fminimizer_nmsimplex;
                   12367:     gsl_multimin_fminimizer *sfm = NULL;
                   12368:     gsl_vector *ss, *x;
                   12369:     gsl_multimin_function minex_func;
                   12370: 
                   12371:     /* Initial vertex size vector */
                   12372:     ss = gsl_vector_alloc (NDIM);
                   12373:     
                   12374:     if (ss == NULL){
                   12375:       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
                   12376:     }
                   12377:     /* Set all step sizes to 1 */
                   12378:     gsl_vector_set_all (ss, 0.001);
                   12379: 
                   12380:     /* Starting point */
1.126     brouard  12381:     
1.136     brouard  12382:     x = gsl_vector_alloc (NDIM);
                   12383:     
                   12384:     if (x == NULL){
                   12385:       gsl_vector_free(ss);
                   12386:       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
                   12387:     }
                   12388:   
                   12389:     /* Initialize method and iterate */
                   12390:     /*     p[1]=0.0268; p[NDIM]=0.083; */
1.186     brouard  12391:     /*     gsl_vector_set(x, 0, 0.0268); */
                   12392:     /*     gsl_vector_set(x, 1, 0.083); */
1.136     brouard  12393:     gsl_vector_set(x, 0, p[1]);
                   12394:     gsl_vector_set(x, 1, p[2]);
                   12395: 
                   12396:     minex_func.f = &gompertz_f;
                   12397:     minex_func.n = NDIM;
                   12398:     minex_func.params = (void *)&p; /* ??? */
                   12399:     
                   12400:     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
                   12401:     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
                   12402:     
                   12403:     printf("Iterations beginning .....\n\n");
                   12404:     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
                   12405: 
                   12406:     iteri=0;
                   12407:     while (rval == GSL_CONTINUE){
                   12408:       iteri++;
                   12409:       status = gsl_multimin_fminimizer_iterate(sfm);
                   12410:       
                   12411:       if (status) printf("error: %s\n", gsl_strerror (status));
                   12412:       fflush(0);
                   12413:       
                   12414:       if (status) 
                   12415:         break;
                   12416:       
                   12417:       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
                   12418:       ssval = gsl_multimin_fminimizer_size (sfm);
                   12419:       
                   12420:       if (rval == GSL_SUCCESS)
                   12421:         printf ("converged to a local maximum at\n");
                   12422:       
                   12423:       printf("%5d ", iteri);
                   12424:       for (it = 0; it < NDIM; it++){
                   12425:        printf ("%10.5f ", gsl_vector_get (sfm->x, it));
                   12426:       }
                   12427:       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
                   12428:     }
                   12429:     
                   12430:     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
                   12431:     
                   12432:     gsl_vector_free(x); /* initial values */
                   12433:     gsl_vector_free(ss); /* inital step size */
                   12434:     for (it=0; it<NDIM; it++){
                   12435:       p[it+1]=gsl_vector_get(sfm->x,it);
                   12436:       fprintf(ficrespow," %.12lf", p[it]);
                   12437:     }
                   12438:     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
                   12439: #endif
                   12440: #ifdef POWELL
                   12441:      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
                   12442: #endif  
1.126     brouard  12443:     fclose(ficrespow);
                   12444:     
1.203     brouard  12445:     hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
1.126     brouard  12446: 
                   12447:     for(i=1; i <=NDIM; i++)
                   12448:       for(j=i+1;j<=NDIM;j++)
1.220     brouard  12449:                                matcov[i][j]=matcov[j][i];
1.126     brouard  12450:     
                   12451:     printf("\nCovariance matrix\n ");
1.203     brouard  12452:     fprintf(ficlog,"\nCovariance matrix\n ");
1.126     brouard  12453:     for(i=1; i <=NDIM; i++) {
                   12454:       for(j=1;j<=NDIM;j++){ 
1.220     brouard  12455:                                printf("%f ",matcov[i][j]);
                   12456:                                fprintf(ficlog,"%f ",matcov[i][j]);
1.126     brouard  12457:       }
1.203     brouard  12458:       printf("\n ");  fprintf(ficlog,"\n ");
1.126     brouard  12459:     }
                   12460:     
                   12461:     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193     brouard  12462:     for (i=1;i<=NDIM;i++) {
1.126     brouard  12463:       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193     brouard  12464:       fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
                   12465:     }
1.302     brouard  12466:     lsurv=vector(agegomp,AGESUP);
                   12467:     lpop=vector(agegomp,AGESUP);
                   12468:     tpop=vector(agegomp,AGESUP);
1.126     brouard  12469:     lsurv[agegomp]=100000;
                   12470:     
                   12471:     for (k=agegomp;k<=AGESUP;k++) {
                   12472:       agemortsup=k;
                   12473:       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
                   12474:     }
                   12475:     
                   12476:     for (k=agegomp;k<agemortsup;k++)
                   12477:       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
                   12478:     
                   12479:     for (k=agegomp;k<agemortsup;k++){
                   12480:       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
                   12481:       sumlpop=sumlpop+lpop[k];
                   12482:     }
                   12483:     
                   12484:     tpop[agegomp]=sumlpop;
                   12485:     for (k=agegomp;k<(agemortsup-3);k++){
                   12486:       /*  tpop[k+1]=2;*/
                   12487:       tpop[k+1]=tpop[k]-lpop[k];
                   12488:     }
                   12489:     
                   12490:     
                   12491:     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
                   12492:     for (k=agegomp;k<(agemortsup-2);k++) 
                   12493:       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
                   12494:     
                   12495:     
                   12496:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220     brouard  12497:                ageminpar=50;
                   12498:                agemaxpar=100;
1.194     brouard  12499:     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
                   12500:        printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
                   12501: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   12502: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
                   12503:        fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
                   12504: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   12505: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220     brouard  12506:     }else{
                   12507:                        printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
                   12508:                        fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
1.201     brouard  12509:       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220     brouard  12510:                }
1.201     brouard  12511:     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126     brouard  12512:                     stepm, weightopt,\
                   12513:                     model,imx,p,matcov,agemortsup);
                   12514:     
1.302     brouard  12515:     free_vector(lsurv,agegomp,AGESUP);
                   12516:     free_vector(lpop,agegomp,AGESUP);
                   12517:     free_vector(tpop,agegomp,AGESUP);
1.220     brouard  12518:     free_matrix(ximort,1,NDIM,1,NDIM);
1.290     brouard  12519:     free_ivector(dcwave,firstobs,lastobs);
                   12520:     free_vector(agecens,firstobs,lastobs);
                   12521:     free_vector(ageexmed,firstobs,lastobs);
                   12522:     free_ivector(cens,firstobs,lastobs);
1.220     brouard  12523: #ifdef GSL
1.136     brouard  12524: #endif
1.186     brouard  12525:   } /* Endof if mle==-3 mortality only */
1.205     brouard  12526:   /* Standard  */
                   12527:   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
                   12528:     globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
                   12529:     /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132     brouard  12530:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126     brouard  12531:     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   12532:     for (k=1; k<=npar;k++)
                   12533:       printf(" %d %8.5f",k,p[k]);
                   12534:     printf("\n");
1.205     brouard  12535:     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
                   12536:       /* mlikeli uses func not funcone */
1.247     brouard  12537:       /* for(i=1;i<nlstate;i++){ */
                   12538:       /*       /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
                   12539:       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
                   12540:       /* } */
1.205     brouard  12541:       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
                   12542:     }
                   12543:     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
                   12544:       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
                   12545:       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
                   12546:       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   12547:     }
                   12548:     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126     brouard  12549:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   12550:     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   12551:     for (k=1; k<=npar;k++)
                   12552:       printf(" %d %8.5f",k,p[k]);
                   12553:     printf("\n");
                   12554:     
                   12555:     /*--------- results files --------------*/
1.283     brouard  12556:     /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
1.126     brouard  12557:     
                   12558:     
                   12559:     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.319     brouard  12560:     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */
1.126     brouard  12561:     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.319     brouard  12562: 
                   12563:     printf("#model=  1      +     age ");
                   12564:     fprintf(ficres,"#model=  1      +     age ");
                   12565:     fprintf(ficlog,"#model=  1      +     age ");
                   12566:     fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
                   12567: </ul>", model);
                   12568: 
                   12569:     fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
                   12570:     fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
                   12571:     if(nagesqr==1){
                   12572:       printf("  + age*age  ");
                   12573:       fprintf(ficres,"  + age*age  ");
                   12574:       fprintf(ficlog,"  + age*age  ");
                   12575:       fprintf(fichtm, "<th>+ age*age</th>");
                   12576:     }
                   12577:     for(j=1;j <=ncovmodel-2;j++){
                   12578:       if(Typevar[j]==0) {
                   12579:        printf("  +      V%d  ",Tvar[j]);
                   12580:        fprintf(ficres,"  +      V%d  ",Tvar[j]);
                   12581:        fprintf(ficlog,"  +      V%d  ",Tvar[j]);
                   12582:        fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
                   12583:       }else if(Typevar[j]==1) {
                   12584:        printf("  +    V%d*age ",Tvar[j]);
                   12585:        fprintf(ficres,"  +    V%d*age ",Tvar[j]);
                   12586:        fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
                   12587:        fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
                   12588:       }else if(Typevar[j]==2) {
                   12589:        printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   12590:        fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   12591:        fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   12592:        fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   12593:       }
                   12594:     }
                   12595:     printf("\n");
                   12596:     fprintf(ficres,"\n");
                   12597:     fprintf(ficlog,"\n");
                   12598:     fprintf(fichtm, "</tr>");
                   12599:     fprintf(fichtm, "\n");
                   12600:     
                   12601:     
1.126     brouard  12602:     for(i=1,jk=1; i <=nlstate; i++){
                   12603:       for(k=1; k <=(nlstate+ndeath); k++){
1.225     brouard  12604:        if (k != i) {
1.319     brouard  12605:          fprintf(fichtm, "<tr>");
1.225     brouard  12606:          printf("%d%d ",i,k);
                   12607:          fprintf(ficlog,"%d%d ",i,k);
                   12608:          fprintf(ficres,"%1d%1d ",i,k);
1.319     brouard  12609:          fprintf(fichtm, "<td>%1d%1d</td>",i,k);
1.225     brouard  12610:          for(j=1; j <=ncovmodel; j++){
                   12611:            printf("%12.7f ",p[jk]);
                   12612:            fprintf(ficlog,"%12.7f ",p[jk]);
                   12613:            fprintf(ficres,"%12.7f ",p[jk]);
1.319     brouard  12614:            fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
1.225     brouard  12615:            jk++; 
                   12616:          }
                   12617:          printf("\n");
                   12618:          fprintf(ficlog,"\n");
                   12619:          fprintf(ficres,"\n");
1.319     brouard  12620:          fprintf(fichtm, "</tr>\n");
1.225     brouard  12621:        }
1.126     brouard  12622:       }
                   12623:     }
1.319     brouard  12624:     /* fprintf(fichtm,"</tr>\n"); */
                   12625:     fprintf(fichtm,"</table>\n");
                   12626:     fprintf(fichtm, "\n");
                   12627: 
1.203     brouard  12628:     if(mle != 0){
                   12629:       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126     brouard  12630:       ftolhess=ftol; /* Usually correct */
1.203     brouard  12631:       hesscov(matcov, hess, p, npar, delti, ftolhess, func);
                   12632:       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
                   12633:       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
1.322     brouard  12634:       fprintf(fichtm, "\n<p>The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n</br>Parameters, Wald tests and Wald-based confidence intervals\n</br> W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n</br> And Wald-based confidence intervals plus and minus 1.96 * W \n </br> It might be better to visualize the covariance matrix. See the page '<a href=\"%s\">Matrix of variance-covariance of one-step probabilities and its graphs</a>'.\n</br>",optionfilehtmcov);
1.319     brouard  12635:       fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
                   12636:       fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
                   12637:       if(nagesqr==1){
                   12638:        printf("  + age*age  ");
                   12639:        fprintf(ficres,"  + age*age  ");
                   12640:        fprintf(ficlog,"  + age*age  ");
                   12641:        fprintf(fichtm, "<th>+ age*age</th>");
                   12642:       }
                   12643:       for(j=1;j <=ncovmodel-2;j++){
                   12644:        if(Typevar[j]==0) {
                   12645:          printf("  +      V%d  ",Tvar[j]);
                   12646:          fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
                   12647:        }else if(Typevar[j]==1) {
                   12648:          printf("  +    V%d*age ",Tvar[j]);
                   12649:          fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
                   12650:        }else if(Typevar[j]==2) {
                   12651:          fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   12652:        }
                   12653:       }
                   12654:       fprintf(fichtm, "</tr>\n");
                   12655:  
1.203     brouard  12656:       for(i=1,jk=1; i <=nlstate; i++){
1.225     brouard  12657:        for(k=1; k <=(nlstate+ndeath); k++){
                   12658:          if (k != i) {
1.319     brouard  12659:            fprintf(fichtm, "<tr valign=top>");
1.225     brouard  12660:            printf("%d%d ",i,k);
                   12661:            fprintf(ficlog,"%d%d ",i,k);
1.319     brouard  12662:            fprintf(fichtm, "<td>%1d%1d</td>",i,k);
1.225     brouard  12663:            for(j=1; j <=ncovmodel; j++){
1.319     brouard  12664:              wald=p[jk]/sqrt(matcov[jk][jk]);
1.324     brouard  12665:              printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                   12666:              fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
1.319     brouard  12667:              if(fabs(wald) > 1.96){
1.321     brouard  12668:                fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
1.319     brouard  12669:              }else{
                   12670:                fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
                   12671:              }
1.324     brouard  12672:              fprintf(fichtm,"W=%8.3f</br>",wald);
1.319     brouard  12673:              fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
1.225     brouard  12674:              jk++; 
                   12675:            }
                   12676:            printf("\n");
                   12677:            fprintf(ficlog,"\n");
1.319     brouard  12678:            fprintf(fichtm, "</tr>\n");
1.225     brouard  12679:          }
                   12680:        }
1.193     brouard  12681:       }
1.203     brouard  12682:     } /* end of hesscov and Wald tests */
1.319     brouard  12683:     fprintf(fichtm,"</table>\n");
1.225     brouard  12684:     
1.203     brouard  12685:     /*  */
1.126     brouard  12686:     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
                   12687:     printf("# Scales (for hessian or gradient estimation)\n");
                   12688:     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
                   12689:     for(i=1,jk=1; i <=nlstate; i++){
                   12690:       for(j=1; j <=nlstate+ndeath; j++){
1.225     brouard  12691:        if (j!=i) {
                   12692:          fprintf(ficres,"%1d%1d",i,j);
                   12693:          printf("%1d%1d",i,j);
                   12694:          fprintf(ficlog,"%1d%1d",i,j);
                   12695:          for(k=1; k<=ncovmodel;k++){
                   12696:            printf(" %.5e",delti[jk]);
                   12697:            fprintf(ficlog," %.5e",delti[jk]);
                   12698:            fprintf(ficres," %.5e",delti[jk]);
                   12699:            jk++;
                   12700:          }
                   12701:          printf("\n");
                   12702:          fprintf(ficlog,"\n");
                   12703:          fprintf(ficres,"\n");
                   12704:        }
1.126     brouard  12705:       }
                   12706:     }
                   12707:     
                   12708:     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
1.203     brouard  12709:     if(mle >= 1) /* To big for the screen */
1.126     brouard  12710:       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
                   12711:     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
                   12712:     /* # 121 Var(a12)\n\ */
                   12713:     /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   12714:     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   12715:     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   12716:     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   12717:     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   12718:     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   12719:     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   12720:     
                   12721:     
                   12722:     /* Just to have a covariance matrix which will be more understandable
                   12723:        even is we still don't want to manage dictionary of variables
                   12724:     */
                   12725:     for(itimes=1;itimes<=2;itimes++){
                   12726:       jj=0;
                   12727:       for(i=1; i <=nlstate; i++){
1.225     brouard  12728:        for(j=1; j <=nlstate+ndeath; j++){
                   12729:          if(j==i) continue;
                   12730:          for(k=1; k<=ncovmodel;k++){
                   12731:            jj++;
                   12732:            ca[0]= k+'a'-1;ca[1]='\0';
                   12733:            if(itimes==1){
                   12734:              if(mle>=1)
                   12735:                printf("#%1d%1d%d",i,j,k);
                   12736:              fprintf(ficlog,"#%1d%1d%d",i,j,k);
                   12737:              fprintf(ficres,"#%1d%1d%d",i,j,k);
                   12738:            }else{
                   12739:              if(mle>=1)
                   12740:                printf("%1d%1d%d",i,j,k);
                   12741:              fprintf(ficlog,"%1d%1d%d",i,j,k);
                   12742:              fprintf(ficres,"%1d%1d%d",i,j,k);
                   12743:            }
                   12744:            ll=0;
                   12745:            for(li=1;li <=nlstate; li++){
                   12746:              for(lj=1;lj <=nlstate+ndeath; lj++){
                   12747:                if(lj==li) continue;
                   12748:                for(lk=1;lk<=ncovmodel;lk++){
                   12749:                  ll++;
                   12750:                  if(ll<=jj){
                   12751:                    cb[0]= lk +'a'-1;cb[1]='\0';
                   12752:                    if(ll<jj){
                   12753:                      if(itimes==1){
                   12754:                        if(mle>=1)
                   12755:                          printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   12756:                        fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   12757:                        fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   12758:                      }else{
                   12759:                        if(mle>=1)
                   12760:                          printf(" %.5e",matcov[jj][ll]); 
                   12761:                        fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   12762:                        fprintf(ficres," %.5e",matcov[jj][ll]); 
                   12763:                      }
                   12764:                    }else{
                   12765:                      if(itimes==1){
                   12766:                        if(mle>=1)
                   12767:                          printf(" Var(%s%1d%1d)",ca,i,j);
                   12768:                        fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                   12769:                        fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                   12770:                      }else{
                   12771:                        if(mle>=1)
                   12772:                          printf(" %.7e",matcov[jj][ll]); 
                   12773:                        fprintf(ficlog," %.7e",matcov[jj][ll]); 
                   12774:                        fprintf(ficres," %.7e",matcov[jj][ll]); 
                   12775:                      }
                   12776:                    }
                   12777:                  }
                   12778:                } /* end lk */
                   12779:              } /* end lj */
                   12780:            } /* end li */
                   12781:            if(mle>=1)
                   12782:              printf("\n");
                   12783:            fprintf(ficlog,"\n");
                   12784:            fprintf(ficres,"\n");
                   12785:            numlinepar++;
                   12786:          } /* end k*/
                   12787:        } /*end j */
1.126     brouard  12788:       } /* end i */
                   12789:     } /* end itimes */
                   12790:     
                   12791:     fflush(ficlog);
                   12792:     fflush(ficres);
1.225     brouard  12793:     while(fgets(line, MAXLINE, ficpar)) {
                   12794:       /* If line starts with a # it is a comment */
                   12795:       if (line[0] == '#') {
                   12796:        numlinepar++;
                   12797:        fputs(line,stdout);
                   12798:        fputs(line,ficparo);
                   12799:        fputs(line,ficlog);
1.299     brouard  12800:        fputs(line,ficres);
1.225     brouard  12801:        continue;
                   12802:       }else
                   12803:        break;
                   12804:     }
                   12805:     
1.209     brouard  12806:     /* while((c=getc(ficpar))=='#' && c!= EOF){ */
                   12807:     /*   ungetc(c,ficpar); */
                   12808:     /*   fgets(line, MAXLINE, ficpar); */
                   12809:     /*   fputs(line,stdout); */
                   12810:     /*   fputs(line,ficparo); */
                   12811:     /* } */
                   12812:     /* ungetc(c,ficpar); */
1.126     brouard  12813:     
                   12814:     estepm=0;
1.209     brouard  12815:     if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
1.225     brouard  12816:       
                   12817:       if (num_filled != 6) {
                   12818:        printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
                   12819:        fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
                   12820:        goto end;
                   12821:       }
                   12822:       printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
                   12823:     }
                   12824:     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
                   12825:     /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
                   12826:     
1.209     brouard  12827:     /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126     brouard  12828:     if (estepm==0 || estepm < stepm) estepm=stepm;
                   12829:     if (fage <= 2) {
                   12830:       bage = ageminpar;
                   12831:       fage = agemaxpar;
                   12832:     }
                   12833:     
                   12834:     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211     brouard  12835:     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                   12836:     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220     brouard  12837:                
1.186     brouard  12838:     /* Other stuffs, more or less useful */    
1.254     brouard  12839:     while(fgets(line, MAXLINE, ficpar)) {
                   12840:       /* If line starts with a # it is a comment */
                   12841:       if (line[0] == '#') {
                   12842:        numlinepar++;
                   12843:        fputs(line,stdout);
                   12844:        fputs(line,ficparo);
                   12845:        fputs(line,ficlog);
1.299     brouard  12846:        fputs(line,ficres);
1.254     brouard  12847:        continue;
                   12848:       }else
                   12849:        break;
                   12850:     }
                   12851: 
                   12852:     if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
                   12853:       
                   12854:       if (num_filled != 7) {
                   12855:        printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
                   12856:        fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
                   12857:        goto end;
                   12858:       }
                   12859:       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   12860:       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   12861:       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   12862:       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.126     brouard  12863:     }
1.254     brouard  12864: 
                   12865:     while(fgets(line, MAXLINE, ficpar)) {
                   12866:       /* If line starts with a # it is a comment */
                   12867:       if (line[0] == '#') {
                   12868:        numlinepar++;
                   12869:        fputs(line,stdout);
                   12870:        fputs(line,ficparo);
                   12871:        fputs(line,ficlog);
1.299     brouard  12872:        fputs(line,ficres);
1.254     brouard  12873:        continue;
                   12874:       }else
                   12875:        break;
1.126     brouard  12876:     }
                   12877:     
                   12878:     
                   12879:     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
                   12880:     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
                   12881:     
1.254     brouard  12882:     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
                   12883:       if (num_filled != 1) {
                   12884:        printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
                   12885:        fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
                   12886:        goto end;
                   12887:       }
                   12888:       printf("pop_based=%d\n",popbased);
                   12889:       fprintf(ficlog,"pop_based=%d\n",popbased);
                   12890:       fprintf(ficparo,"pop_based=%d\n",popbased);   
                   12891:       fprintf(ficres,"pop_based=%d\n",popbased);   
                   12892:     }
                   12893:      
1.258     brouard  12894:     /* Results */
1.307     brouard  12895:     endishere=0;
1.258     brouard  12896:     nresult=0;
1.308     brouard  12897:     parameterline=0;
1.258     brouard  12898:     do{
                   12899:       if(!fgets(line, MAXLINE, ficpar)){
                   12900:        endishere=1;
1.308     brouard  12901:        parameterline=15;
1.258     brouard  12902:       }else if (line[0] == '#') {
                   12903:        /* If line starts with a # it is a comment */
1.254     brouard  12904:        numlinepar++;
                   12905:        fputs(line,stdout);
                   12906:        fputs(line,ficparo);
                   12907:        fputs(line,ficlog);
1.299     brouard  12908:        fputs(line,ficres);
1.254     brouard  12909:        continue;
1.258     brouard  12910:       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
                   12911:        parameterline=11;
1.296     brouard  12912:       else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258     brouard  12913:        parameterline=12;
1.307     brouard  12914:       else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
1.258     brouard  12915:        parameterline=13;
1.307     brouard  12916:       }
1.258     brouard  12917:       else{
                   12918:        parameterline=14;
1.254     brouard  12919:       }
1.308     brouard  12920:       switch (parameterline){ /* =0 only if only comments */
1.258     brouard  12921:       case 11:
1.296     brouard  12922:        if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
                   12923:                  fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.258     brouard  12924:          printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
                   12925:          fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
                   12926:          fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
                   12927:          /* day and month of proj2 are not used but only year anproj2.*/
1.273     brouard  12928:          dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
                   12929:          dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296     brouard  12930:           prvforecast = 1;
                   12931:        } 
                   12932:        else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.313     brouard  12933:          printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
                   12934:          fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
                   12935:          fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296     brouard  12936:           prvforecast = 2;
                   12937:        }
                   12938:        else {
                   12939:          printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
                   12940:          fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
                   12941:          goto end;
1.258     brouard  12942:        }
1.254     brouard  12943:        break;
1.258     brouard  12944:       case 12:
1.296     brouard  12945:        if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
                   12946:           fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
                   12947:          printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
                   12948:          fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
                   12949:          fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
                   12950:          /* day and month of back2 are not used but only year anback2.*/
1.273     brouard  12951:          dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
                   12952:          dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296     brouard  12953:           prvbackcast = 1;
                   12954:        } 
                   12955:        else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.313     brouard  12956:          printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
                   12957:          fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
                   12958:          fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296     brouard  12959:           prvbackcast = 2;
                   12960:        }
                   12961:        else {
                   12962:          printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
                   12963:          fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
                   12964:          goto end;
1.258     brouard  12965:        }
1.230     brouard  12966:        break;
1.258     brouard  12967:       case 13:
1.307     brouard  12968:        num_filled=sscanf(line,"result:%[^\n]\n",resultline);
                   12969:        nresult++; /* Sum of resultlines */
                   12970:        printf("Result %d: result:%s\n",nresult, resultline);
1.318     brouard  12971:        if(nresult > MAXRESULTLINESPONE-1){
                   12972:          printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
                   12973:          fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
1.307     brouard  12974:          goto end;
                   12975:        }
1.310     brouard  12976:        if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.314     brouard  12977:          fprintf(ficparo,"result: %s\n",resultline);
                   12978:          fprintf(ficres,"result: %s\n",resultline);
                   12979:          fprintf(ficlog,"result: %s\n",resultline);
1.310     brouard  12980:        } else
                   12981:          goto end;
1.307     brouard  12982:        break;
                   12983:       case 14:
                   12984:        printf("Error: Unknown command '%s'\n",line);
                   12985:        fprintf(ficlog,"Error: Unknown command '%s'\n",line);
1.314     brouard  12986:        if(line[0] == ' ' || line[0] == '\n'){
                   12987:          printf("It should not be an empty line '%s'\n",line);
                   12988:          fprintf(ficlog,"It should not be an empty line '%s'\n",line);
                   12989:        }         
1.307     brouard  12990:        if(ncovmodel >=2 && nresult==0 ){
                   12991:          printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
                   12992:          fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258     brouard  12993:        }
1.307     brouard  12994:        /* goto end; */
                   12995:        break;
1.308     brouard  12996:       case 15:
                   12997:        printf("End of resultlines.\n");
                   12998:        fprintf(ficlog,"End of resultlines.\n");
                   12999:        break;
                   13000:       default: /* parameterline =0 */
1.307     brouard  13001:        nresult=1;
                   13002:        decoderesult(".",nresult ); /* No covariate */
1.258     brouard  13003:       } /* End switch parameterline */
                   13004:     }while(endishere==0); /* End do */
1.126     brouard  13005:     
1.230     brouard  13006:     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145     brouard  13007:     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126     brouard  13008:     
                   13009:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194     brouard  13010:     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230     brouard  13011:       printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194     brouard  13012: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   13013: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230     brouard  13014:       fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194     brouard  13015: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   13016: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220     brouard  13017:     }else{
1.270     brouard  13018:       /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296     brouard  13019:       /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
                   13020:       /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
                   13021:       if(prvforecast==1){
                   13022:         dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
                   13023:         jprojd=jproj1;
                   13024:         mprojd=mproj1;
                   13025:         anprojd=anproj1;
                   13026:         dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
                   13027:         jprojf=jproj2;
                   13028:         mprojf=mproj2;
                   13029:         anprojf=anproj2;
                   13030:       } else if(prvforecast == 2){
                   13031:         dateprojd=dateintmean;
                   13032:         date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
                   13033:         dateprojf=dateintmean+yrfproj;
                   13034:         date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
                   13035:       }
                   13036:       if(prvbackcast==1){
                   13037:         datebackd=(jback1+12*mback1+365*anback1)/365;
                   13038:         jbackd=jback1;
                   13039:         mbackd=mback1;
                   13040:         anbackd=anback1;
                   13041:         datebackf=(jback2+12*mback2+365*anback2)/365;
                   13042:         jbackf=jback2;
                   13043:         mbackf=mback2;
                   13044:         anbackf=anback2;
                   13045:       } else if(prvbackcast == 2){
                   13046:         datebackd=dateintmean;
                   13047:         date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
                   13048:         datebackf=dateintmean-yrbproj;
                   13049:         date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
                   13050:       }
                   13051:       
                   13052:       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220     brouard  13053:     }
                   13054:     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296     brouard  13055:                 model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
                   13056:                 jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220     brouard  13057:                
1.225     brouard  13058:     /*------------ free_vector  -------------*/
                   13059:     /*  chdir(path); */
1.220     brouard  13060:                
1.215     brouard  13061:     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
                   13062:     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
                   13063:     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
                   13064:     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
1.290     brouard  13065:     free_lvector(num,firstobs,lastobs);
                   13066:     free_vector(agedc,firstobs,lastobs);
1.126     brouard  13067:     /*free_matrix(covar,0,NCOVMAX,1,n);*/
                   13068:     /*free_matrix(covar,1,NCOVMAX,1,n);*/
                   13069:     fclose(ficparo);
                   13070:     fclose(ficres);
1.220     brouard  13071:                
                   13072:                
1.186     brouard  13073:     /* Other results (useful)*/
1.220     brouard  13074:                
                   13075:                
1.126     brouard  13076:     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
1.180     brouard  13077:     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
                   13078:     prlim=matrix(1,nlstate,1,nlstate);
1.209     brouard  13079:     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126     brouard  13080:     fclose(ficrespl);
                   13081: 
                   13082:     /*------------- h Pij x at various ages ------------*/
1.180     brouard  13083:     /*#include "hpijx.h"*/
                   13084:     hPijx(p, bage, fage);
1.145     brouard  13085:     fclose(ficrespij);
1.227     brouard  13086:     
1.220     brouard  13087:     /* ncovcombmax=  pow(2,cptcoveff); */
1.219     brouard  13088:     /*-------------- Variance of one-step probabilities---*/
1.145     brouard  13089:     k=1;
1.126     brouard  13090:     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227     brouard  13091:     
1.269     brouard  13092:     /* Prevalence for each covariate combination in probs[age][status][cov] */
                   13093:     probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
                   13094:     for(i=AGEINF;i<=AGESUP;i++)
1.219     brouard  13095:       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225     brouard  13096:        for(k=1;k<=ncovcombmax;k++)
                   13097:          probs[i][j][k]=0.;
1.269     brouard  13098:     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, 
                   13099:               ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219     brouard  13100:     if (mobilav!=0 ||mobilavproj !=0 ) {
1.269     brouard  13101:       mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
                   13102:       for(i=AGEINF;i<=AGESUP;i++)
1.268     brouard  13103:        for(j=1;j<=nlstate+ndeath;j++)
1.227     brouard  13104:          for(k=1;k<=ncovcombmax;k++)
                   13105:            mobaverages[i][j][k]=0.;
1.219     brouard  13106:       mobaverage=mobaverages;
                   13107:       if (mobilav!=0) {
1.235     brouard  13108:        printf("Movingaveraging observed prevalence\n");
1.258     brouard  13109:        fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227     brouard  13110:        if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
                   13111:          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   13112:          printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   13113:        }
1.269     brouard  13114:       } else if (mobilavproj !=0) {
1.235     brouard  13115:        printf("Movingaveraging projected observed prevalence\n");
1.258     brouard  13116:        fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227     brouard  13117:        if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
                   13118:          fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
                   13119:          printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
                   13120:        }
1.269     brouard  13121:       }else{
                   13122:        printf("Internal error moving average\n");
                   13123:        fflush(stdout);
                   13124:        exit(1);
1.219     brouard  13125:       }
                   13126:     }/* end if moving average */
1.227     brouard  13127:     
1.126     brouard  13128:     /*---------- Forecasting ------------------*/
1.296     brouard  13129:     if(prevfcast==1){ 
                   13130:       /*   /\*    if(stepm ==1){*\/ */
                   13131:       /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
                   13132:       /*This done previously after freqsummary.*/
                   13133:       /*   dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
                   13134:       /*   dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
                   13135:       
                   13136:       /* } else if (prvforecast==2){ */
                   13137:       /*   /\*    if(stepm ==1){*\/ */
                   13138:       /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
                   13139:       /* } */
                   13140:       /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
                   13141:       prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126     brouard  13142:     }
1.269     brouard  13143: 
1.296     brouard  13144:     /* Prevbcasting */
                   13145:     if(prevbcast==1){
1.219     brouard  13146:       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);       
                   13147:       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);       
                   13148:       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
                   13149: 
                   13150:       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
                   13151: 
                   13152:       bprlim=matrix(1,nlstate,1,nlstate);
1.269     brouard  13153: 
1.219     brouard  13154:       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
                   13155:       fclose(ficresplb);
                   13156: 
1.222     brouard  13157:       hBijx(p, bage, fage, mobaverage);
                   13158:       fclose(ficrespijb);
1.219     brouard  13159: 
1.296     brouard  13160:       /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
                   13161:       /* /\*                  mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
                   13162:       /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
                   13163:       /*                      mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
                   13164:       prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
                   13165:                       mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
                   13166: 
                   13167:       
1.269     brouard  13168:       varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268     brouard  13169: 
                   13170:       
1.269     brouard  13171:       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219     brouard  13172:       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
                   13173:       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
                   13174:       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296     brouard  13175:     }    /* end  Prevbcasting */
1.268     brouard  13176:  
1.186     brouard  13177:  
                   13178:     /* ------ Other prevalence ratios------------ */
1.126     brouard  13179: 
1.215     brouard  13180:     free_ivector(wav,1,imx);
                   13181:     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
                   13182:     free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
                   13183:     free_imatrix(mw,1,lastpass-firstpass+2,1,imx);   
1.218     brouard  13184:                
                   13185:                
1.127     brouard  13186:     /*---------- Health expectancies, no variances ------------*/
1.218     brouard  13187:                
1.201     brouard  13188:     strcpy(filerese,"E_");
                   13189:     strcat(filerese,fileresu);
1.126     brouard  13190:     if((ficreseij=fopen(filerese,"w"))==NULL) {
                   13191:       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   13192:       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   13193:     }
1.208     brouard  13194:     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
                   13195:     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238     brouard  13196: 
                   13197:     pstamp(ficreseij);
1.219     brouard  13198:                
1.235     brouard  13199:     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
                   13200:     if (cptcovn < 1){i1=1;}
                   13201:     
                   13202:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   13203:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253     brouard  13204:       if(i1 != 1 && TKresult[nres]!= k)
1.235     brouard  13205:        continue;
1.219     brouard  13206:       fprintf(ficreseij,"\n#****** ");
1.235     brouard  13207:       printf("\n#****** ");
1.225     brouard  13208:       for(j=1;j<=cptcoveff;j++) {
1.227     brouard  13209:        fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235     brouard  13210:        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   13211:       }
                   13212:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   13213:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   13214:        fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219     brouard  13215:       }
                   13216:       fprintf(ficreseij,"******\n");
1.235     brouard  13217:       printf("******\n");
1.219     brouard  13218:       
                   13219:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   13220:       oldm=oldms;savm=savms;
1.235     brouard  13221:       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
1.127     brouard  13222:       
1.219     brouard  13223:       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127     brouard  13224:     }
                   13225:     fclose(ficreseij);
1.208     brouard  13226:     printf("done evsij\n");fflush(stdout);
                   13227:     fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269     brouard  13228: 
1.218     brouard  13229:                
1.227     brouard  13230:     /*---------- State-specific expectancies and variances ------------*/
1.218     brouard  13231:                
1.201     brouard  13232:     strcpy(filerest,"T_");
                   13233:     strcat(filerest,fileresu);
1.127     brouard  13234:     if((ficrest=fopen(filerest,"w"))==NULL) {
                   13235:       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
                   13236:       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
                   13237:     }
1.208     brouard  13238:     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
                   13239:     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201     brouard  13240:     strcpy(fileresstde,"STDE_");
                   13241:     strcat(fileresstde,fileresu);
1.126     brouard  13242:     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227     brouard  13243:       printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
                   13244:       fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126     brouard  13245:     }
1.227     brouard  13246:     printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
                   13247:     fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126     brouard  13248: 
1.201     brouard  13249:     strcpy(filerescve,"CVE_");
                   13250:     strcat(filerescve,fileresu);
1.126     brouard  13251:     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227     brouard  13252:       printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
                   13253:       fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126     brouard  13254:     }
1.227     brouard  13255:     printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
                   13256:     fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126     brouard  13257: 
1.201     brouard  13258:     strcpy(fileresv,"V_");
                   13259:     strcat(fileresv,fileresu);
1.126     brouard  13260:     if((ficresvij=fopen(fileresv,"w"))==NULL) {
                   13261:       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
                   13262:       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
                   13263:     }
1.227     brouard  13264:     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
                   13265:     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126     brouard  13266: 
1.235     brouard  13267:     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
                   13268:     if (cptcovn < 1){i1=1;}
                   13269:     
                   13270:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   13271:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253     brouard  13272:       if(i1 != 1 && TKresult[nres]!= k)
1.235     brouard  13273:        continue;
1.321     brouard  13274:       printf("\n# model %s \n#****** Result for:", model);
                   13275:       fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
                   13276:       fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
1.227     brouard  13277:       for(j=1;j<=cptcoveff;j++){ 
                   13278:        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   13279:        fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   13280:        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   13281:       }
1.235     brouard  13282:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   13283:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   13284:        fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   13285:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   13286:       }        
1.208     brouard  13287:       fprintf(ficrest,"******\n");
1.227     brouard  13288:       fprintf(ficlog,"******\n");
                   13289:       printf("******\n");
1.208     brouard  13290:       
                   13291:       fprintf(ficresstdeij,"\n#****** ");
                   13292:       fprintf(ficrescveij,"\n#****** ");
1.225     brouard  13293:       for(j=1;j<=cptcoveff;j++) {
1.227     brouard  13294:        fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   13295:        fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208     brouard  13296:       }
1.235     brouard  13297:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   13298:        fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   13299:        fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   13300:       }        
1.208     brouard  13301:       fprintf(ficresstdeij,"******\n");
                   13302:       fprintf(ficrescveij,"******\n");
                   13303:       
                   13304:       fprintf(ficresvij,"\n#****** ");
1.238     brouard  13305:       /* pstamp(ficresvij); */
1.225     brouard  13306:       for(j=1;j<=cptcoveff;j++) 
1.227     brouard  13307:        fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235     brouard  13308:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   13309:        fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   13310:       }        
1.208     brouard  13311:       fprintf(ficresvij,"******\n");
                   13312:       
                   13313:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   13314:       oldm=oldms;savm=savms;
1.235     brouard  13315:       printf(" cvevsij ");
                   13316:       fprintf(ficlog, " cvevsij ");
                   13317:       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208     brouard  13318:       printf(" end cvevsij \n ");
                   13319:       fprintf(ficlog, " end cvevsij \n ");
                   13320:       
                   13321:       /*
                   13322:        */
                   13323:       /* goto endfree; */
                   13324:       
                   13325:       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   13326:       pstamp(ficrest);
                   13327:       
1.269     brouard  13328:       epj=vector(1,nlstate+1);
1.208     brouard  13329:       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227     brouard  13330:        oldm=oldms;savm=savms; /* ZZ Segmentation fault */
                   13331:        cptcod= 0; /* To be deleted */
                   13332:        printf("varevsij vpopbased=%d \n",vpopbased);
                   13333:        fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235     brouard  13334:        varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
1.227     brouard  13335:        fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
                   13336:        if(vpopbased==1)
                   13337:          fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
                   13338:        else
1.288     brouard  13339:          fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227     brouard  13340:        fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
                   13341:        for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                   13342:        fprintf(ficrest,"\n");
                   13343:        /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288     brouard  13344:        printf("Computing age specific forward period (stable) prevalences in each health state \n");
                   13345:        fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227     brouard  13346:        for(age=bage; age <=fage ;age++){
1.235     brouard  13347:          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227     brouard  13348:          if (vpopbased==1) {
                   13349:            if(mobilav ==0){
                   13350:              for(i=1; i<=nlstate;i++)
                   13351:                prlim[i][i]=probs[(int)age][i][k];
                   13352:            }else{ /* mobilav */ 
                   13353:              for(i=1; i<=nlstate;i++)
                   13354:                prlim[i][i]=mobaverage[(int)age][i][k];
                   13355:            }
                   13356:          }
1.219     brouard  13357:          
1.227     brouard  13358:          fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
                   13359:          /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
                   13360:          /* printf(" age %4.0f ",age); */
                   13361:          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                   13362:            for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   13363:              epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   13364:              /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                   13365:              /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
                   13366:            }
                   13367:            epj[nlstate+1] +=epj[j];
                   13368:          }
                   13369:          /* printf(" age %4.0f \n",age); */
1.219     brouard  13370:          
1.227     brouard  13371:          for(i=1, vepp=0.;i <=nlstate;i++)
                   13372:            for(j=1;j <=nlstate;j++)
                   13373:              vepp += vareij[i][j][(int)age];
                   13374:          fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                   13375:          for(j=1;j <=nlstate;j++){
                   13376:            fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                   13377:          }
                   13378:          fprintf(ficrest,"\n");
                   13379:        }
1.208     brouard  13380:       } /* End vpopbased */
1.269     brouard  13381:       free_vector(epj,1,nlstate+1);
1.208     brouard  13382:       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   13383:       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235     brouard  13384:       printf("done selection\n");fflush(stdout);
                   13385:       fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208     brouard  13386:       
1.235     brouard  13387:     } /* End k selection */
1.227     brouard  13388: 
                   13389:     printf("done State-specific expectancies\n");fflush(stdout);
                   13390:     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
                   13391: 
1.288     brouard  13392:     /* variance-covariance of forward period prevalence*/
1.269     brouard  13393:     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268     brouard  13394: 
1.227     brouard  13395:     
1.290     brouard  13396:     free_vector(weight,firstobs,lastobs);
1.227     brouard  13397:     free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290     brouard  13398:     free_imatrix(s,1,maxwav+1,firstobs,lastobs);
                   13399:     free_matrix(anint,1,maxwav,firstobs,lastobs); 
                   13400:     free_matrix(mint,1,maxwav,firstobs,lastobs);
                   13401:     free_ivector(cod,firstobs,lastobs);
1.227     brouard  13402:     free_ivector(tab,1,NCOVMAX);
                   13403:     fclose(ficresstdeij);
                   13404:     fclose(ficrescveij);
                   13405:     fclose(ficresvij);
                   13406:     fclose(ficrest);
                   13407:     fclose(ficpar);
                   13408:     
                   13409:     
1.126     brouard  13410:     /*---------- End : free ----------------*/
1.219     brouard  13411:     if (mobilav!=0 ||mobilavproj !=0)
1.269     brouard  13412:       free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
                   13413:     free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220     brouard  13414:     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
                   13415:     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126     brouard  13416:   }  /* mle==-3 arrives here for freeing */
1.227     brouard  13417:   /* endfree:*/
                   13418:   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   13419:   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   13420:   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290     brouard  13421:   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
                   13422:   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
                   13423:   if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
                   13424:   free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227     brouard  13425:   free_matrix(matcov,1,npar,1,npar);
                   13426:   free_matrix(hess,1,npar,1,npar);
                   13427:   /*free_vector(delti,1,npar);*/
                   13428:   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   13429:   free_matrix(agev,1,maxwav,1,imx);
1.269     brouard  13430:   free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227     brouard  13431:   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
                   13432:   
                   13433:   free_ivector(ncodemax,1,NCOVMAX);
                   13434:   free_ivector(ncodemaxwundef,1,NCOVMAX);
                   13435:   free_ivector(Dummy,-1,NCOVMAX);
                   13436:   free_ivector(Fixed,-1,NCOVMAX);
1.238     brouard  13437:   free_ivector(DummyV,1,NCOVMAX);
                   13438:   free_ivector(FixedV,1,NCOVMAX);
1.227     brouard  13439:   free_ivector(Typevar,-1,NCOVMAX);
                   13440:   free_ivector(Tvar,1,NCOVMAX);
1.234     brouard  13441:   free_ivector(TvarsQ,1,NCOVMAX);
                   13442:   free_ivector(TvarsQind,1,NCOVMAX);
                   13443:   free_ivector(TvarsD,1,NCOVMAX);
                   13444:   free_ivector(TvarsDind,1,NCOVMAX);
1.231     brouard  13445:   free_ivector(TvarFD,1,NCOVMAX);
                   13446:   free_ivector(TvarFDind,1,NCOVMAX);
1.232     brouard  13447:   free_ivector(TvarF,1,NCOVMAX);
                   13448:   free_ivector(TvarFind,1,NCOVMAX);
                   13449:   free_ivector(TvarV,1,NCOVMAX);
                   13450:   free_ivector(TvarVind,1,NCOVMAX);
                   13451:   free_ivector(TvarA,1,NCOVMAX);
                   13452:   free_ivector(TvarAind,1,NCOVMAX);
1.231     brouard  13453:   free_ivector(TvarFQ,1,NCOVMAX);
                   13454:   free_ivector(TvarFQind,1,NCOVMAX);
                   13455:   free_ivector(TvarVD,1,NCOVMAX);
                   13456:   free_ivector(TvarVDind,1,NCOVMAX);
                   13457:   free_ivector(TvarVQ,1,NCOVMAX);
                   13458:   free_ivector(TvarVQind,1,NCOVMAX);
1.230     brouard  13459:   free_ivector(Tvarsel,1,NCOVMAX);
                   13460:   free_vector(Tvalsel,1,NCOVMAX);
1.227     brouard  13461:   free_ivector(Tposprod,1,NCOVMAX);
                   13462:   free_ivector(Tprod,1,NCOVMAX);
                   13463:   free_ivector(Tvaraff,1,NCOVMAX);
                   13464:   free_ivector(invalidvarcomb,1,ncovcombmax);
                   13465:   free_ivector(Tage,1,NCOVMAX);
                   13466:   free_ivector(Tmodelind,1,NCOVMAX);
1.228     brouard  13467:   free_ivector(TmodelInvind,1,NCOVMAX);
                   13468:   free_ivector(TmodelInvQind,1,NCOVMAX);
1.227     brouard  13469:   
                   13470:   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
                   13471:   /* free_imatrix(codtab,1,100,1,10); */
1.126     brouard  13472:   fflush(fichtm);
                   13473:   fflush(ficgp);
                   13474:   
1.227     brouard  13475:   
1.126     brouard  13476:   if((nberr >0) || (nbwarn>0)){
1.216     brouard  13477:     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
                   13478:     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
1.126     brouard  13479:   }else{
                   13480:     printf("End of Imach\n");
                   13481:     fprintf(ficlog,"End of Imach\n");
                   13482:   }
                   13483:   printf("See log file on %s\n",filelog);
                   13484:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
1.157     brouard  13485:   /*(void) gettimeofday(&end_time,&tzp);*/
                   13486:   rend_time = time(NULL);  
                   13487:   end_time = *localtime(&rend_time);
                   13488:   /* tml = *localtime(&end_time.tm_sec); */
                   13489:   strcpy(strtend,asctime(&end_time));
1.126     brouard  13490:   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
                   13491:   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
1.157     brouard  13492:   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227     brouard  13493:   
1.157     brouard  13494:   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
                   13495:   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
                   13496:   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126     brouard  13497:   /*  printf("Total time was %d uSec.\n", total_usecs);*/
                   13498: /*   if(fileappend(fichtm,optionfilehtm)){ */
                   13499:   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   13500:   fclose(fichtm);
                   13501:   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   13502:   fclose(fichtmcov);
                   13503:   fclose(ficgp);
                   13504:   fclose(ficlog);
                   13505:   /*------ End -----------*/
1.227     brouard  13506:   
1.281     brouard  13507: 
                   13508: /* Executes gnuplot */
1.227     brouard  13509:   
                   13510:   printf("Before Current directory %s!\n",pathcd);
1.184     brouard  13511: #ifdef WIN32
1.227     brouard  13512:   if (_chdir(pathcd) != 0)
                   13513:     printf("Can't move to directory %s!\n",path);
                   13514:   if(_getcwd(pathcd,MAXLINE) > 0)
1.184     brouard  13515: #else
1.227     brouard  13516:     if(chdir(pathcd) != 0)
                   13517:       printf("Can't move to directory %s!\n", path);
                   13518:   if (getcwd(pathcd, MAXLINE) > 0)
1.184     brouard  13519: #endif 
1.126     brouard  13520:     printf("Current directory %s!\n",pathcd);
                   13521:   /*strcat(plotcmd,CHARSEPARATOR);*/
                   13522:   sprintf(plotcmd,"gnuplot");
1.157     brouard  13523: #ifdef _WIN32
1.126     brouard  13524:   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
                   13525: #endif
                   13526:   if(!stat(plotcmd,&info)){
1.158     brouard  13527:     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126     brouard  13528:     if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158     brouard  13529:       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126     brouard  13530:     }else
                   13531:       strcpy(pplotcmd,plotcmd);
1.157     brouard  13532: #ifdef __unix
1.126     brouard  13533:     strcpy(plotcmd,GNUPLOTPROGRAM);
                   13534:     if(!stat(plotcmd,&info)){
1.158     brouard  13535:       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126     brouard  13536:     }else
                   13537:       strcpy(pplotcmd,plotcmd);
                   13538: #endif
                   13539:   }else
                   13540:     strcpy(pplotcmd,plotcmd);
                   13541:   
                   13542:   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158     brouard  13543:   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292     brouard  13544:   strcpy(pplotcmd,plotcmd);
1.227     brouard  13545:   
1.126     brouard  13546:   if((outcmd=system(plotcmd)) != 0){
1.292     brouard  13547:     printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154     brouard  13548:     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152     brouard  13549:     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292     brouard  13550:     if((outcmd=system(plotcmd)) != 0){
1.153     brouard  13551:       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292     brouard  13552:       strcpy(plotcmd,pplotcmd);
                   13553:     }
1.126     brouard  13554:   }
1.158     brouard  13555:   printf(" Successful, please wait...");
1.126     brouard  13556:   while (z[0] != 'q') {
                   13557:     /* chdir(path); */
1.154     brouard  13558:     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126     brouard  13559:     scanf("%s",z);
                   13560: /*     if (z[0] == 'c') system("./imach"); */
                   13561:     if (z[0] == 'e') {
1.158     brouard  13562: #ifdef __APPLE__
1.152     brouard  13563:       sprintf(pplotcmd, "open %s", optionfilehtm);
1.157     brouard  13564: #elif __linux
                   13565:       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153     brouard  13566: #else
1.152     brouard  13567:       sprintf(pplotcmd, "%s", optionfilehtm);
1.153     brouard  13568: #endif
                   13569:       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
                   13570:       system(pplotcmd);
1.126     brouard  13571:     }
                   13572:     else if (z[0] == 'g') system(plotcmd);
                   13573:     else if (z[0] == 'q') exit(0);
                   13574:   }
1.227     brouard  13575: end:
1.126     brouard  13576:   while (z[0] != 'q') {
1.195     brouard  13577:     printf("\nType  q for exiting: "); fflush(stdout);
1.126     brouard  13578:     scanf("%s",z);
                   13579:   }
1.283     brouard  13580:   printf("End\n");
1.282     brouard  13581:   exit(0);
1.126     brouard  13582: }

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