Annotation of imach/src/imach.c, revision 1.252

1.252   ! brouard     1: /* $Id: imach.c,v 1.251 2016/09/15 15:01:13 brouard Exp $
1.126     brouard     2:   $State: Exp $
1.163     brouard     3:   $Log: imach.c,v $
1.252   ! brouard     4:   Revision 1.251  2016/09/15 15:01:13  brouard
        !             5:   Summary: not working
        !             6: 
1.251     brouard     7:   Revision 1.250  2016/09/08 16:07:27  brouard
                      8:   Summary: continue
                      9: 
1.250     brouard    10:   Revision 1.249  2016/09/07 17:14:18  brouard
                     11:   Summary: Starting values from frequencies
                     12: 
1.249     brouard    13:   Revision 1.248  2016/09/07 14:10:18  brouard
                     14:   *** empty log message ***
                     15: 
1.248     brouard    16:   Revision 1.247  2016/09/02 11:11:21  brouard
                     17:   *** empty log message ***
                     18: 
1.247     brouard    19:   Revision 1.246  2016/09/02 08:49:22  brouard
                     20:   *** empty log message ***
                     21: 
1.246     brouard    22:   Revision 1.245  2016/09/02 07:25:01  brouard
                     23:   *** empty log message ***
                     24: 
1.245     brouard    25:   Revision 1.244  2016/09/02 07:17:34  brouard
                     26:   *** empty log message ***
                     27: 
1.244     brouard    28:   Revision 1.243  2016/09/02 06:45:35  brouard
                     29:   *** empty log message ***
                     30: 
1.243     brouard    31:   Revision 1.242  2016/08/30 15:01:20  brouard
                     32:   Summary: Fixing a lots
                     33: 
1.242     brouard    34:   Revision 1.241  2016/08/29 17:17:25  brouard
                     35:   Summary: gnuplot problem in Back projection to fix
                     36: 
1.241     brouard    37:   Revision 1.240  2016/08/29 07:53:18  brouard
                     38:   Summary: Better
                     39: 
1.240     brouard    40:   Revision 1.239  2016/08/26 15:51:03  brouard
                     41:   Summary: Improvement in Powell output in order to copy and paste
                     42: 
                     43:   Author:
                     44: 
1.239     brouard    45:   Revision 1.238  2016/08/26 14:23:35  brouard
                     46:   Summary: Starting tests of 0.99
                     47: 
1.238     brouard    48:   Revision 1.237  2016/08/26 09:20:19  brouard
                     49:   Summary: to valgrind
                     50: 
1.237     brouard    51:   Revision 1.236  2016/08/25 10:50:18  brouard
                     52:   *** empty log message ***
                     53: 
1.236     brouard    54:   Revision 1.235  2016/08/25 06:59:23  brouard
                     55:   *** empty log message ***
                     56: 
1.235     brouard    57:   Revision 1.234  2016/08/23 16:51:20  brouard
                     58:   *** empty log message ***
                     59: 
1.234     brouard    60:   Revision 1.233  2016/08/23 07:40:50  brouard
                     61:   Summary: not working
                     62: 
1.233     brouard    63:   Revision 1.232  2016/08/22 14:20:21  brouard
                     64:   Summary: not working
                     65: 
1.232     brouard    66:   Revision 1.231  2016/08/22 07:17:15  brouard
                     67:   Summary: not working
                     68: 
1.231     brouard    69:   Revision 1.230  2016/08/22 06:55:53  brouard
                     70:   Summary: Not working
                     71: 
1.230     brouard    72:   Revision 1.229  2016/07/23 09:45:53  brouard
                     73:   Summary: Completing for func too
                     74: 
1.229     brouard    75:   Revision 1.228  2016/07/22 17:45:30  brouard
                     76:   Summary: Fixing some arrays, still debugging
                     77: 
1.227     brouard    78:   Revision 1.226  2016/07/12 18:42:34  brouard
                     79:   Summary: temp
                     80: 
1.226     brouard    81:   Revision 1.225  2016/07/12 08:40:03  brouard
                     82:   Summary: saving but not running
                     83: 
1.225     brouard    84:   Revision 1.224  2016/07/01 13:16:01  brouard
                     85:   Summary: Fixes
                     86: 
1.224     brouard    87:   Revision 1.223  2016/02/19 09:23:35  brouard
                     88:   Summary: temporary
                     89: 
1.223     brouard    90:   Revision 1.222  2016/02/17 08:14:50  brouard
                     91:   Summary: Probably last 0.98 stable version 0.98r6
                     92: 
1.222     brouard    93:   Revision 1.221  2016/02/15 23:35:36  brouard
                     94:   Summary: minor bug
                     95: 
1.220     brouard    96:   Revision 1.219  2016/02/15 00:48:12  brouard
                     97:   *** empty log message ***
                     98: 
1.219     brouard    99:   Revision 1.218  2016/02/12 11:29:23  brouard
                    100:   Summary: 0.99 Back projections
                    101: 
1.218     brouard   102:   Revision 1.217  2015/12/23 17:18:31  brouard
                    103:   Summary: Experimental backcast
                    104: 
1.217     brouard   105:   Revision 1.216  2015/12/18 17:32:11  brouard
                    106:   Summary: 0.98r4 Warning and status=-2
                    107: 
                    108:   Version 0.98r4 is now:
                    109:    - displaying an error when status is -1, date of interview unknown and date of death known;
                    110:    - permitting a status -2 when the vital status is unknown at a known date of right truncation.
                    111:   Older changes concerning s=-2, dating from 2005 have been supersed.
                    112: 
1.216     brouard   113:   Revision 1.215  2015/12/16 08:52:24  brouard
                    114:   Summary: 0.98r4 working
                    115: 
1.215     brouard   116:   Revision 1.214  2015/12/16 06:57:54  brouard
                    117:   Summary: temporary not working
                    118: 
1.214     brouard   119:   Revision 1.213  2015/12/11 18:22:17  brouard
                    120:   Summary: 0.98r4
                    121: 
1.213     brouard   122:   Revision 1.212  2015/11/21 12:47:24  brouard
                    123:   Summary: minor typo
                    124: 
1.212     brouard   125:   Revision 1.211  2015/11/21 12:41:11  brouard
                    126:   Summary: 0.98r3 with some graph of projected cross-sectional
                    127: 
                    128:   Author: Nicolas Brouard
                    129: 
1.211     brouard   130:   Revision 1.210  2015/11/18 17:41:20  brouard
1.252   ! brouard   131:   Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
1.210     brouard   132:   Summary: Adding ftolpl parameter
                    133:   Author: N Brouard
                    134: 
                    135:   We had difficulties to get smoothed confidence intervals. It was due
                    136:   to the period prevalence which wasn't computed accurately. The inner
                    137:   parameter ftolpl is now an outer parameter of the .imach parameter
                    138:   file after estepm. If ftolpl is small 1.e-4 and estepm too,
                    139:   computation are long.
                    140: 
1.209     brouard   141:   Revision 1.208  2015/11/17 14:31:57  brouard
                    142:   Summary: temporary
                    143: 
1.208     brouard   144:   Revision 1.207  2015/10/27 17:36:57  brouard
                    145:   *** empty log message ***
                    146: 
1.207     brouard   147:   Revision 1.206  2015/10/24 07:14:11  brouard
                    148:   *** empty log message ***
                    149: 
1.206     brouard   150:   Revision 1.205  2015/10/23 15:50:53  brouard
                    151:   Summary: 0.98r3 some clarification for graphs on likelihood contributions
                    152: 
1.205     brouard   153:   Revision 1.204  2015/10/01 16:20:26  brouard
                    154:   Summary: Some new graphs of contribution to likelihood
                    155: 
1.204     brouard   156:   Revision 1.203  2015/09/30 17:45:14  brouard
                    157:   Summary: looking at better estimation of the hessian
                    158: 
                    159:   Also a better criteria for convergence to the period prevalence And
                    160:   therefore adding the number of years needed to converge. (The
                    161:   prevalence in any alive state shold sum to one
                    162: 
1.203     brouard   163:   Revision 1.202  2015/09/22 19:45:16  brouard
                    164:   Summary: Adding some overall graph on contribution to likelihood. Might change
                    165: 
1.202     brouard   166:   Revision 1.201  2015/09/15 17:34:58  brouard
                    167:   Summary: 0.98r0
                    168: 
                    169:   - Some new graphs like suvival functions
                    170:   - Some bugs fixed like model=1+age+V2.
                    171: 
1.201     brouard   172:   Revision 1.200  2015/09/09 16:53:55  brouard
                    173:   Summary: Big bug thanks to Flavia
                    174: 
                    175:   Even model=1+age+V2. did not work anymore
                    176: 
1.200     brouard   177:   Revision 1.199  2015/09/07 14:09:23  brouard
                    178:   Summary: 0.98q6 changing default small png format for graph to vectorized svg.
                    179: 
1.199     brouard   180:   Revision 1.198  2015/09/03 07:14:39  brouard
                    181:   Summary: 0.98q5 Flavia
                    182: 
1.198     brouard   183:   Revision 1.197  2015/09/01 18:24:39  brouard
                    184:   *** empty log message ***
                    185: 
1.197     brouard   186:   Revision 1.196  2015/08/18 23:17:52  brouard
                    187:   Summary: 0.98q5
                    188: 
1.196     brouard   189:   Revision 1.195  2015/08/18 16:28:39  brouard
                    190:   Summary: Adding a hack for testing purpose
                    191: 
                    192:   After reading the title, ftol and model lines, if the comment line has
                    193:   a q, starting with #q, the answer at the end of the run is quit. It
                    194:   permits to run test files in batch with ctest. The former workaround was
                    195:   $ echo q | imach foo.imach
                    196: 
1.195     brouard   197:   Revision 1.194  2015/08/18 13:32:00  brouard
                    198:   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
                    199: 
1.194     brouard   200:   Revision 1.193  2015/08/04 07:17:42  brouard
                    201:   Summary: 0.98q4
                    202: 
1.193     brouard   203:   Revision 1.192  2015/07/16 16:49:02  brouard
                    204:   Summary: Fixing some outputs
                    205: 
1.192     brouard   206:   Revision 1.191  2015/07/14 10:00:33  brouard
                    207:   Summary: Some fixes
                    208: 
1.191     brouard   209:   Revision 1.190  2015/05/05 08:51:13  brouard
                    210:   Summary: Adding digits in output parameters (7 digits instead of 6)
                    211: 
                    212:   Fix 1+age+.
                    213: 
1.190     brouard   214:   Revision 1.189  2015/04/30 14:45:16  brouard
                    215:   Summary: 0.98q2
                    216: 
1.189     brouard   217:   Revision 1.188  2015/04/30 08:27:53  brouard
                    218:   *** empty log message ***
                    219: 
1.188     brouard   220:   Revision 1.187  2015/04/29 09:11:15  brouard
                    221:   *** empty log message ***
                    222: 
1.187     brouard   223:   Revision 1.186  2015/04/23 12:01:52  brouard
                    224:   Summary: V1*age is working now, version 0.98q1
                    225: 
                    226:   Some codes had been disabled in order to simplify and Vn*age was
                    227:   working in the optimization phase, ie, giving correct MLE parameters,
                    228:   but, as usual, outputs were not correct and program core dumped.
                    229: 
1.186     brouard   230:   Revision 1.185  2015/03/11 13:26:42  brouard
                    231:   Summary: Inclusion of compile and links command line for Intel Compiler
                    232: 
1.185     brouard   233:   Revision 1.184  2015/03/11 11:52:39  brouard
                    234:   Summary: Back from Windows 8. Intel Compiler
                    235: 
1.184     brouard   236:   Revision 1.183  2015/03/10 20:34:32  brouard
                    237:   Summary: 0.98q0, trying with directest, mnbrak fixed
                    238: 
                    239:   We use directest instead of original Powell test; probably no
                    240:   incidence on the results, but better justifications;
                    241:   We fixed Numerical Recipes mnbrak routine which was wrong and gave
                    242:   wrong results.
                    243: 
1.183     brouard   244:   Revision 1.182  2015/02/12 08:19:57  brouard
                    245:   Summary: Trying to keep directest which seems simpler and more general
                    246:   Author: Nicolas Brouard
                    247: 
1.182     brouard   248:   Revision 1.181  2015/02/11 23:22:24  brouard
                    249:   Summary: Comments on Powell added
                    250: 
                    251:   Author:
                    252: 
1.181     brouard   253:   Revision 1.180  2015/02/11 17:33:45  brouard
                    254:   Summary: Finishing move from main to function (hpijx and prevalence_limit)
                    255: 
1.180     brouard   256:   Revision 1.179  2015/01/04 09:57:06  brouard
                    257:   Summary: back to OS/X
                    258: 
1.179     brouard   259:   Revision 1.178  2015/01/04 09:35:48  brouard
                    260:   *** empty log message ***
                    261: 
1.178     brouard   262:   Revision 1.177  2015/01/03 18:40:56  brouard
                    263:   Summary: Still testing ilc32 on OSX
                    264: 
1.177     brouard   265:   Revision 1.176  2015/01/03 16:45:04  brouard
                    266:   *** empty log message ***
                    267: 
1.176     brouard   268:   Revision 1.175  2015/01/03 16:33:42  brouard
                    269:   *** empty log message ***
                    270: 
1.175     brouard   271:   Revision 1.174  2015/01/03 16:15:49  brouard
                    272:   Summary: Still in cross-compilation
                    273: 
1.174     brouard   274:   Revision 1.173  2015/01/03 12:06:26  brouard
                    275:   Summary: trying to detect cross-compilation
                    276: 
1.173     brouard   277:   Revision 1.172  2014/12/27 12:07:47  brouard
                    278:   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
                    279: 
1.172     brouard   280:   Revision 1.171  2014/12/23 13:26:59  brouard
                    281:   Summary: Back from Visual C
                    282: 
                    283:   Still problem with utsname.h on Windows
                    284: 
1.171     brouard   285:   Revision 1.170  2014/12/23 11:17:12  brouard
                    286:   Summary: Cleaning some \%% back to %%
                    287: 
                    288:   The escape was mandatory for a specific compiler (which one?), but too many warnings.
                    289: 
1.170     brouard   290:   Revision 1.169  2014/12/22 23:08:31  brouard
                    291:   Summary: 0.98p
                    292: 
                    293:   Outputs some informations on compiler used, OS etc. Testing on different platforms.
                    294: 
1.169     brouard   295:   Revision 1.168  2014/12/22 15:17:42  brouard
1.170     brouard   296:   Summary: update
1.169     brouard   297: 
1.168     brouard   298:   Revision 1.167  2014/12/22 13:50:56  brouard
                    299:   Summary: Testing uname and compiler version and if compiled 32 or 64
                    300: 
                    301:   Testing on Linux 64
                    302: 
1.167     brouard   303:   Revision 1.166  2014/12/22 11:40:47  brouard
                    304:   *** empty log message ***
                    305: 
1.166     brouard   306:   Revision 1.165  2014/12/16 11:20:36  brouard
                    307:   Summary: After compiling on Visual C
                    308: 
                    309:   * imach.c (Module): Merging 1.61 to 1.162
                    310: 
1.165     brouard   311:   Revision 1.164  2014/12/16 10:52:11  brouard
                    312:   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
                    313: 
                    314:   * imach.c (Module): Merging 1.61 to 1.162
                    315: 
1.164     brouard   316:   Revision 1.163  2014/12/16 10:30:11  brouard
                    317:   * imach.c (Module): Merging 1.61 to 1.162
                    318: 
1.163     brouard   319:   Revision 1.162  2014/09/25 11:43:39  brouard
                    320:   Summary: temporary backup 0.99!
                    321: 
1.162     brouard   322:   Revision 1.1  2014/09/16 11:06:58  brouard
                    323:   Summary: With some code (wrong) for nlopt
                    324: 
                    325:   Author:
                    326: 
                    327:   Revision 1.161  2014/09/15 20:41:41  brouard
                    328:   Summary: Problem with macro SQR on Intel compiler
                    329: 
1.161     brouard   330:   Revision 1.160  2014/09/02 09:24:05  brouard
                    331:   *** empty log message ***
                    332: 
1.160     brouard   333:   Revision 1.159  2014/09/01 10:34:10  brouard
                    334:   Summary: WIN32
                    335:   Author: Brouard
                    336: 
1.159     brouard   337:   Revision 1.158  2014/08/27 17:11:51  brouard
                    338:   *** empty log message ***
                    339: 
1.158     brouard   340:   Revision 1.157  2014/08/27 16:26:55  brouard
                    341:   Summary: Preparing windows Visual studio version
                    342:   Author: Brouard
                    343: 
                    344:   In order to compile on Visual studio, time.h is now correct and time_t
                    345:   and tm struct should be used. difftime should be used but sometimes I
                    346:   just make the differences in raw time format (time(&now).
                    347:   Trying to suppress #ifdef LINUX
                    348:   Add xdg-open for __linux in order to open default browser.
                    349: 
1.157     brouard   350:   Revision 1.156  2014/08/25 20:10:10  brouard
                    351:   *** empty log message ***
                    352: 
1.156     brouard   353:   Revision 1.155  2014/08/25 18:32:34  brouard
                    354:   Summary: New compile, minor changes
                    355:   Author: Brouard
                    356: 
1.155     brouard   357:   Revision 1.154  2014/06/20 17:32:08  brouard
                    358:   Summary: Outputs now all graphs of convergence to period prevalence
                    359: 
1.154     brouard   360:   Revision 1.153  2014/06/20 16:45:46  brouard
                    361:   Summary: If 3 live state, convergence to period prevalence on same graph
                    362:   Author: Brouard
                    363: 
1.153     brouard   364:   Revision 1.152  2014/06/18 17:54:09  brouard
                    365:   Summary: open browser, use gnuplot on same dir than imach if not found in the path
                    366: 
1.152     brouard   367:   Revision 1.151  2014/06/18 16:43:30  brouard
                    368:   *** empty log message ***
                    369: 
1.151     brouard   370:   Revision 1.150  2014/06/18 16:42:35  brouard
                    371:   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
                    372:   Author: brouard
                    373: 
1.150     brouard   374:   Revision 1.149  2014/06/18 15:51:14  brouard
                    375:   Summary: Some fixes in parameter files errors
                    376:   Author: Nicolas Brouard
                    377: 
1.149     brouard   378:   Revision 1.148  2014/06/17 17:38:48  brouard
                    379:   Summary: Nothing new
                    380:   Author: Brouard
                    381: 
                    382:   Just a new packaging for OS/X version 0.98nS
                    383: 
1.148     brouard   384:   Revision 1.147  2014/06/16 10:33:11  brouard
                    385:   *** empty log message ***
                    386: 
1.147     brouard   387:   Revision 1.146  2014/06/16 10:20:28  brouard
                    388:   Summary: Merge
                    389:   Author: Brouard
                    390: 
                    391:   Merge, before building revised version.
                    392: 
1.146     brouard   393:   Revision 1.145  2014/06/10 21:23:15  brouard
                    394:   Summary: Debugging with valgrind
                    395:   Author: Nicolas Brouard
                    396: 
                    397:   Lot of changes in order to output the results with some covariates
                    398:   After the Edimburgh REVES conference 2014, it seems mandatory to
                    399:   improve the code.
                    400:   No more memory valgrind error but a lot has to be done in order to
                    401:   continue the work of splitting the code into subroutines.
                    402:   Also, decodemodel has been improved. Tricode is still not
                    403:   optimal. nbcode should be improved. Documentation has been added in
                    404:   the source code.
                    405: 
1.144     brouard   406:   Revision 1.143  2014/01/26 09:45:38  brouard
                    407:   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
                    408: 
                    409:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    410:   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
                    411: 
1.143     brouard   412:   Revision 1.142  2014/01/26 03:57:36  brouard
                    413:   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
                    414: 
                    415:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    416: 
1.142     brouard   417:   Revision 1.141  2014/01/26 02:42:01  brouard
                    418:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    419: 
1.141     brouard   420:   Revision 1.140  2011/09/02 10:37:54  brouard
                    421:   Summary: times.h is ok with mingw32 now.
                    422: 
1.140     brouard   423:   Revision 1.139  2010/06/14 07:50:17  brouard
                    424:   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
                    425:   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
                    426: 
1.139     brouard   427:   Revision 1.138  2010/04/30 18:19:40  brouard
                    428:   *** empty log message ***
                    429: 
1.138     brouard   430:   Revision 1.137  2010/04/29 18:11:38  brouard
                    431:   (Module): Checking covariates for more complex models
                    432:   than V1+V2. A lot of change to be done. Unstable.
                    433: 
1.137     brouard   434:   Revision 1.136  2010/04/26 20:30:53  brouard
                    435:   (Module): merging some libgsl code. Fixing computation
                    436:   of likelione (using inter/intrapolation if mle = 0) in order to
                    437:   get same likelihood as if mle=1.
                    438:   Some cleaning of code and comments added.
                    439: 
1.136     brouard   440:   Revision 1.135  2009/10/29 15:33:14  brouard
                    441:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                    442: 
1.135     brouard   443:   Revision 1.134  2009/10/29 13:18:53  brouard
                    444:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                    445: 
1.134     brouard   446:   Revision 1.133  2009/07/06 10:21:25  brouard
                    447:   just nforces
                    448: 
1.133     brouard   449:   Revision 1.132  2009/07/06 08:22:05  brouard
                    450:   Many tings
                    451: 
1.132     brouard   452:   Revision 1.131  2009/06/20 16:22:47  brouard
                    453:   Some dimensions resccaled
                    454: 
1.131     brouard   455:   Revision 1.130  2009/05/26 06:44:34  brouard
                    456:   (Module): Max Covariate is now set to 20 instead of 8. A
                    457:   lot of cleaning with variables initialized to 0. Trying to make
                    458:   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
                    459: 
1.130     brouard   460:   Revision 1.129  2007/08/31 13:49:27  lievre
                    461:   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
                    462: 
1.129     lievre    463:   Revision 1.128  2006/06/30 13:02:05  brouard
                    464:   (Module): Clarifications on computing e.j
                    465: 
1.128     brouard   466:   Revision 1.127  2006/04/28 18:11:50  brouard
                    467:   (Module): Yes the sum of survivors was wrong since
                    468:   imach-114 because nhstepm was no more computed in the age
                    469:   loop. Now we define nhstepma in the age loop.
                    470:   (Module): In order to speed up (in case of numerous covariates) we
                    471:   compute health expectancies (without variances) in a first step
                    472:   and then all the health expectancies with variances or standard
                    473:   deviation (needs data from the Hessian matrices) which slows the
                    474:   computation.
                    475:   In the future we should be able to stop the program is only health
                    476:   expectancies and graph are needed without standard deviations.
                    477: 
1.127     brouard   478:   Revision 1.126  2006/04/28 17:23:28  brouard
                    479:   (Module): Yes the sum of survivors was wrong since
                    480:   imach-114 because nhstepm was no more computed in the age
                    481:   loop. Now we define nhstepma in the age loop.
                    482:   Version 0.98h
                    483: 
1.126     brouard   484:   Revision 1.125  2006/04/04 15:20:31  lievre
                    485:   Errors in calculation of health expectancies. Age was not initialized.
                    486:   Forecasting file added.
                    487: 
                    488:   Revision 1.124  2006/03/22 17:13:53  lievre
                    489:   Parameters are printed with %lf instead of %f (more numbers after the comma).
                    490:   The log-likelihood is printed in the log file
                    491: 
                    492:   Revision 1.123  2006/03/20 10:52:43  brouard
                    493:   * imach.c (Module): <title> changed, corresponds to .htm file
                    494:   name. <head> headers where missing.
                    495: 
                    496:   * imach.c (Module): Weights can have a decimal point as for
                    497:   English (a comma might work with a correct LC_NUMERIC environment,
                    498:   otherwise the weight is truncated).
                    499:   Modification of warning when the covariates values are not 0 or
                    500:   1.
                    501:   Version 0.98g
                    502: 
                    503:   Revision 1.122  2006/03/20 09:45:41  brouard
                    504:   (Module): Weights can have a decimal point as for
                    505:   English (a comma might work with a correct LC_NUMERIC environment,
                    506:   otherwise the weight is truncated).
                    507:   Modification of warning when the covariates values are not 0 or
                    508:   1.
                    509:   Version 0.98g
                    510: 
                    511:   Revision 1.121  2006/03/16 17:45:01  lievre
                    512:   * imach.c (Module): Comments concerning covariates added
                    513: 
                    514:   * imach.c (Module): refinements in the computation of lli if
                    515:   status=-2 in order to have more reliable computation if stepm is
                    516:   not 1 month. Version 0.98f
                    517: 
                    518:   Revision 1.120  2006/03/16 15:10:38  lievre
                    519:   (Module): refinements in the computation of lli if
                    520:   status=-2 in order to have more reliable computation if stepm is
                    521:   not 1 month. Version 0.98f
                    522: 
                    523:   Revision 1.119  2006/03/15 17:42:26  brouard
                    524:   (Module): Bug if status = -2, the loglikelihood was
                    525:   computed as likelihood omitting the logarithm. Version O.98e
                    526: 
                    527:   Revision 1.118  2006/03/14 18:20:07  brouard
                    528:   (Module): varevsij Comments added explaining the second
                    529:   table of variances if popbased=1 .
                    530:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    531:   (Module): Function pstamp added
                    532:   (Module): Version 0.98d
                    533: 
                    534:   Revision 1.117  2006/03/14 17:16:22  brouard
                    535:   (Module): varevsij Comments added explaining the second
                    536:   table of variances if popbased=1 .
                    537:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    538:   (Module): Function pstamp added
                    539:   (Module): Version 0.98d
                    540: 
                    541:   Revision 1.116  2006/03/06 10:29:27  brouard
                    542:   (Module): Variance-covariance wrong links and
                    543:   varian-covariance of ej. is needed (Saito).
                    544: 
                    545:   Revision 1.115  2006/02/27 12:17:45  brouard
                    546:   (Module): One freematrix added in mlikeli! 0.98c
                    547: 
                    548:   Revision 1.114  2006/02/26 12:57:58  brouard
                    549:   (Module): Some improvements in processing parameter
                    550:   filename with strsep.
                    551: 
                    552:   Revision 1.113  2006/02/24 14:20:24  brouard
                    553:   (Module): Memory leaks checks with valgrind and:
                    554:   datafile was not closed, some imatrix were not freed and on matrix
                    555:   allocation too.
                    556: 
                    557:   Revision 1.112  2006/01/30 09:55:26  brouard
                    558:   (Module): Back to gnuplot.exe instead of wgnuplot.exe
                    559: 
                    560:   Revision 1.111  2006/01/25 20:38:18  brouard
                    561:   (Module): Lots of cleaning and bugs added (Gompertz)
                    562:   (Module): Comments can be added in data file. Missing date values
                    563:   can be a simple dot '.'.
                    564: 
                    565:   Revision 1.110  2006/01/25 00:51:50  brouard
                    566:   (Module): Lots of cleaning and bugs added (Gompertz)
                    567: 
                    568:   Revision 1.109  2006/01/24 19:37:15  brouard
                    569:   (Module): Comments (lines starting with a #) are allowed in data.
                    570: 
                    571:   Revision 1.108  2006/01/19 18:05:42  lievre
                    572:   Gnuplot problem appeared...
                    573:   To be fixed
                    574: 
                    575:   Revision 1.107  2006/01/19 16:20:37  brouard
                    576:   Test existence of gnuplot in imach path
                    577: 
                    578:   Revision 1.106  2006/01/19 13:24:36  brouard
                    579:   Some cleaning and links added in html output
                    580: 
                    581:   Revision 1.105  2006/01/05 20:23:19  lievre
                    582:   *** empty log message ***
                    583: 
                    584:   Revision 1.104  2005/09/30 16:11:43  lievre
                    585:   (Module): sump fixed, loop imx fixed, and simplifications.
                    586:   (Module): If the status is missing at the last wave but we know
                    587:   that the person is alive, then we can code his/her status as -2
                    588:   (instead of missing=-1 in earlier versions) and his/her
                    589:   contributions to the likelihood is 1 - Prob of dying from last
                    590:   health status (= 1-p13= p11+p12 in the easiest case of somebody in
                    591:   the healthy state at last known wave). Version is 0.98
                    592: 
                    593:   Revision 1.103  2005/09/30 15:54:49  lievre
                    594:   (Module): sump fixed, loop imx fixed, and simplifications.
                    595: 
                    596:   Revision 1.102  2004/09/15 17:31:30  brouard
                    597:   Add the possibility to read data file including tab characters.
                    598: 
                    599:   Revision 1.101  2004/09/15 10:38:38  brouard
                    600:   Fix on curr_time
                    601: 
                    602:   Revision 1.100  2004/07/12 18:29:06  brouard
                    603:   Add version for Mac OS X. Just define UNIX in Makefile
                    604: 
                    605:   Revision 1.99  2004/06/05 08:57:40  brouard
                    606:   *** empty log message ***
                    607: 
                    608:   Revision 1.98  2004/05/16 15:05:56  brouard
                    609:   New version 0.97 . First attempt to estimate force of mortality
                    610:   directly from the data i.e. without the need of knowing the health
                    611:   state at each age, but using a Gompertz model: log u =a + b*age .
                    612:   This is the basic analysis of mortality and should be done before any
                    613:   other analysis, in order to test if the mortality estimated from the
                    614:   cross-longitudinal survey is different from the mortality estimated
                    615:   from other sources like vital statistic data.
                    616: 
                    617:   The same imach parameter file can be used but the option for mle should be -3.
                    618: 
1.133     brouard   619:   Agnès, who wrote this part of the code, tried to keep most of the
1.126     brouard   620:   former routines in order to include the new code within the former code.
                    621: 
                    622:   The output is very simple: only an estimate of the intercept and of
                    623:   the slope with 95% confident intervals.
                    624: 
                    625:   Current limitations:
                    626:   A) Even if you enter covariates, i.e. with the
                    627:   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
                    628:   B) There is no computation of Life Expectancy nor Life Table.
                    629: 
                    630:   Revision 1.97  2004/02/20 13:25:42  lievre
                    631:   Version 0.96d. Population forecasting command line is (temporarily)
                    632:   suppressed.
                    633: 
                    634:   Revision 1.96  2003/07/15 15:38:55  brouard
                    635:   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
                    636:   rewritten within the same printf. Workaround: many printfs.
                    637: 
                    638:   Revision 1.95  2003/07/08 07:54:34  brouard
                    639:   * imach.c (Repository):
                    640:   (Repository): Using imachwizard code to output a more meaningful covariance
                    641:   matrix (cov(a12,c31) instead of numbers.
                    642: 
                    643:   Revision 1.94  2003/06/27 13:00:02  brouard
                    644:   Just cleaning
                    645: 
                    646:   Revision 1.93  2003/06/25 16:33:55  brouard
                    647:   (Module): On windows (cygwin) function asctime_r doesn't
                    648:   exist so I changed back to asctime which exists.
                    649:   (Module): Version 0.96b
                    650: 
                    651:   Revision 1.92  2003/06/25 16:30:45  brouard
                    652:   (Module): On windows (cygwin) function asctime_r doesn't
                    653:   exist so I changed back to asctime which exists.
                    654: 
                    655:   Revision 1.91  2003/06/25 15:30:29  brouard
                    656:   * imach.c (Repository): Duplicated warning errors corrected.
                    657:   (Repository): Elapsed time after each iteration is now output. It
                    658:   helps to forecast when convergence will be reached. Elapsed time
                    659:   is stamped in powell.  We created a new html file for the graphs
                    660:   concerning matrix of covariance. It has extension -cov.htm.
                    661: 
                    662:   Revision 1.90  2003/06/24 12:34:15  brouard
                    663:   (Module): Some bugs corrected for windows. Also, when
                    664:   mle=-1 a template is output in file "or"mypar.txt with the design
                    665:   of the covariance matrix to be input.
                    666: 
                    667:   Revision 1.89  2003/06/24 12:30:52  brouard
                    668:   (Module): Some bugs corrected for windows. Also, when
                    669:   mle=-1 a template is output in file "or"mypar.txt with the design
                    670:   of the covariance matrix to be input.
                    671: 
                    672:   Revision 1.88  2003/06/23 17:54:56  brouard
                    673:   * 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.
                    674: 
                    675:   Revision 1.87  2003/06/18 12:26:01  brouard
                    676:   Version 0.96
                    677: 
                    678:   Revision 1.86  2003/06/17 20:04:08  brouard
                    679:   (Module): Change position of html and gnuplot routines and added
                    680:   routine fileappend.
                    681: 
                    682:   Revision 1.85  2003/06/17 13:12:43  brouard
                    683:   * imach.c (Repository): Check when date of death was earlier that
                    684:   current date of interview. It may happen when the death was just
                    685:   prior to the death. In this case, dh was negative and likelihood
                    686:   was wrong (infinity). We still send an "Error" but patch by
                    687:   assuming that the date of death was just one stepm after the
                    688:   interview.
                    689:   (Repository): Because some people have very long ID (first column)
                    690:   we changed int to long in num[] and we added a new lvector for
                    691:   memory allocation. But we also truncated to 8 characters (left
                    692:   truncation)
                    693:   (Repository): No more line truncation errors.
                    694: 
                    695:   Revision 1.84  2003/06/13 21:44:43  brouard
                    696:   * imach.c (Repository): Replace "freqsummary" at a correct
                    697:   place. It differs from routine "prevalence" which may be called
                    698:   many times. Probs is memory consuming and must be used with
                    699:   parcimony.
                    700:   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
                    701: 
                    702:   Revision 1.83  2003/06/10 13:39:11  lievre
                    703:   *** empty log message ***
                    704: 
                    705:   Revision 1.82  2003/06/05 15:57:20  brouard
                    706:   Add log in  imach.c and  fullversion number is now printed.
                    707: 
                    708: */
                    709: /*
                    710:    Interpolated Markov Chain
                    711: 
                    712:   Short summary of the programme:
                    713:   
1.227     brouard   714:   This program computes Healthy Life Expectancies or State-specific
                    715:   (if states aren't health statuses) Expectancies from
                    716:   cross-longitudinal data. Cross-longitudinal data consist in: 
                    717: 
                    718:   -1- a first survey ("cross") where individuals from different ages
                    719:   are interviewed on their health status or degree of disability (in
                    720:   the case of a health survey which is our main interest)
                    721: 
                    722:   -2- at least a second wave of interviews ("longitudinal") which
                    723:   measure each change (if any) in individual health status.  Health
                    724:   expectancies are computed from the time spent in each health state
                    725:   according to a model. More health states you consider, more time is
                    726:   necessary to reach the Maximum Likelihood of the parameters involved
                    727:   in the model.  The simplest model is the multinomial logistic model
                    728:   where pij is the probability to be observed in state j at the second
                    729:   wave conditional to be observed in state i at the first
                    730:   wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
                    731:   etc , where 'age' is age and 'sex' is a covariate. If you want to
                    732:   have a more complex model than "constant and age", you should modify
                    733:   the program where the markup *Covariates have to be included here
                    734:   again* invites you to do it.  More covariates you add, slower the
1.126     brouard   735:   convergence.
                    736: 
                    737:   The advantage of this computer programme, compared to a simple
                    738:   multinomial logistic model, is clear when the delay between waves is not
                    739:   identical for each individual. Also, if a individual missed an
                    740:   intermediate interview, the information is lost, but taken into
                    741:   account using an interpolation or extrapolation.  
                    742: 
                    743:   hPijx is the probability to be observed in state i at age x+h
                    744:   conditional to the observed state i at age x. The delay 'h' can be
                    745:   split into an exact number (nh*stepm) of unobserved intermediate
                    746:   states. This elementary transition (by month, quarter,
                    747:   semester or year) is modelled as a multinomial logistic.  The hPx
                    748:   matrix is simply the matrix product of nh*stepm elementary matrices
                    749:   and the contribution of each individual to the likelihood is simply
                    750:   hPijx.
                    751: 
                    752:   Also this programme outputs the covariance matrix of the parameters but also
1.218     brouard   753:   of the life expectancies. It also computes the period (stable) prevalence.
                    754: 
                    755: Back prevalence and projections:
1.227     brouard   756: 
                    757:  - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
                    758:    double agemaxpar, double ftolpl, int *ncvyearp, double
                    759:    dateprev1,double dateprev2, int firstpass, int lastpass, int
                    760:    mobilavproj)
                    761: 
                    762:     Computes the back prevalence limit for any combination of
                    763:     covariate values k at any age between ageminpar and agemaxpar and
                    764:     returns it in **bprlim. In the loops,
                    765: 
                    766:    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
                    767:        **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
                    768: 
                    769:    - hBijx Back Probability to be in state i at age x-h being in j at x
1.218     brouard   770:    Computes for any combination of covariates k and any age between bage and fage 
                    771:    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                    772:                        oldm=oldms;savm=savms;
1.227     brouard   773: 
                    774:    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218     brouard   775:      Computes the transition matrix starting at age 'age' over
                    776:      'nhstepm*hstepm*stepm' months (i.e. until
                    777:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
1.227     brouard   778:      nhstepm*hstepm matrices. 
                    779: 
                    780:      Returns p3mat[i][j][h] after calling
                    781:      p3mat[i][j][h]=matprod2(newm,
                    782:      bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
                    783:      dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
                    784:      oldm);
1.226     brouard   785: 
                    786: Important routines
                    787: 
                    788: - func (or funcone), computes logit (pij) distinguishing
                    789:   o fixed variables (single or product dummies or quantitative);
                    790:   o varying variables by:
                    791:    (1) wave (single, product dummies, quantitative), 
                    792:    (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
                    793:        % fixed dummy (treated) or quantitative (not done because time-consuming);
                    794:        % varying dummy (not done) or quantitative (not done);
                    795: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
                    796:   and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
                    797: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
                    798:   o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
                    799:     race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218     brouard   800: 
1.226     brouard   801: 
                    802:   
1.133     brouard   803:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                    804:            Institut national d'études démographiques, Paris.
1.126     brouard   805:   This software have been partly granted by Euro-REVES, a concerted action
                    806:   from the European Union.
                    807:   It is copyrighted identically to a GNU software product, ie programme and
                    808:   software can be distributed freely for non commercial use. Latest version
                    809:   can be accessed at http://euroreves.ined.fr/imach .
                    810: 
                    811:   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
                    812:   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
                    813:   
                    814:   **********************************************************************/
                    815: /*
                    816:   main
                    817:   read parameterfile
                    818:   read datafile
                    819:   concatwav
                    820:   freqsummary
                    821:   if (mle >= 1)
                    822:     mlikeli
                    823:   print results files
                    824:   if mle==1 
                    825:      computes hessian
                    826:   read end of parameter file: agemin, agemax, bage, fage, estepm
                    827:       begin-prev-date,...
                    828:   open gnuplot file
                    829:   open html file
1.145     brouard   830:   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
                    831:    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
                    832:                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
                    833:     freexexit2 possible for memory heap.
                    834: 
                    835:   h Pij x                         | pij_nom  ficrestpij
                    836:    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
                    837:        1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
                    838:        1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
                    839: 
                    840:        1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
                    841:        1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
                    842:   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
                    843:    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
                    844:    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
                    845: 
1.126     brouard   846:   forecasting if prevfcast==1 prevforecast call prevalence()
                    847:   health expectancies
                    848:   Variance-covariance of DFLE
                    849:   prevalence()
                    850:    movingaverage()
                    851:   varevsij() 
                    852:   if popbased==1 varevsij(,popbased)
                    853:   total life expectancies
                    854:   Variance of period (stable) prevalence
                    855:  end
                    856: */
                    857: 
1.187     brouard   858: /* #define DEBUG */
                    859: /* #define DEBUGBRENT */
1.203     brouard   860: /* #define DEBUGLINMIN */
                    861: /* #define DEBUGHESS */
                    862: #define DEBUGHESSIJ
1.224     brouard   863: /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165     brouard   864: #define POWELL /* Instead of NLOPT */
1.224     brouard   865: #define POWELLNOF3INFF1TEST /* Skip test */
1.186     brouard   866: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
                    867: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126     brouard   868: 
                    869: #include <math.h>
                    870: #include <stdio.h>
                    871: #include <stdlib.h>
                    872: #include <string.h>
1.226     brouard   873: #include <ctype.h>
1.159     brouard   874: 
                    875: #ifdef _WIN32
                    876: #include <io.h>
1.172     brouard   877: #include <windows.h>
                    878: #include <tchar.h>
1.159     brouard   879: #else
1.126     brouard   880: #include <unistd.h>
1.159     brouard   881: #endif
1.126     brouard   882: 
                    883: #include <limits.h>
                    884: #include <sys/types.h>
1.171     brouard   885: 
                    886: #if defined(__GNUC__)
                    887: #include <sys/utsname.h> /* Doesn't work on Windows */
                    888: #endif
                    889: 
1.126     brouard   890: #include <sys/stat.h>
                    891: #include <errno.h>
1.159     brouard   892: /* extern int errno; */
1.126     brouard   893: 
1.157     brouard   894: /* #ifdef LINUX */
                    895: /* #include <time.h> */
                    896: /* #include "timeval.h" */
                    897: /* #else */
                    898: /* #include <sys/time.h> */
                    899: /* #endif */
                    900: 
1.126     brouard   901: #include <time.h>
                    902: 
1.136     brouard   903: #ifdef GSL
                    904: #include <gsl/gsl_errno.h>
                    905: #include <gsl/gsl_multimin.h>
                    906: #endif
                    907: 
1.167     brouard   908: 
1.162     brouard   909: #ifdef NLOPT
                    910: #include <nlopt.h>
                    911: typedef struct {
                    912:   double (* function)(double [] );
                    913: } myfunc_data ;
                    914: #endif
                    915: 
1.126     brouard   916: /* #include <libintl.h> */
                    917: /* #define _(String) gettext (String) */
                    918: 
1.251     brouard   919: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126     brouard   920: 
                    921: #define GNUPLOTPROGRAM "gnuplot"
                    922: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
                    923: #define FILENAMELENGTH 132
                    924: 
                    925: #define        GLOCK_ERROR_NOPATH              -1      /* empty path */
                    926: #define        GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
                    927: 
1.144     brouard   928: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
                    929: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126     brouard   930: 
                    931: #define NINTERVMAX 8
1.144     brouard   932: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
                    933: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
                    934: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197     brouard   935: #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
1.211     brouard   936: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
                    937: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
1.126     brouard   938: #define MAXN 20000
1.144     brouard   939: #define YEARM 12. /**< Number of months per year */
1.218     brouard   940: /* #define AGESUP 130 */
                    941: #define AGESUP 150
                    942: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126     brouard   943: #define AGEBASE 40
1.194     brouard   944: #define AGEOVERFLOW 1.e20
1.164     brouard   945: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157     brouard   946: #ifdef _WIN32
                    947: #define DIRSEPARATOR '\\'
                    948: #define CHARSEPARATOR "\\"
                    949: #define ODIRSEPARATOR '/'
                    950: #else
1.126     brouard   951: #define DIRSEPARATOR '/'
                    952: #define CHARSEPARATOR "/"
                    953: #define ODIRSEPARATOR '\\'
                    954: #endif
                    955: 
1.252   ! brouard   956: /* $Id: imach.c,v 1.251 2016/09/15 15:01:13 brouard Exp $ */
1.126     brouard   957: /* $State: Exp $ */
1.196     brouard   958: #include "version.h"
                    959: char version[]=__IMACH_VERSION__;
1.224     brouard   960: char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
1.252   ! brouard   961: char fullversion[]="$Revision: 1.251 $ $Date: 2016/09/15 15:01:13 $"; 
1.126     brouard   962: char strstart[80];
                    963: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130     brouard   964: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
1.187     brouard   965: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145     brouard   966: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
                    967: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
                    968: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225     brouard   969: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
                    970: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145     brouard   971: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
                    972: int cptcovprodnoage=0; /**< Number of covariate products without age */   
                    973: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233     brouard   974: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
                    975: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232     brouard   976: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234     brouard   977: int nsd=0; /**< Total number of single dummy variables (output) */
                    978: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232     brouard   979: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225     brouard   980: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224     brouard   981: int ntveff=0; /**< ntveff number of effective time varying variables */
                    982: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145     brouard   983: int cptcov=0; /* Working variable */
1.218     brouard   984: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126     brouard   985: int npar=NPARMAX;
                    986: int nlstate=2; /* Number of live states */
                    987: int ndeath=1; /* Number of dead states */
1.130     brouard   988: int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223     brouard   989: int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
1.126     brouard   990: int popbased=0;
                    991: 
                    992: int *wav; /* Number of waves for this individuual 0 is possible */
1.130     brouard   993: int maxwav=0; /* Maxim number of waves */
                    994: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
                    995: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
                    996: int gipmx=0, gsw=0; /* Global variables on the number of contributions 
1.126     brouard   997:                   to the likelihood and the sum of weights (done by funcone)*/
1.130     brouard   998: int mle=1, weightopt=0;
1.126     brouard   999: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
                   1000: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
                   1001: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
                   1002:           * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162     brouard  1003: int countcallfunc=0;  /* Count the number of calls to func */
1.230     brouard  1004: int selected(int kvar); /* Is covariate kvar selected for printing results */
                   1005: 
1.130     brouard  1006: double jmean=1; /* Mean space between 2 waves */
1.145     brouard  1007: double **matprod2(); /* test */
1.126     brouard  1008: double **oldm, **newm, **savm; /* Working pointers to matrices */
                   1009: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218     brouard  1010: double  **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
                   1011: 
1.136     brouard  1012: /*FILE *fic ; */ /* Used in readdata only */
1.217     brouard  1013: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126     brouard  1014: FILE *ficlog, *ficrespow;
1.130     brouard  1015: int globpr=0; /* Global variable for printing or not */
1.126     brouard  1016: double fretone; /* Only one call to likelihood */
1.130     brouard  1017: long ipmx=0; /* Number of contributions */
1.126     brouard  1018: double sw; /* Sum of weights */
                   1019: char filerespow[FILENAMELENGTH];
                   1020: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
                   1021: FILE *ficresilk;
                   1022: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
                   1023: FILE *ficresprobmorprev;
                   1024: FILE *fichtm, *fichtmcov; /* Html File */
                   1025: FILE *ficreseij;
                   1026: char filerese[FILENAMELENGTH];
                   1027: FILE *ficresstdeij;
                   1028: char fileresstde[FILENAMELENGTH];
                   1029: FILE *ficrescveij;
                   1030: char filerescve[FILENAMELENGTH];
                   1031: FILE  *ficresvij;
                   1032: char fileresv[FILENAMELENGTH];
                   1033: FILE  *ficresvpl;
                   1034: char fileresvpl[FILENAMELENGTH];
                   1035: char title[MAXLINE];
1.234     brouard  1036: char model[MAXLINE]; /**< The model line */
1.217     brouard  1037: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
1.126     brouard  1038: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
                   1039: char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
                   1040: char command[FILENAMELENGTH];
                   1041: int  outcmd=0;
                   1042: 
1.217     brouard  1043: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202     brouard  1044: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126     brouard  1045: char filelog[FILENAMELENGTH]; /* Log file */
                   1046: char filerest[FILENAMELENGTH];
                   1047: char fileregp[FILENAMELENGTH];
                   1048: char popfile[FILENAMELENGTH];
                   1049: 
                   1050: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
                   1051: 
1.157     brouard  1052: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
                   1053: /* struct timezone tzp; */
                   1054: /* extern int gettimeofday(); */
                   1055: struct tm tml, *gmtime(), *localtime();
                   1056: 
                   1057: extern time_t time();
                   1058: 
                   1059: struct tm start_time, end_time, curr_time, last_time, forecast_time;
                   1060: time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
                   1061: struct tm tm;
                   1062: 
1.126     brouard  1063: char strcurr[80], strfor[80];
                   1064: 
                   1065: char *endptr;
                   1066: long lval;
                   1067: double dval;
                   1068: 
                   1069: #define NR_END 1
                   1070: #define FREE_ARG char*
                   1071: #define FTOL 1.0e-10
                   1072: 
                   1073: #define NRANSI 
1.240     brouard  1074: #define ITMAX 200
                   1075: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ 
1.126     brouard  1076: 
                   1077: #define TOL 2.0e-4 
                   1078: 
                   1079: #define CGOLD 0.3819660 
                   1080: #define ZEPS 1.0e-10 
                   1081: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
                   1082: 
                   1083: #define GOLD 1.618034 
                   1084: #define GLIMIT 100.0 
                   1085: #define TINY 1.0e-20 
                   1086: 
                   1087: static double maxarg1,maxarg2;
                   1088: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
                   1089: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                   1090:   
                   1091: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
                   1092: #define rint(a) floor(a+0.5)
1.166     brouard  1093: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183     brouard  1094: #define mytinydouble 1.0e-16
1.166     brouard  1095: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
                   1096: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
                   1097: /* static double dsqrarg; */
                   1098: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126     brouard  1099: static double sqrarg;
                   1100: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
                   1101: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                   1102: int agegomp= AGEGOMP;
                   1103: 
                   1104: int imx; 
                   1105: int stepm=1;
                   1106: /* Stepm, step in month: minimum step interpolation*/
                   1107: 
                   1108: int estepm;
                   1109: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
                   1110: 
                   1111: int m,nb;
                   1112: long *num;
1.197     brouard  1113: int firstpass=0, lastpass=4,*cod, *cens;
1.192     brouard  1114: int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                   1115:                   covariate for which somebody answered excluding 
                   1116:                   undefined. Usually 2: 0 and 1. */
                   1117: int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
                   1118:                             covariate for which somebody answered including 
                   1119:                             undefined. Usually 3: -1, 0 and 1. */
1.126     brouard  1120: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218     brouard  1121: double **pmmij, ***probs; /* Global pointer */
1.219     brouard  1122: double ***mobaverage, ***mobaverages; /* New global variable */
1.126     brouard  1123: double *ageexmed,*agecens;
                   1124: double dateintmean=0;
                   1125: 
                   1126: double *weight;
                   1127: int **s; /* Status */
1.141     brouard  1128: double *agedc;
1.145     brouard  1129: double  **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141     brouard  1130:                  * covar=matrix(0,NCOVMAX,1,n); 
1.187     brouard  1131:                  * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225     brouard  1132: double **coqvar; /* Fixed quantitative covariate iqv */
                   1133: double ***cotvar; /* Time varying covariate itv */
                   1134: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141     brouard  1135: double  idx; 
                   1136: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234     brouard  1137: /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1138: /*k          1  2   3   4     5    6    7     8    9 */
                   1139: /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
                   1140: /* Tndvar[k]    1   2   3               4          5 */
                   1141: /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
                   1142: /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
                   1143: /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
                   1144: /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
                   1145: /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
                   1146: /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
                   1147: /* Tprod[i]=k           4               7            */
                   1148: /* Tage[i]=k                  5               8      */
                   1149: /* */
                   1150: /* Type                    */
                   1151: /* V         1  2  3  4  5 */
                   1152: /*           F  F  V  V  V */
                   1153: /*           D  Q  D  D  Q */
                   1154: /*                         */
                   1155: int *TvarsD;
                   1156: int *TvarsDind;
                   1157: int *TvarsQ;
                   1158: int *TvarsQind;
                   1159: 
1.235     brouard  1160: #define MAXRESULTLINES 10
                   1161: int nresult=0;
                   1162: int TKresult[MAXRESULTLINES];
1.237     brouard  1163: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
                   1164: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235     brouard  1165: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
                   1166: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237     brouard  1167: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235     brouard  1168: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
                   1169: 
1.234     brouard  1170: /* 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  1171: 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 */
                   1172: 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 */
                   1173: 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 */
                   1174: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1175: 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 */
                   1176: 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  1177: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1178: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   1179: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1180: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1181: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1182: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
                   1183: 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 */
                   1184: 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 */
                   1185: 
1.230     brouard  1186: int *Tvarsel; /**< Selected covariates for output */
                   1187: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226     brouard  1188: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
1.227     brouard  1189: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
                   1190: 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  1191: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
                   1192: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197     brouard  1193: int *Tage;
1.227     brouard  1194: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
1.228     brouard  1195: 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  1196: 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*/ 
                   1197: 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  1198: int *Ndum; /** Freq of modality (tricode */
1.200     brouard  1199: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227     brouard  1200: int **Tvard;
                   1201: int *Tprod;/**< Gives the k position of the k1 product */
1.238     brouard  1202: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
1.227     brouard  1203: int *Tposprod; /**< Gives the k1 product from the k position */
1.238     brouard  1204:    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
                   1205:    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227     brouard  1206: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126     brouard  1207: double *lsurv, *lpop, *tpop;
                   1208: 
1.231     brouard  1209: #define FD 1; /* Fixed dummy covariate */
                   1210: #define FQ 2; /* Fixed quantitative covariate */
                   1211: #define FP 3; /* Fixed product covariate */
                   1212: #define FPDD 7; /* Fixed product dummy*dummy covariate */
                   1213: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
                   1214: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
                   1215: #define VD 10; /* Varying dummy covariate */
                   1216: #define VQ 11; /* Varying quantitative covariate */
                   1217: #define VP 12; /* Varying product covariate */
                   1218: #define VPDD 13; /* Varying product dummy*dummy covariate */
                   1219: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
                   1220: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
                   1221: #define APFD 16; /* Age product * fixed dummy covariate */
                   1222: #define APFQ 17; /* Age product * fixed quantitative covariate */
                   1223: #define APVD 18; /* Age product * varying dummy covariate */
                   1224: #define APVQ 19; /* Age product * varying quantitative covariate */
                   1225: 
                   1226: #define FTYPE 1; /* Fixed covariate */
                   1227: #define VTYPE 2; /* Varying covariate (loop in wave) */
                   1228: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
                   1229: 
                   1230: struct kmodel{
                   1231:        int maintype; /* main type */
                   1232:        int subtype; /* subtype */
                   1233: };
                   1234: struct kmodel modell[NCOVMAX];
                   1235: 
1.143     brouard  1236: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
                   1237: double ftolhess; /**< Tolerance for computing hessian */
1.126     brouard  1238: 
                   1239: /**************** split *************************/
                   1240: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
                   1241: {
                   1242:   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
                   1243:      the name of the file (name), its extension only (ext) and its first part of the name (finame)
                   1244:   */ 
                   1245:   char *ss;                            /* pointer */
1.186     brouard  1246:   int  l1=0, l2=0;                             /* length counters */
1.126     brouard  1247: 
                   1248:   l1 = strlen(path );                  /* length of path */
                   1249:   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
                   1250:   ss= strrchr( path, DIRSEPARATOR );           /* find last / */
                   1251:   if ( ss == NULL ) {                  /* no directory, so determine current directory */
                   1252:     strcpy( name, path );              /* we got the fullname name because no directory */
                   1253:     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
                   1254:       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
                   1255:     /* get current working directory */
                   1256:     /*    extern  char* getcwd ( char *buf , int len);*/
1.184     brouard  1257: #ifdef WIN32
                   1258:     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
                   1259: #else
                   1260:        if (getcwd(dirc, FILENAME_MAX) == NULL) {
                   1261: #endif
1.126     brouard  1262:       return( GLOCK_ERROR_GETCWD );
                   1263:     }
                   1264:     /* got dirc from getcwd*/
                   1265:     printf(" DIRC = %s \n",dirc);
1.205     brouard  1266:   } else {                             /* strip directory from path */
1.126     brouard  1267:     ss++;                              /* after this, the filename */
                   1268:     l2 = strlen( ss );                 /* length of filename */
                   1269:     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
                   1270:     strcpy( name, ss );                /* save file name */
                   1271:     strncpy( dirc, path, l1 - l2 );    /* now the directory */
1.186     brouard  1272:     dirc[l1-l2] = '\0';                        /* add zero */
1.126     brouard  1273:     printf(" DIRC2 = %s \n",dirc);
                   1274:   }
                   1275:   /* We add a separator at the end of dirc if not exists */
                   1276:   l1 = strlen( dirc );                 /* length of directory */
                   1277:   if( dirc[l1-1] != DIRSEPARATOR ){
                   1278:     dirc[l1] =  DIRSEPARATOR;
                   1279:     dirc[l1+1] = 0; 
                   1280:     printf(" DIRC3 = %s \n",dirc);
                   1281:   }
                   1282:   ss = strrchr( name, '.' );           /* find last / */
                   1283:   if (ss >0){
                   1284:     ss++;
                   1285:     strcpy(ext,ss);                    /* save extension */
                   1286:     l1= strlen( name);
                   1287:     l2= strlen(ss)+1;
                   1288:     strncpy( finame, name, l1-l2);
                   1289:     finame[l1-l2]= 0;
                   1290:   }
                   1291: 
                   1292:   return( 0 );                         /* we're done */
                   1293: }
                   1294: 
                   1295: 
                   1296: /******************************************/
                   1297: 
                   1298: void replace_back_to_slash(char *s, char*t)
                   1299: {
                   1300:   int i;
                   1301:   int lg=0;
                   1302:   i=0;
                   1303:   lg=strlen(t);
                   1304:   for(i=0; i<= lg; i++) {
                   1305:     (s[i] = t[i]);
                   1306:     if (t[i]== '\\') s[i]='/';
                   1307:   }
                   1308: }
                   1309: 
1.132     brouard  1310: char *trimbb(char *out, char *in)
1.137     brouard  1311: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132     brouard  1312:   char *s;
                   1313:   s=out;
                   1314:   while (*in != '\0'){
1.137     brouard  1315:     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132     brouard  1316:       in++;
                   1317:     }
                   1318:     *out++ = *in++;
                   1319:   }
                   1320:   *out='\0';
                   1321:   return s;
                   1322: }
                   1323: 
1.187     brouard  1324: /* char *substrchaine(char *out, char *in, char *chain) */
                   1325: /* { */
                   1326: /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
                   1327: /*   char *s, *t; */
                   1328: /*   t=in;s=out; */
                   1329: /*   while ((*in != *chain) && (*in != '\0')){ */
                   1330: /*     *out++ = *in++; */
                   1331: /*   } */
                   1332: 
                   1333: /*   /\* *in matches *chain *\/ */
                   1334: /*   while ((*in++ == *chain++) && (*in != '\0')){ */
                   1335: /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
                   1336: /*   } */
                   1337: /*   in--; chain--; */
                   1338: /*   while ( (*in != '\0')){ */
                   1339: /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
                   1340: /*     *out++ = *in++; */
                   1341: /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
                   1342: /*   } */
                   1343: /*   *out='\0'; */
                   1344: /*   out=s; */
                   1345: /*   return out; */
                   1346: /* } */
                   1347: char *substrchaine(char *out, char *in, char *chain)
                   1348: {
                   1349:   /* Substract chain 'chain' from 'in', return and output 'out' */
                   1350:   /* in="V1+V1*age+age*age+V2", chain="age*age" */
                   1351: 
                   1352:   char *strloc;
                   1353: 
                   1354:   strcpy (out, in); 
                   1355:   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
                   1356:   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
                   1357:   if(strloc != NULL){ 
                   1358:     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
                   1359:     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
                   1360:     /* strcpy (strloc, strloc +strlen(chain));*/
                   1361:   }
                   1362:   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
                   1363:   return out;
                   1364: }
                   1365: 
                   1366: 
1.145     brouard  1367: char *cutl(char *blocc, char *alocc, char *in, char occ)
                   1368: {
1.187     brouard  1369:   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
1.145     brouard  1370:      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187     brouard  1371:      gives blocc="abcdef" and alocc="ghi2j".
1.145     brouard  1372:      If occ is not found blocc is null and alocc is equal to in. Returns blocc
                   1373:   */
1.160     brouard  1374:   char *s, *t;
1.145     brouard  1375:   t=in;s=in;
                   1376:   while ((*in != occ) && (*in != '\0')){
                   1377:     *alocc++ = *in++;
                   1378:   }
                   1379:   if( *in == occ){
                   1380:     *(alocc)='\0';
                   1381:     s=++in;
                   1382:   }
                   1383:  
                   1384:   if (s == t) {/* occ not found */
                   1385:     *(alocc-(in-s))='\0';
                   1386:     in=s;
                   1387:   }
                   1388:   while ( *in != '\0'){
                   1389:     *blocc++ = *in++;
                   1390:   }
                   1391: 
                   1392:   *blocc='\0';
                   1393:   return t;
                   1394: }
1.137     brouard  1395: char *cutv(char *blocc, char *alocc, char *in, char occ)
                   1396: {
1.187     brouard  1397:   /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
1.137     brouard  1398:      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                   1399:      gives blocc="abcdef2ghi" and alocc="j".
                   1400:      If occ is not found blocc is null and alocc is equal to in. Returns alocc
                   1401:   */
                   1402:   char *s, *t;
                   1403:   t=in;s=in;
                   1404:   while (*in != '\0'){
                   1405:     while( *in == occ){
                   1406:       *blocc++ = *in++;
                   1407:       s=in;
                   1408:     }
                   1409:     *blocc++ = *in++;
                   1410:   }
                   1411:   if (s == t) /* occ not found */
                   1412:     *(blocc-(in-s))='\0';
                   1413:   else
                   1414:     *(blocc-(in-s)-1)='\0';
                   1415:   in=s;
                   1416:   while ( *in != '\0'){
                   1417:     *alocc++ = *in++;
                   1418:   }
                   1419: 
                   1420:   *alocc='\0';
                   1421:   return s;
                   1422: }
                   1423: 
1.126     brouard  1424: int nbocc(char *s, char occ)
                   1425: {
                   1426:   int i,j=0;
                   1427:   int lg=20;
                   1428:   i=0;
                   1429:   lg=strlen(s);
                   1430:   for(i=0; i<= lg; i++) {
1.234     brouard  1431:     if  (s[i] == occ ) j++;
1.126     brouard  1432:   }
                   1433:   return j;
                   1434: }
                   1435: 
1.137     brouard  1436: /* void cutv(char *u,char *v, char*t, char occ) */
                   1437: /* { */
                   1438: /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
                   1439: /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
                   1440: /*      gives u="abcdef2ghi" and v="j" *\/ */
                   1441: /*   int i,lg,j,p=0; */
                   1442: /*   i=0; */
                   1443: /*   lg=strlen(t); */
                   1444: /*   for(j=0; j<=lg-1; j++) { */
                   1445: /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
                   1446: /*   } */
1.126     brouard  1447: 
1.137     brouard  1448: /*   for(j=0; j<p; j++) { */
                   1449: /*     (u[j] = t[j]); */
                   1450: /*   } */
                   1451: /*      u[p]='\0'; */
1.126     brouard  1452: 
1.137     brouard  1453: /*    for(j=0; j<= lg; j++) { */
                   1454: /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
                   1455: /*   } */
                   1456: /* } */
1.126     brouard  1457: 
1.160     brouard  1458: #ifdef _WIN32
                   1459: char * strsep(char **pp, const char *delim)
                   1460: {
                   1461:   char *p, *q;
                   1462:          
                   1463:   if ((p = *pp) == NULL)
                   1464:     return 0;
                   1465:   if ((q = strpbrk (p, delim)) != NULL)
                   1466:   {
                   1467:     *pp = q + 1;
                   1468:     *q = '\0';
                   1469:   }
                   1470:   else
                   1471:     *pp = 0;
                   1472:   return p;
                   1473: }
                   1474: #endif
                   1475: 
1.126     brouard  1476: /********************** nrerror ********************/
                   1477: 
                   1478: void nrerror(char error_text[])
                   1479: {
                   1480:   fprintf(stderr,"ERREUR ...\n");
                   1481:   fprintf(stderr,"%s\n",error_text);
                   1482:   exit(EXIT_FAILURE);
                   1483: }
                   1484: /*********************** vector *******************/
                   1485: double *vector(int nl, int nh)
                   1486: {
                   1487:   double *v;
                   1488:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
                   1489:   if (!v) nrerror("allocation failure in vector");
                   1490:   return v-nl+NR_END;
                   1491: }
                   1492: 
                   1493: /************************ free vector ******************/
                   1494: void free_vector(double*v, int nl, int nh)
                   1495: {
                   1496:   free((FREE_ARG)(v+nl-NR_END));
                   1497: }
                   1498: 
                   1499: /************************ivector *******************************/
                   1500: int *ivector(long nl,long nh)
                   1501: {
                   1502:   int *v;
                   1503:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                   1504:   if (!v) nrerror("allocation failure in ivector");
                   1505:   return v-nl+NR_END;
                   1506: }
                   1507: 
                   1508: /******************free ivector **************************/
                   1509: void free_ivector(int *v, long nl, long nh)
                   1510: {
                   1511:   free((FREE_ARG)(v+nl-NR_END));
                   1512: }
                   1513: 
                   1514: /************************lvector *******************************/
                   1515: long *lvector(long nl,long nh)
                   1516: {
                   1517:   long *v;
                   1518:   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
                   1519:   if (!v) nrerror("allocation failure in ivector");
                   1520:   return v-nl+NR_END;
                   1521: }
                   1522: 
                   1523: /******************free lvector **************************/
                   1524: void free_lvector(long *v, long nl, long nh)
                   1525: {
                   1526:   free((FREE_ARG)(v+nl-NR_END));
                   1527: }
                   1528: 
                   1529: /******************* imatrix *******************************/
                   1530: int **imatrix(long nrl, long nrh, long ncl, long nch) 
                   1531:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
                   1532: { 
                   1533:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
                   1534:   int **m; 
                   1535:   
                   1536:   /* allocate pointers to rows */ 
                   1537:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
                   1538:   if (!m) nrerror("allocation failure 1 in matrix()"); 
                   1539:   m += NR_END; 
                   1540:   m -= nrl; 
                   1541:   
                   1542:   
                   1543:   /* allocate rows and set pointers to them */ 
                   1544:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
                   1545:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
                   1546:   m[nrl] += NR_END; 
                   1547:   m[nrl] -= ncl; 
                   1548:   
                   1549:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
                   1550:   
                   1551:   /* return pointer to array of pointers to rows */ 
                   1552:   return m; 
                   1553: } 
                   1554: 
                   1555: /****************** free_imatrix *************************/
                   1556: void free_imatrix(m,nrl,nrh,ncl,nch)
                   1557:       int **m;
                   1558:       long nch,ncl,nrh,nrl; 
                   1559:      /* free an int matrix allocated by imatrix() */ 
                   1560: { 
                   1561:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
                   1562:   free((FREE_ARG) (m+nrl-NR_END)); 
                   1563: } 
                   1564: 
                   1565: /******************* matrix *******************************/
                   1566: double **matrix(long nrl, long nrh, long ncl, long nch)
                   1567: {
                   1568:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
                   1569:   double **m;
                   1570: 
                   1571:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                   1572:   if (!m) nrerror("allocation failure 1 in matrix()");
                   1573:   m += NR_END;
                   1574:   m -= nrl;
                   1575: 
                   1576:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                   1577:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                   1578:   m[nrl] += NR_END;
                   1579:   m[nrl] -= ncl;
                   1580: 
                   1581:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                   1582:   return m;
1.145     brouard  1583:   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
                   1584: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
                   1585: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126     brouard  1586:    */
                   1587: }
                   1588: 
                   1589: /*************************free matrix ************************/
                   1590: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
                   1591: {
                   1592:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                   1593:   free((FREE_ARG)(m+nrl-NR_END));
                   1594: }
                   1595: 
                   1596: /******************* ma3x *******************************/
                   1597: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
                   1598: {
                   1599:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
                   1600:   double ***m;
                   1601: 
                   1602:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                   1603:   if (!m) nrerror("allocation failure 1 in matrix()");
                   1604:   m += NR_END;
                   1605:   m -= nrl;
                   1606: 
                   1607:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                   1608:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                   1609:   m[nrl] += NR_END;
                   1610:   m[nrl] -= ncl;
                   1611: 
                   1612:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                   1613: 
                   1614:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                   1615:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
                   1616:   m[nrl][ncl] += NR_END;
                   1617:   m[nrl][ncl] -= nll;
                   1618:   for (j=ncl+1; j<=nch; j++) 
                   1619:     m[nrl][j]=m[nrl][j-1]+nlay;
                   1620:   
                   1621:   for (i=nrl+1; i<=nrh; i++) {
                   1622:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
                   1623:     for (j=ncl+1; j<=nch; j++) 
                   1624:       m[i][j]=m[i][j-1]+nlay;
                   1625:   }
                   1626:   return m; 
                   1627:   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                   1628:            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
                   1629:   */
                   1630: }
                   1631: 
                   1632: /*************************free ma3x ************************/
                   1633: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                   1634: {
                   1635:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                   1636:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                   1637:   free((FREE_ARG)(m+nrl-NR_END));
                   1638: }
                   1639: 
                   1640: /*************** function subdirf ***********/
                   1641: char *subdirf(char fileres[])
                   1642: {
                   1643:   /* Caution optionfilefiname is hidden */
                   1644:   strcpy(tmpout,optionfilefiname);
                   1645:   strcat(tmpout,"/"); /* Add to the right */
                   1646:   strcat(tmpout,fileres);
                   1647:   return tmpout;
                   1648: }
                   1649: 
                   1650: /*************** function subdirf2 ***********/
                   1651: char *subdirf2(char fileres[], char *preop)
                   1652: {
                   1653:   
                   1654:   /* Caution optionfilefiname is hidden */
                   1655:   strcpy(tmpout,optionfilefiname);
                   1656:   strcat(tmpout,"/");
                   1657:   strcat(tmpout,preop);
                   1658:   strcat(tmpout,fileres);
                   1659:   return tmpout;
                   1660: }
                   1661: 
                   1662: /*************** function subdirf3 ***********/
                   1663: char *subdirf3(char fileres[], char *preop, char *preop2)
                   1664: {
                   1665:   
                   1666:   /* Caution optionfilefiname is hidden */
                   1667:   strcpy(tmpout,optionfilefiname);
                   1668:   strcat(tmpout,"/");
                   1669:   strcat(tmpout,preop);
                   1670:   strcat(tmpout,preop2);
                   1671:   strcat(tmpout,fileres);
                   1672:   return tmpout;
                   1673: }
1.213     brouard  1674:  
                   1675: /*************** function subdirfext ***********/
                   1676: char *subdirfext(char fileres[], char *preop, char *postop)
                   1677: {
                   1678:   
                   1679:   strcpy(tmpout,preop);
                   1680:   strcat(tmpout,fileres);
                   1681:   strcat(tmpout,postop);
                   1682:   return tmpout;
                   1683: }
1.126     brouard  1684: 
1.213     brouard  1685: /*************** function subdirfext3 ***********/
                   1686: char *subdirfext3(char fileres[], char *preop, char *postop)
                   1687: {
                   1688:   
                   1689:   /* Caution optionfilefiname is hidden */
                   1690:   strcpy(tmpout,optionfilefiname);
                   1691:   strcat(tmpout,"/");
                   1692:   strcat(tmpout,preop);
                   1693:   strcat(tmpout,fileres);
                   1694:   strcat(tmpout,postop);
                   1695:   return tmpout;
                   1696: }
                   1697:  
1.162     brouard  1698: char *asc_diff_time(long time_sec, char ascdiff[])
                   1699: {
                   1700:   long sec_left, days, hours, minutes;
                   1701:   days = (time_sec) / (60*60*24);
                   1702:   sec_left = (time_sec) % (60*60*24);
                   1703:   hours = (sec_left) / (60*60) ;
                   1704:   sec_left = (sec_left) %(60*60);
                   1705:   minutes = (sec_left) /60;
                   1706:   sec_left = (sec_left) % (60);
                   1707:   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
                   1708:   return ascdiff;
                   1709: }
                   1710: 
1.126     brouard  1711: /***************** f1dim *************************/
                   1712: extern int ncom; 
                   1713: extern double *pcom,*xicom;
                   1714: extern double (*nrfunc)(double []); 
                   1715:  
                   1716: double f1dim(double x) 
                   1717: { 
                   1718:   int j; 
                   1719:   double f;
                   1720:   double *xt; 
                   1721:  
                   1722:   xt=vector(1,ncom); 
                   1723:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
                   1724:   f=(*nrfunc)(xt); 
                   1725:   free_vector(xt,1,ncom); 
                   1726:   return f; 
                   1727: } 
                   1728: 
                   1729: /*****************brent *************************/
                   1730: double brent(double ax, double bx, double cx, double (*f)(double), double tol,         double *xmin) 
1.187     brouard  1731: {
                   1732:   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
                   1733:    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
                   1734:    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
                   1735:    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
                   1736:    * returned function value. 
                   1737:   */
1.126     brouard  1738:   int iter; 
                   1739:   double a,b,d,etemp;
1.159     brouard  1740:   double fu=0,fv,fw,fx;
1.164     brouard  1741:   double ftemp=0.;
1.126     brouard  1742:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
                   1743:   double e=0.0; 
                   1744:  
                   1745:   a=(ax < cx ? ax : cx); 
                   1746:   b=(ax > cx ? ax : cx); 
                   1747:   x=w=v=bx; 
                   1748:   fw=fv=fx=(*f)(x); 
                   1749:   for (iter=1;iter<=ITMAX;iter++) { 
                   1750:     xm=0.5*(a+b); 
                   1751:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                   1752:     /*         if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                   1753:     printf(".");fflush(stdout);
                   1754:     fprintf(ficlog,".");fflush(ficlog);
1.162     brouard  1755: #ifdef DEBUGBRENT
1.126     brouard  1756:     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);
                   1757:     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);
                   1758:     /*         if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                   1759: #endif
                   1760:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                   1761:       *xmin=x; 
                   1762:       return fx; 
                   1763:     } 
                   1764:     ftemp=fu;
                   1765:     if (fabs(e) > tol1) { 
                   1766:       r=(x-w)*(fx-fv); 
                   1767:       q=(x-v)*(fx-fw); 
                   1768:       p=(x-v)*q-(x-w)*r; 
                   1769:       q=2.0*(q-r); 
                   1770:       if (q > 0.0) p = -p; 
                   1771:       q=fabs(q); 
                   1772:       etemp=e; 
                   1773:       e=d; 
                   1774:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
1.224     brouard  1775:                                d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
1.126     brouard  1776:       else { 
1.224     brouard  1777:                                d=p/q; 
                   1778:                                u=x+d; 
                   1779:                                if (u-a < tol2 || b-u < tol2) 
                   1780:                                        d=SIGN(tol1,xm-x); 
1.126     brouard  1781:       } 
                   1782:     } else { 
                   1783:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                   1784:     } 
                   1785:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                   1786:     fu=(*f)(u); 
                   1787:     if (fu <= fx) { 
                   1788:       if (u >= x) a=x; else b=x; 
                   1789:       SHFT(v,w,x,u) 
1.183     brouard  1790:       SHFT(fv,fw,fx,fu) 
                   1791:     } else { 
                   1792:       if (u < x) a=u; else b=u; 
                   1793:       if (fu <= fw || w == x) { 
1.224     brouard  1794:                                v=w; 
                   1795:                                w=u; 
                   1796:                                fv=fw; 
                   1797:                                fw=fu; 
1.183     brouard  1798:       } else if (fu <= fv || v == x || v == w) { 
1.224     brouard  1799:                                v=u; 
                   1800:                                fv=fu; 
1.183     brouard  1801:       } 
                   1802:     } 
1.126     brouard  1803:   } 
                   1804:   nrerror("Too many iterations in brent"); 
                   1805:   *xmin=x; 
                   1806:   return fx; 
                   1807: } 
                   1808: 
                   1809: /****************** mnbrak ***********************/
                   1810: 
                   1811: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                   1812:            double (*func)(double)) 
1.183     brouard  1813: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
                   1814: the downhill direction (defined by the function as evaluated at the initial points) and returns
                   1815: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
                   1816: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
                   1817:    */
1.126     brouard  1818:   double ulim,u,r,q, dum;
                   1819:   double fu; 
1.187     brouard  1820: 
                   1821:   double scale=10.;
                   1822:   int iterscale=0;
                   1823: 
                   1824:   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
                   1825:   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
                   1826: 
                   1827: 
                   1828:   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
                   1829:   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
                   1830:   /*   *bx = *ax - (*ax - *bx)/scale; */
                   1831:   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
                   1832:   /* } */
                   1833: 
1.126     brouard  1834:   if (*fb > *fa) { 
                   1835:     SHFT(dum,*ax,*bx,dum) 
1.183     brouard  1836:     SHFT(dum,*fb,*fa,dum) 
                   1837:   } 
1.126     brouard  1838:   *cx=(*bx)+GOLD*(*bx-*ax); 
                   1839:   *fc=(*func)(*cx); 
1.183     brouard  1840: #ifdef DEBUG
1.224     brouard  1841:   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
                   1842:   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  1843: #endif
1.224     brouard  1844:   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  1845:     r=(*bx-*ax)*(*fb-*fc); 
1.224     brouard  1846:     q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126     brouard  1847:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
1.183     brouard  1848:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
                   1849:     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
                   1850:     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126     brouard  1851:       fu=(*func)(u); 
1.163     brouard  1852: #ifdef DEBUG
                   1853:       /* f(x)=A(x-u)**2+f(u) */
                   1854:       double A, fparabu; 
                   1855:       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
                   1856:       fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224     brouard  1857:       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);
                   1858:       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  1859:       /* And thus,it can be that fu > *fc even if fparabu < *fc */
                   1860:       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
                   1861:         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
                   1862:       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163     brouard  1863: #endif 
1.184     brouard  1864: #ifdef MNBRAKORIGINAL
1.183     brouard  1865: #else
1.191     brouard  1866: /*       if (fu > *fc) { */
                   1867: /* #ifdef DEBUG */
                   1868: /*       printf("mnbrak4  fu > fc \n"); */
                   1869: /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
                   1870: /* #endif */
                   1871: /*     /\* 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 *\\/  *\/ */
                   1872: /*     /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
                   1873: /*     dum=u; /\* Shifting c and u *\/ */
                   1874: /*     u = *cx; */
                   1875: /*     *cx = dum; */
                   1876: /*     dum = fu; */
                   1877: /*     fu = *fc; */
                   1878: /*     *fc =dum; */
                   1879: /*       } else { /\* end *\/ */
                   1880: /* #ifdef DEBUG */
                   1881: /*       printf("mnbrak3  fu < fc \n"); */
                   1882: /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
                   1883: /* #endif */
                   1884: /*     dum=u; /\* Shifting c and u *\/ */
                   1885: /*     u = *cx; */
                   1886: /*     *cx = dum; */
                   1887: /*     dum = fu; */
                   1888: /*     fu = *fc; */
                   1889: /*     *fc =dum; */
                   1890: /*       } */
1.224     brouard  1891: #ifdef DEBUGMNBRAK
                   1892:                 double A, fparabu; 
                   1893:      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
                   1894:      fparabu= *fa - A*(*ax-u)*(*ax-u);
                   1895:      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);
                   1896:      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  1897: #endif
1.191     brouard  1898:       dum=u; /* Shifting c and u */
                   1899:       u = *cx;
                   1900:       *cx = dum;
                   1901:       dum = fu;
                   1902:       fu = *fc;
                   1903:       *fc =dum;
1.183     brouard  1904: #endif
1.162     brouard  1905:     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183     brouard  1906: #ifdef DEBUG
1.224     brouard  1907:       printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
                   1908:       fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
1.183     brouard  1909: #endif
1.126     brouard  1910:       fu=(*func)(u); 
                   1911:       if (fu < *fc) { 
1.183     brouard  1912: #ifdef DEBUG
1.224     brouard  1913:                                printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
                   1914:                          fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
                   1915: #endif
                   1916:                          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                   1917:                                SHFT(*fb,*fc,fu,(*func)(u)) 
                   1918: #ifdef DEBUG
                   1919:                                        printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183     brouard  1920: #endif
                   1921:       } 
1.162     brouard  1922:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183     brouard  1923: #ifdef DEBUG
1.224     brouard  1924:       printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
                   1925:       fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183     brouard  1926: #endif
1.126     brouard  1927:       u=ulim; 
                   1928:       fu=(*func)(u); 
1.183     brouard  1929:     } else { /* u could be left to b (if r > q parabola has a maximum) */
                   1930: #ifdef DEBUG
1.224     brouard  1931:       printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
                   1932:       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  1933: #endif
1.126     brouard  1934:       u=(*cx)+GOLD*(*cx-*bx); 
                   1935:       fu=(*func)(u); 
1.224     brouard  1936: #ifdef DEBUG
                   1937:       printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
                   1938:       fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
                   1939: #endif
1.183     brouard  1940:     } /* end tests */
1.126     brouard  1941:     SHFT(*ax,*bx,*cx,u) 
1.183     brouard  1942:     SHFT(*fa,*fb,*fc,fu) 
                   1943: #ifdef DEBUG
1.224     brouard  1944:       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
                   1945:       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  1946: #endif
                   1947:   } /* 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  1948: } 
                   1949: 
                   1950: /*************** linmin ************************/
1.162     brouard  1951: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
                   1952: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
                   1953: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
                   1954: the value of func at the returned location p . This is actually all accomplished by calling the
                   1955: routines mnbrak and brent .*/
1.126     brouard  1956: int ncom; 
                   1957: double *pcom,*xicom;
                   1958: double (*nrfunc)(double []); 
                   1959:  
1.224     brouard  1960: #ifdef LINMINORIGINAL
1.126     brouard  1961: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
1.224     brouard  1962: #else
                   1963: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
                   1964: #endif
1.126     brouard  1965: { 
                   1966:   double brent(double ax, double bx, double cx, 
                   1967:               double (*f)(double), double tol, double *xmin); 
                   1968:   double f1dim(double x); 
                   1969:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                   1970:              double *fc, double (*func)(double)); 
                   1971:   int j; 
                   1972:   double xx,xmin,bx,ax; 
                   1973:   double fx,fb,fa;
1.187     brouard  1974: 
1.203     brouard  1975: #ifdef LINMINORIGINAL
                   1976: #else
                   1977:   double scale=10., axs, xxs; /* Scale added for infinity */
                   1978: #endif
                   1979:   
1.126     brouard  1980:   ncom=n; 
                   1981:   pcom=vector(1,n); 
                   1982:   xicom=vector(1,n); 
                   1983:   nrfunc=func; 
                   1984:   for (j=1;j<=n;j++) { 
                   1985:     pcom[j]=p[j]; 
1.202     brouard  1986:     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126     brouard  1987:   } 
1.187     brouard  1988: 
1.203     brouard  1989: #ifdef LINMINORIGINAL
                   1990:   xx=1.;
                   1991: #else
                   1992:   axs=0.0;
                   1993:   xxs=1.;
                   1994:   do{
                   1995:     xx= xxs;
                   1996: #endif
1.187     brouard  1997:     ax=0.;
                   1998:     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
                   1999:     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
                   2000:     /* 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))   */
                   2001:     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
                   2002:     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
                   2003:     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
                   2004:     /* 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  2005: #ifdef LINMINORIGINAL
                   2006: #else
                   2007:     if (fx != fx){
1.224     brouard  2008:                        xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
                   2009:                        printf("|");
                   2010:                        fprintf(ficlog,"|");
1.203     brouard  2011: #ifdef DEBUGLINMIN
1.224     brouard  2012:                        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  2013: #endif
                   2014:     }
1.224     brouard  2015:   }while(fx != fx && xxs > 1.e-5);
1.203     brouard  2016: #endif
                   2017:   
1.191     brouard  2018: #ifdef DEBUGLINMIN
                   2019:   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  2020:   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  2021: #endif
1.224     brouard  2022: #ifdef LINMINORIGINAL
                   2023: #else
                   2024:        if(fb == fx){ /* Flat function in the direction */
                   2025:                xmin=xx;
                   2026:     *flat=1;
                   2027:        }else{
                   2028:     *flat=0;
                   2029: #endif
                   2030:                /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187     brouard  2031:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
                   2032:   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
                   2033:   /* fmin = f(p[j] + xmin * xi[j]) */
                   2034:   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
                   2035:   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126     brouard  2036: #ifdef DEBUG
1.224     brouard  2037:   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);
                   2038:   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);
                   2039: #endif
                   2040: #ifdef LINMINORIGINAL
                   2041: #else
                   2042:                        }
1.126     brouard  2043: #endif
1.191     brouard  2044: #ifdef DEBUGLINMIN
                   2045:   printf("linmin end ");
1.202     brouard  2046:   fprintf(ficlog,"linmin end ");
1.191     brouard  2047: #endif
1.126     brouard  2048:   for (j=1;j<=n;j++) { 
1.203     brouard  2049: #ifdef LINMINORIGINAL
                   2050:     xi[j] *= xmin; 
                   2051: #else
                   2052: #ifdef DEBUGLINMIN
                   2053:     if(xxs <1.0)
                   2054:       printf(" before xi[%d]=%12.8f", j,xi[j]);
                   2055: #endif
                   2056:     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) */
                   2057: #ifdef DEBUGLINMIN
                   2058:     if(xxs <1.0)
                   2059:       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 );
                   2060: #endif
                   2061: #endif
1.187     brouard  2062:     p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126     brouard  2063:   } 
1.191     brouard  2064: #ifdef DEBUGLINMIN
1.203     brouard  2065:   printf("\n");
1.191     brouard  2066:   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202     brouard  2067:   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  2068:   for (j=1;j<=n;j++) { 
1.202     brouard  2069:     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
                   2070:     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
                   2071:     if(j % ncovmodel == 0){
1.191     brouard  2072:       printf("\n");
1.202     brouard  2073:       fprintf(ficlog,"\n");
                   2074:     }
1.191     brouard  2075:   }
1.203     brouard  2076: #else
1.191     brouard  2077: #endif
1.126     brouard  2078:   free_vector(xicom,1,n); 
                   2079:   free_vector(pcom,1,n); 
                   2080: } 
                   2081: 
                   2082: 
                   2083: /*************** powell ************************/
1.162     brouard  2084: /*
                   2085: Minimization of a function func of n variables. Input consists of an initial starting point
                   2086: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
                   2087: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
                   2088: such that failure to decrease by more than this amount on one iteration signals doneness. On
                   2089: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
                   2090: function value at p , and iter is the number of iterations taken. The routine linmin is used.
                   2091:  */
1.224     brouard  2092: #ifdef LINMINORIGINAL
                   2093: #else
                   2094:        int *flatdir; /* Function is vanishing in that direction */
1.225     brouard  2095:        int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224     brouard  2096: #endif
1.126     brouard  2097: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                   2098:            double (*func)(double [])) 
                   2099: { 
1.224     brouard  2100: #ifdef LINMINORIGINAL
                   2101:  void linmin(double p[], double xi[], int n, double *fret, 
1.126     brouard  2102:              double (*func)(double [])); 
1.224     brouard  2103: #else 
1.241     brouard  2104:  void linmin(double p[], double xi[], int n, double *fret,
                   2105:             double (*func)(double []),int *flat); 
1.224     brouard  2106: #endif
1.239     brouard  2107:  int i,ibig,j,jk,k; 
1.126     brouard  2108:   double del,t,*pt,*ptt,*xit;
1.181     brouard  2109:   double directest;
1.126     brouard  2110:   double fp,fptt;
                   2111:   double *xits;
                   2112:   int niterf, itmp;
1.224     brouard  2113: #ifdef LINMINORIGINAL
                   2114: #else
                   2115: 
                   2116:   flatdir=ivector(1,n); 
                   2117:   for (j=1;j<=n;j++) flatdir[j]=0; 
                   2118: #endif
1.126     brouard  2119: 
                   2120:   pt=vector(1,n); 
                   2121:   ptt=vector(1,n); 
                   2122:   xit=vector(1,n); 
                   2123:   xits=vector(1,n); 
                   2124:   *fret=(*func)(p); 
                   2125:   for (j=1;j<=n;j++) pt[j]=p[j]; 
1.202     brouard  2126:   rcurr_time = time(NULL);  
1.126     brouard  2127:   for (*iter=1;;++(*iter)) { 
1.187     brouard  2128:     fp=(*fret); /* From former iteration or initial value */
1.126     brouard  2129:     ibig=0; 
                   2130:     del=0.0; 
1.157     brouard  2131:     rlast_time=rcurr_time;
                   2132:     /* (void) gettimeofday(&curr_time,&tzp); */
                   2133:     rcurr_time = time(NULL);  
                   2134:     curr_time = *localtime(&rcurr_time);
                   2135:     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
                   2136:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
                   2137: /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192     brouard  2138:     for (i=1;i<=n;i++) {
1.126     brouard  2139:       fprintf(ficrespow," %.12lf", p[i]);
                   2140:     }
1.239     brouard  2141:     fprintf(ficrespow,"\n");fflush(ficrespow);
                   2142:     printf("\n#model=  1      +     age ");
                   2143:     fprintf(ficlog,"\n#model=  1      +     age ");
                   2144:     if(nagesqr==1){
1.241     brouard  2145:        printf("  + age*age  ");
                   2146:        fprintf(ficlog,"  + age*age  ");
1.239     brouard  2147:     }
                   2148:     for(j=1;j <=ncovmodel-2;j++){
                   2149:       if(Typevar[j]==0) {
                   2150:        printf("  +      V%d  ",Tvar[j]);
                   2151:        fprintf(ficlog,"  +      V%d  ",Tvar[j]);
                   2152:       }else if(Typevar[j]==1) {
                   2153:        printf("  +    V%d*age ",Tvar[j]);
                   2154:        fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
                   2155:       }else if(Typevar[j]==2) {
                   2156:        printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   2157:        fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
                   2158:       }
                   2159:     }
1.126     brouard  2160:     printf("\n");
1.239     brouard  2161: /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
                   2162: /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
1.126     brouard  2163:     fprintf(ficlog,"\n");
1.239     brouard  2164:     for(i=1,jk=1; i <=nlstate; i++){
                   2165:       for(k=1; k <=(nlstate+ndeath); k++){
                   2166:        if (k != i) {
                   2167:          printf("%d%d ",i,k);
                   2168:          fprintf(ficlog,"%d%d ",i,k);
                   2169:          for(j=1; j <=ncovmodel; j++){
                   2170:            printf("%12.7f ",p[jk]);
                   2171:            fprintf(ficlog,"%12.7f ",p[jk]);
                   2172:            jk++; 
                   2173:          }
                   2174:          printf("\n");
                   2175:          fprintf(ficlog,"\n");
                   2176:        }
                   2177:       }
                   2178:     }
1.241     brouard  2179:     if(*iter <=3 && *iter >1){
1.157     brouard  2180:       tml = *localtime(&rcurr_time);
                   2181:       strcpy(strcurr,asctime(&tml));
                   2182:       rforecast_time=rcurr_time; 
1.126     brouard  2183:       itmp = strlen(strcurr);
                   2184:       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
1.241     brouard  2185:        strcurr[itmp-1]='\0';
1.162     brouard  2186:       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157     brouard  2187:       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126     brouard  2188:       for(niterf=10;niterf<=30;niterf+=10){
1.241     brouard  2189:        rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                   2190:        forecast_time = *localtime(&rforecast_time);
                   2191:        strcpy(strfor,asctime(&forecast_time));
                   2192:        itmp = strlen(strfor);
                   2193:        if(strfor[itmp-1]=='\n')
                   2194:          strfor[itmp-1]='\0';
                   2195:        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);
                   2196:        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  2197:       }
                   2198:     }
1.187     brouard  2199:     for (i=1;i<=n;i++) { /* For each direction i */
                   2200:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126     brouard  2201:       fptt=(*fret); 
                   2202: #ifdef DEBUG
1.203     brouard  2203:       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
                   2204:       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126     brouard  2205: #endif
1.203     brouard  2206:       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126     brouard  2207:       fprintf(ficlog,"%d",i);fflush(ficlog);
1.224     brouard  2208: #ifdef LINMINORIGINAL
1.188     brouard  2209:       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224     brouard  2210: #else
                   2211:       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                   2212:                        flatdir[i]=flat; /* Function is vanishing in that direction i */
                   2213: #endif
                   2214:                        /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188     brouard  2215:       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224     brouard  2216:                                /* because that direction will be replaced unless the gain del is small */
                   2217:                                /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
                   2218:                                /* Unless the n directions are conjugate some gain in the determinant may be obtained */
                   2219:                                /* with the new direction. */
                   2220:                                del=fabs(fptt-(*fret)); 
                   2221:                                ibig=i; 
1.126     brouard  2222:       } 
                   2223: #ifdef DEBUG
                   2224:       printf("%d %.12e",i,(*fret));
                   2225:       fprintf(ficlog,"%d %.12e",i,(*fret));
                   2226:       for (j=1;j<=n;j++) {
1.224     brouard  2227:                                xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                   2228:                                printf(" x(%d)=%.12e",j,xit[j]);
                   2229:                                fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126     brouard  2230:       }
                   2231:       for(j=1;j<=n;j++) {
1.225     brouard  2232:                                printf(" p(%d)=%.12e",j,p[j]);
                   2233:                                fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126     brouard  2234:       }
                   2235:       printf("\n");
                   2236:       fprintf(ficlog,"\n");
                   2237: #endif
1.187     brouard  2238:     } /* end loop on each direction i */
                   2239:     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
1.188     brouard  2240:     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
1.187     brouard  2241:     /* New value of last point Pn is not computed, P(n-1) */
1.224     brouard  2242:       for(j=1;j<=n;j++) {
1.225     brouard  2243:                                if(flatdir[j] >0){
                   2244:                                        printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                   2245:                                        fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                   2246:                                }
                   2247:                                /* printf("\n"); */
                   2248:                                /* fprintf(ficlog,"\n"); */
                   2249:                        }
1.243     brouard  2250:     /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
                   2251:     if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188     brouard  2252:       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
                   2253:       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
                   2254:       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
                   2255:       /* decreased of more than 3.84  */
                   2256:       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
                   2257:       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
                   2258:       /* By adding 10 parameters more the gain should be 18.31 */
1.224     brouard  2259:                        
1.188     brouard  2260:       /* Starting the program with initial values given by a former maximization will simply change */
                   2261:       /* the scales of the directions and the directions, because the are reset to canonical directions */
                   2262:       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
                   2263:       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
1.126     brouard  2264: #ifdef DEBUG
                   2265:       int k[2],l;
                   2266:       k[0]=1;
                   2267:       k[1]=-1;
                   2268:       printf("Max: %.12e",(*func)(p));
                   2269:       fprintf(ficlog,"Max: %.12e",(*func)(p));
                   2270:       for (j=1;j<=n;j++) {
                   2271:        printf(" %.12e",p[j]);
                   2272:        fprintf(ficlog," %.12e",p[j]);
                   2273:       }
                   2274:       printf("\n");
                   2275:       fprintf(ficlog,"\n");
                   2276:       for(l=0;l<=1;l++) {
                   2277:        for (j=1;j<=n;j++) {
                   2278:          ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                   2279:          printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   2280:          fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   2281:        }
                   2282:        printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   2283:        fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   2284:       }
                   2285: #endif
                   2286: 
1.224     brouard  2287: #ifdef LINMINORIGINAL
                   2288: #else
                   2289:       free_ivector(flatdir,1,n); 
                   2290: #endif
1.126     brouard  2291:       free_vector(xit,1,n); 
                   2292:       free_vector(xits,1,n); 
                   2293:       free_vector(ptt,1,n); 
                   2294:       free_vector(pt,1,n); 
                   2295:       return; 
1.192     brouard  2296:     } /* enough precision */ 
1.240     brouard  2297:     if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); 
1.181     brouard  2298:     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126     brouard  2299:       ptt[j]=2.0*p[j]-pt[j]; 
                   2300:       xit[j]=p[j]-pt[j]; 
                   2301:       pt[j]=p[j]; 
                   2302:     } 
1.181     brouard  2303:     fptt=(*func)(ptt); /* f_3 */
1.224     brouard  2304: #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   2305:                if (*iter <=4) {
1.225     brouard  2306: #else
                   2307: #endif
1.224     brouard  2308: #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
1.192     brouard  2309: #else
1.161     brouard  2310:     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192     brouard  2311: #endif
1.162     brouard  2312:       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161     brouard  2313:       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162     brouard  2314:       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
                   2315:       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
                   2316:       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224     brouard  2317:       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
                   2318:       /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
                   2319:       /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161     brouard  2320:       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224     brouard  2321:       /*  Even if f3 <f1, directest can be negative and t >0 */
                   2322:       /* mu² and del² are equal when f3=f1 */
                   2323:                        /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
                   2324:                        /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
                   2325:                        /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
                   2326:                        /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
1.183     brouard  2327: #ifdef NRCORIGINAL
                   2328:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
                   2329: #else
                   2330:       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  2331:       t= t- del*SQR(fp-fptt);
1.183     brouard  2332: #endif
1.202     brouard  2333:       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161     brouard  2334: #ifdef DEBUG
1.181     brouard  2335:       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);
                   2336:       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  2337:       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                   2338:             (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
                   2339:       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                   2340:             (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
                   2341:       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);
                   2342:       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);
                   2343: #endif
1.183     brouard  2344: #ifdef POWELLORIGINAL
                   2345:       if (t < 0.0) { /* Then we use it for new direction */
                   2346: #else
1.182     brouard  2347:       if (directest*t < 0.0) { /* Contradiction between both tests */
1.224     brouard  2348:                                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  2349:         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  2350:         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  2351:         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
                   2352:       } 
1.181     brouard  2353:       if (directest < 0.0) { /* Then we use it for new direction */
                   2354: #endif
1.191     brouard  2355: #ifdef DEBUGLINMIN
1.234     brouard  2356:        printf("Before linmin in direction P%d-P0\n",n);
                   2357:        for (j=1;j<=n;j++) {
                   2358:          printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2359:          fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2360:          if(j % ncovmodel == 0){
                   2361:            printf("\n");
                   2362:            fprintf(ficlog,"\n");
                   2363:          }
                   2364:        }
1.224     brouard  2365: #endif
                   2366: #ifdef LINMINORIGINAL
1.234     brouard  2367:        linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224     brouard  2368: #else
1.234     brouard  2369:        linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
                   2370:        flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191     brouard  2371: #endif
1.234     brouard  2372:        
1.191     brouard  2373: #ifdef DEBUGLINMIN
1.234     brouard  2374:        for (j=1;j<=n;j++) { 
                   2375:          printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2376:          fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                   2377:          if(j % ncovmodel == 0){
                   2378:            printf("\n");
                   2379:            fprintf(ficlog,"\n");
                   2380:          }
                   2381:        }
1.224     brouard  2382: #endif
1.234     brouard  2383:        for (j=1;j<=n;j++) { 
                   2384:          xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                   2385:          xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                   2386:        }
1.224     brouard  2387: #ifdef LINMINORIGINAL
                   2388: #else
1.234     brouard  2389:        for (j=1, flatd=0;j<=n;j++) {
                   2390:          if(flatdir[j]>0)
                   2391:            flatd++;
                   2392:        }
                   2393:        if(flatd >0){
                   2394:          printf("%d flat directions\n",flatd);
                   2395:          fprintf(ficlog,"%d flat directions\n",flatd);
                   2396:          for (j=1;j<=n;j++) { 
                   2397:            if(flatdir[j]>0){
                   2398:              printf("%d ",j);
                   2399:              fprintf(ficlog,"%d ",j);
                   2400:            }
                   2401:          }
                   2402:          printf("\n");
                   2403:          fprintf(ficlog,"\n");
                   2404:        }
1.191     brouard  2405: #endif
1.234     brouard  2406:        printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                   2407:        fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                   2408:        
1.126     brouard  2409: #ifdef DEBUG
1.234     brouard  2410:        printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                   2411:        fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                   2412:        for(j=1;j<=n;j++){
                   2413:          printf(" %lf",xit[j]);
                   2414:          fprintf(ficlog," %lf",xit[j]);
                   2415:        }
                   2416:        printf("\n");
                   2417:        fprintf(ficlog,"\n");
1.126     brouard  2418: #endif
1.192     brouard  2419:       } /* end of t or directest negative */
1.224     brouard  2420: #ifdef POWELLNOF3INFF1TEST
1.192     brouard  2421: #else
1.234     brouard  2422:       } /* end if (fptt < fp)  */
1.192     brouard  2423: #endif
1.225     brouard  2424: #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
1.234     brouard  2425:     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
1.225     brouard  2426: #else
1.224     brouard  2427: #endif
1.234     brouard  2428:                } /* loop iteration */ 
1.126     brouard  2429: } 
1.234     brouard  2430:   
1.126     brouard  2431: /**** Prevalence limit (stable or period prevalence)  ****************/
1.234     brouard  2432:   
1.235     brouard  2433:   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  2434:   {
1.235     brouard  2435:     /* Computes the prevalence limit in each live state at age x and for covariate combination ij 
                   2436:        (and selected quantitative values in nres)
                   2437:        by left multiplying the unit
1.234     brouard  2438:        matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206     brouard  2439:   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
                   2440:   /* Wx is row vector: population in state 1, population in state 2, population dead */
                   2441:   /* or prevalence in state 1, prevalence in state 2, 0 */
                   2442:   /* newm is the matrix after multiplications, its rows are identical at a factor */
                   2443:   /* Initial matrix pimij */
                   2444:   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
                   2445:   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
                   2446:   /*  0,                   0                  , 1} */
                   2447:   /*
                   2448:    * and after some iteration: */
                   2449:   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
                   2450:   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
                   2451:   /*  0,                   0                  , 1} */
                   2452:   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
                   2453:   /* {0.51571254859325999, 0.4842874514067399, */
                   2454:   /*  0.51326036147820708, 0.48673963852179264} */
                   2455:   /* If we start from prlim again, prlim tends to a constant matrix */
1.234     brouard  2456:     
1.126     brouard  2457:   int i, ii,j,k;
1.209     brouard  2458:   double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145     brouard  2459:   /* double **matprod2(); */ /* test */
1.218     brouard  2460:   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126     brouard  2461:   double **newm;
1.209     brouard  2462:   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203     brouard  2463:   int ncvloop=0;
1.169     brouard  2464:   
1.209     brouard  2465:   min=vector(1,nlstate);
                   2466:   max=vector(1,nlstate);
                   2467:   meandiff=vector(1,nlstate);
                   2468: 
1.218     brouard  2469:        /* Starting with matrix unity */
1.126     brouard  2470:   for (ii=1;ii<=nlstate+ndeath;ii++)
                   2471:     for (j=1;j<=nlstate+ndeath;j++){
                   2472:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2473:     }
1.169     brouard  2474:   
                   2475:   cov[1]=1.;
                   2476:   
                   2477:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202     brouard  2478:   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126     brouard  2479:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202     brouard  2480:     ncvloop++;
1.126     brouard  2481:     newm=savm;
                   2482:     /* Covariates have to be included here again */
1.138     brouard  2483:     cov[2]=agefin;
1.187     brouard  2484:     if(nagesqr==1)
                   2485:       cov[3]= agefin*agefin;;
1.234     brouard  2486:     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                   2487:                        /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                   2488:       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235     brouard  2489:       /* 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  2490:     }
                   2491:     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                   2492:                        /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235     brouard  2493:       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
                   2494:       /* 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  2495:     }
1.237     brouard  2496:     for (k=1; k<=cptcovage;k++){  /* For product with age */
1.234     brouard  2497:       if(Dummy[Tvar[Tage[k]]]){
                   2498:        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                   2499:       } else{
1.235     brouard  2500:        cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
1.234     brouard  2501:       }
1.235     brouard  2502:       /* 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  2503:     }
1.237     brouard  2504:     for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235     brouard  2505:       /* 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  2506:       if(Dummy[Tvard[k][1]==0]){
                   2507:        if(Dummy[Tvard[k][2]==0]){
                   2508:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
                   2509:        }else{
                   2510:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
                   2511:        }
                   2512:       }else{
                   2513:        if(Dummy[Tvard[k][2]==0]){
                   2514:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
                   2515:        }else{
                   2516:          cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
                   2517:        }
                   2518:       }
1.234     brouard  2519:     }
1.138     brouard  2520:     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                   2521:     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                   2522:     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145     brouard  2523:     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   2524:     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218     brouard  2525:                /* age and covariate values of ij are in 'cov' */
1.142     brouard  2526:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138     brouard  2527:     
1.126     brouard  2528:     savm=oldm;
                   2529:     oldm=newm;
1.209     brouard  2530: 
                   2531:     for(j=1; j<=nlstate; j++){
                   2532:       max[j]=0.;
                   2533:       min[j]=1.;
                   2534:     }
                   2535:     for(i=1;i<=nlstate;i++){
                   2536:       sumnew=0;
                   2537:       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                   2538:       for(j=1; j<=nlstate; j++){ 
                   2539:        prlim[i][j]= newm[i][j]/(1-sumnew);
                   2540:        max[j]=FMAX(max[j],prlim[i][j]);
                   2541:        min[j]=FMIN(min[j],prlim[i][j]);
                   2542:       }
                   2543:     }
                   2544: 
1.126     brouard  2545:     maxmax=0.;
1.209     brouard  2546:     for(j=1; j<=nlstate; j++){
                   2547:       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
                   2548:       maxmax=FMAX(maxmax,meandiff[j]);
                   2549:       /* 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  2550:     } /* j loop */
1.203     brouard  2551:     *ncvyear= (int)age- (int)agefin;
1.208     brouard  2552:     /* 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  2553:     if(maxmax < ftolpl){
1.209     brouard  2554:       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
                   2555:       free_vector(min,1,nlstate);
                   2556:       free_vector(max,1,nlstate);
                   2557:       free_vector(meandiff,1,nlstate);
1.126     brouard  2558:       return prlim;
                   2559:     }
1.169     brouard  2560:   } /* age loop */
1.208     brouard  2561:     /* After some age loop it doesn't converge */
1.209     brouard  2562:   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.208     brouard  2563: Earliest 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);
1.209     brouard  2564:   /* 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); */
                   2565:   free_vector(min,1,nlstate);
                   2566:   free_vector(max,1,nlstate);
                   2567:   free_vector(meandiff,1,nlstate);
1.208     brouard  2568:   
1.169     brouard  2569:   return prlim; /* should not reach here */
1.126     brouard  2570: }
                   2571: 
1.217     brouard  2572: 
                   2573:  /**** Back Prevalence limit (stable or period prevalence)  ****************/
                   2574: 
1.218     brouard  2575:  /* 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) */
                   2576:  /* 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  2577:   double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217     brouard  2578: {
1.218     brouard  2579:   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217     brouard  2580:      matrix by transitions matrix until convergence is reached with precision ftolpl */
                   2581:   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
                   2582:   /* Wx is row vector: population in state 1, population in state 2, population dead */
                   2583:   /* or prevalence in state 1, prevalence in state 2, 0 */
                   2584:   /* newm is the matrix after multiplications, its rows are identical at a factor */
                   2585:   /* Initial matrix pimij */
                   2586:   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
                   2587:   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
                   2588:   /*  0,                   0                  , 1} */
                   2589:   /*
                   2590:    * and after some iteration: */
                   2591:   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
                   2592:   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
                   2593:   /*  0,                   0                  , 1} */
                   2594:   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
                   2595:   /* {0.51571254859325999, 0.4842874514067399, */
                   2596:   /*  0.51326036147820708, 0.48673963852179264} */
                   2597:   /* If we start from prlim again, prlim tends to a constant matrix */
                   2598: 
                   2599:   int i, ii,j,k;
1.247     brouard  2600:   int first=0;
1.217     brouard  2601:   double *min, *max, *meandiff, maxmax,sumnew=0.;
                   2602:   /* double **matprod2(); */ /* test */
                   2603:   double **out, cov[NCOVMAX+1], **bmij();
                   2604:   double **newm;
1.218     brouard  2605:   double        **dnewm, **doldm, **dsavm;  /* for use */
                   2606:   double        **oldm, **savm;  /* for use */
                   2607: 
1.217     brouard  2608:   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
                   2609:   int ncvloop=0;
                   2610:   
                   2611:   min=vector(1,nlstate);
                   2612:   max=vector(1,nlstate);
                   2613:   meandiff=vector(1,nlstate);
                   2614: 
1.218     brouard  2615:        dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
                   2616:        oldm=oldms; savm=savms;
                   2617: 
                   2618:        /* Starting with matrix unity */
                   2619:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   2620:                for (j=1;j<=nlstate+ndeath;j++){
1.217     brouard  2621:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2622:     }
                   2623:   
                   2624:   cov[1]=1.;
                   2625:   
                   2626:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   2627:   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218     brouard  2628:   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
                   2629:   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217     brouard  2630:     ncvloop++;
1.218     brouard  2631:     newm=savm; /* oldm should be kept from previous iteration or unity at start */
                   2632:                /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217     brouard  2633:     /* Covariates have to be included here again */
                   2634:     cov[2]=agefin;
                   2635:     if(nagesqr==1)
                   2636:       cov[3]= agefin*agefin;;
1.242     brouard  2637:     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                   2638:                        /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                   2639:       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
                   2640:       /* printf("bprevalim 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)); */
                   2641:     }
                   2642:     /* for (k=1; k<=cptcovn;k++) { */
                   2643:     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
                   2644:     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
                   2645:     /*   /\* 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])]); *\/ */
                   2646:     /* } */
                   2647:     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                   2648:                        /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
                   2649:       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
                   2650:       /* 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]); */
                   2651:     }
                   2652:     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
                   2653:     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
                   2654:     /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
                   2655:     /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
                   2656:     for (k=1; k<=cptcovage;k++){  /* For product with age */
                   2657:       if(Dummy[Tvar[Tage[k]]]){
                   2658:        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                   2659:       } else{
                   2660:        cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
                   2661:       }
                   2662:       /* 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]); */
                   2663:     }
                   2664:     for (k=1; k<=cptcovprod;k++){ /* For product without age */
                   2665:       /* 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]); */
                   2666:       if(Dummy[Tvard[k][1]==0]){
                   2667:        if(Dummy[Tvard[k][2]==0]){
                   2668:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
                   2669:        }else{
                   2670:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
                   2671:        }
                   2672:       }else{
                   2673:        if(Dummy[Tvard[k][2]==0]){
                   2674:          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
                   2675:        }else{
                   2676:          cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
                   2677:        }
                   2678:       }
1.217     brouard  2679:     }
                   2680:     
                   2681:     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                   2682:     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                   2683:     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
                   2684:     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   2685:     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218     brouard  2686:                /* ij should be linked to the correct index of cov */
                   2687:                /* age and covariate values ij are in 'cov', but we need to pass
                   2688:                 * ij for the observed prevalence at age and status and covariate
                   2689:                 * number:  prevacurrent[(int)agefin][ii][ij]
                   2690:                 */
                   2691:     /* 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 *\/ */
                   2692:     /* 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 *\/ */
                   2693:     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
1.217     brouard  2694:     savm=oldm;
                   2695:     oldm=newm;
                   2696:     for(j=1; j<=nlstate; j++){
                   2697:       max[j]=0.;
                   2698:       min[j]=1.;
                   2699:     }
                   2700:     for(j=1; j<=nlstate; j++){ 
                   2701:       for(i=1;i<=nlstate;i++){
1.234     brouard  2702:        /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                   2703:        bprlim[i][j]= newm[i][j];
                   2704:        max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                   2705:        min[i]=FMIN(min[i],bprlim[i][j]);
1.217     brouard  2706:       }
                   2707:     }
1.218     brouard  2708:                
1.217     brouard  2709:     maxmax=0.;
                   2710:     for(i=1; i<=nlstate; i++){
                   2711:       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
                   2712:       maxmax=FMAX(maxmax,meandiff[i]);
                   2713:       /* 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); */
                   2714:     } /* j loop */
                   2715:     *ncvyear= -( (int)age- (int)agefin);
1.218     brouard  2716:     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217     brouard  2717:     if(maxmax < ftolpl){
1.220     brouard  2718:       /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217     brouard  2719:       free_vector(min,1,nlstate);
                   2720:       free_vector(max,1,nlstate);
                   2721:       free_vector(meandiff,1,nlstate);
                   2722:       return bprlim;
                   2723:     }
                   2724:   } /* age loop */
                   2725:     /* After some age loop it doesn't converge */
1.247     brouard  2726:   if(first){
                   2727:     first=1;
                   2728:     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\
                   2729: 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);
                   2730:   }
                   2731:   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  2732: 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);
                   2733:   /* 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); */
                   2734:   free_vector(min,1,nlstate);
                   2735:   free_vector(max,1,nlstate);
                   2736:   free_vector(meandiff,1,nlstate);
                   2737:   
                   2738:   return bprlim; /* should not reach here */
                   2739: }
                   2740: 
1.126     brouard  2741: /*************** transition probabilities ***************/ 
                   2742: 
                   2743: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                   2744: {
1.138     brouard  2745:   /* According to parameters values stored in x and the covariate's values stored in cov,
                   2746:      computes the probability to be observed in state j being in state i by appying the
                   2747:      model to the ncovmodel covariates (including constant and age).
                   2748:      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
                   2749:      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
                   2750:      ncth covariate in the global vector x is given by the formula:
                   2751:      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
                   2752:      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
                   2753:      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
                   2754:      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
                   2755:      Outputs ps[i][j] the probability to be observed in j being in j according to
                   2756:      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
                   2757:   */
                   2758:   double s1, lnpijopii;
1.126     brouard  2759:   /*double t34;*/
1.164     brouard  2760:   int i,j, nc, ii, jj;
1.126     brouard  2761: 
1.223     brouard  2762:   for(i=1; i<= nlstate; i++){
                   2763:     for(j=1; j<i;j++){
                   2764:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   2765:        /*lnpijopii += param[i][j][nc]*cov[nc];*/
                   2766:        lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                   2767:        /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   2768:       }
                   2769:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   2770:       /*       printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   2771:     }
                   2772:     for(j=i+1; j<=nlstate+ndeath;j++){
                   2773:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   2774:        /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                   2775:        lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                   2776:        /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                   2777:       }
                   2778:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   2779:     }
                   2780:   }
1.218     brouard  2781:   
1.223     brouard  2782:   for(i=1; i<= nlstate; i++){
                   2783:     s1=0;
                   2784:     for(j=1; j<i; j++){
                   2785:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   2786:       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   2787:     }
                   2788:     for(j=i+1; j<=nlstate+ndeath; j++){
                   2789:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   2790:       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   2791:     }
                   2792:     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   2793:     ps[i][i]=1./(s1+1.);
                   2794:     /* Computing other pijs */
                   2795:     for(j=1; j<i; j++)
                   2796:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   2797:     for(j=i+1; j<=nlstate+ndeath; j++)
                   2798:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   2799:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                   2800:   } /* end i */
1.218     brouard  2801:   
1.223     brouard  2802:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   2803:     for(jj=1; jj<= nlstate+ndeath; jj++){
                   2804:       ps[ii][jj]=0;
                   2805:       ps[ii][ii]=1;
                   2806:     }
                   2807:   }
1.218     brouard  2808:   
                   2809:   
1.223     brouard  2810:   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
                   2811:   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
                   2812:   /*   printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
                   2813:   /*   } */
                   2814:   /*   printf("\n "); */
                   2815:   /* } */
                   2816:   /* printf("\n ");printf("%lf ",cov[2]);*/
                   2817:   /*
                   2818:     for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218     brouard  2819:                goto end;*/
1.223     brouard  2820:   return ps;
1.126     brouard  2821: }
                   2822: 
1.218     brouard  2823: /*************** backward transition probabilities ***************/ 
                   2824: 
                   2825:  /* 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 ) */
                   2826: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
                   2827:  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
                   2828: {
1.222     brouard  2829:   /* Computes the backward probability at age agefin and covariate ij
                   2830:    * and returns in **ps as well as **bmij.
                   2831:    */
1.218     brouard  2832:   int i, ii, j,k;
1.222     brouard  2833:   
                   2834:   double **out, **pmij();
                   2835:   double sumnew=0.;
1.218     brouard  2836:   double agefin;
1.222     brouard  2837:   
                   2838:   double **dnewm, **dsavm, **doldm;
                   2839:   double **bbmij;
                   2840:   
1.218     brouard  2841:   doldm=ddoldms; /* global pointers */
1.222     brouard  2842:   dnewm=ddnewms;
                   2843:   dsavm=ddsavms;
                   2844:   
                   2845:   agefin=cov[2];
                   2846:   /* bmij *//* age is cov[2], ij is included in cov, but we need for
                   2847:      the observed prevalence (with this covariate ij) */
                   2848:   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
                   2849:   /* We do have the matrix Px in savm  and we need pij */
                   2850:   for (j=1;j<=nlstate+ndeath;j++){
                   2851:     sumnew=0.; /* w1 p11 + w2 p21 only on live states */
                   2852:     for (ii=1;ii<=nlstate;ii++){
                   2853:       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
                   2854:     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
                   2855:     for (ii=1;ii<=nlstate+ndeath;ii++){
                   2856:       if(sumnew >= 1.e-10){
                   2857:        /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
                   2858:        /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
                   2859:        /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
                   2860:        /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
                   2861:        /* }else */
                   2862:        doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
                   2863:       }else{
1.242     brouard  2864:        ;
                   2865:        /* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */
1.222     brouard  2866:       }
                   2867:     } /*End ii */
                   2868:   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
                   2869:   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
                   2870:   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
                   2871:   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
                   2872:   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
                   2873:   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
                   2874:   /* left Product of this matrix by diag matrix of prevalences (savm) */
                   2875:   for (j=1;j<=nlstate+ndeath;j++){
                   2876:     for (ii=1;ii<=nlstate+ndeath;ii++){
                   2877:       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
                   2878:     }
                   2879:   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
                   2880:   ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
                   2881:   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
                   2882:   /* end bmij */
                   2883:   return ps; 
1.218     brouard  2884: }
1.217     brouard  2885: /*************** transition probabilities ***************/ 
                   2886: 
1.218     brouard  2887: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217     brouard  2888: {
                   2889:   /* According to parameters values stored in x and the covariate's values stored in cov,
                   2890:      computes the probability to be observed in state j being in state i by appying the
                   2891:      model to the ncovmodel covariates (including constant and age).
                   2892:      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
                   2893:      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
                   2894:      ncth covariate in the global vector x is given by the formula:
                   2895:      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
                   2896:      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
                   2897:      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
                   2898:      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
                   2899:      Outputs ps[i][j] the probability to be observed in j being in j according to
                   2900:      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
                   2901:   */
                   2902:   double s1, lnpijopii;
                   2903:   /*double t34;*/
                   2904:   int i,j, nc, ii, jj;
                   2905: 
1.234     brouard  2906:   for(i=1; i<= nlstate; i++){
                   2907:     for(j=1; j<i;j++){
                   2908:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   2909:        /*lnpijopii += param[i][j][nc]*cov[nc];*/
                   2910:        lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                   2911:        /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   2912:       }
                   2913:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   2914:       /*       printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   2915:     }
                   2916:     for(j=i+1; j<=nlstate+ndeath;j++){
                   2917:       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   2918:        /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                   2919:        lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                   2920:        /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                   2921:       }
                   2922:       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   2923:     }
                   2924:   }
                   2925:   
                   2926:   for(i=1; i<= nlstate; i++){
                   2927:     s1=0;
                   2928:     for(j=1; j<i; j++){
                   2929:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   2930:       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   2931:     }
                   2932:     for(j=i+1; j<=nlstate+ndeath; j++){
                   2933:       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                   2934:       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   2935:     }
                   2936:     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   2937:     ps[i][i]=1./(s1+1.);
                   2938:     /* Computing other pijs */
                   2939:     for(j=1; j<i; j++)
                   2940:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   2941:     for(j=i+1; j<=nlstate+ndeath; j++)
                   2942:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   2943:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                   2944:   } /* end i */
                   2945:   
                   2946:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   2947:     for(jj=1; jj<= nlstate+ndeath; jj++){
                   2948:       ps[ii][jj]=0;
                   2949:       ps[ii][ii]=1;
                   2950:     }
                   2951:   }
                   2952:   /* Added for backcast */ /* Transposed matrix too */
                   2953:   for(jj=1; jj<= nlstate+ndeath; jj++){
                   2954:     s1=0.;
                   2955:     for(ii=1; ii<= nlstate+ndeath; ii++){
                   2956:       s1+=ps[ii][jj];
                   2957:     }
                   2958:     for(ii=1; ii<= nlstate; ii++){
                   2959:       ps[ii][jj]=ps[ii][jj]/s1;
                   2960:     }
                   2961:   }
                   2962:   /* Transposition */
                   2963:   for(jj=1; jj<= nlstate+ndeath; jj++){
                   2964:     for(ii=jj; ii<= nlstate+ndeath; ii++){
                   2965:       s1=ps[ii][jj];
                   2966:       ps[ii][jj]=ps[jj][ii];
                   2967:       ps[jj][ii]=s1;
                   2968:     }
                   2969:   }
                   2970:   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
                   2971:   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
                   2972:   /*   printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
                   2973:   /*   } */
                   2974:   /*   printf("\n "); */
                   2975:   /* } */
                   2976:   /* printf("\n ");printf("%lf ",cov[2]);*/
                   2977:   /*
                   2978:     for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   2979:     goto end;*/
                   2980:   return ps;
1.217     brouard  2981: }
                   2982: 
                   2983: 
1.126     brouard  2984: /**************** Product of 2 matrices ******************/
                   2985: 
1.145     brouard  2986: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126     brouard  2987: {
                   2988:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                   2989:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                   2990:   /* in, b, out are matrice of pointers which should have been initialized 
                   2991:      before: only the contents of out is modified. The function returns
                   2992:      a pointer to pointers identical to out */
1.145     brouard  2993:   int i, j, k;
1.126     brouard  2994:   for(i=nrl; i<= nrh; i++)
1.145     brouard  2995:     for(k=ncolol; k<=ncoloh; k++){
                   2996:       out[i][k]=0.;
                   2997:       for(j=ncl; j<=nch; j++)
                   2998:        out[i][k] +=in[i][j]*b[j][k];
                   2999:     }
1.126     brouard  3000:   return out;
                   3001: }
                   3002: 
                   3003: 
                   3004: /************* Higher Matrix Product ***************/
                   3005: 
1.235     brouard  3006: 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  3007: {
1.218     brouard  3008:   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
1.126     brouard  3009:      'nhstepm*hstepm*stepm' months (i.e. until
                   3010:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                   3011:      nhstepm*hstepm matrices. 
                   3012:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
                   3013:      (typically every 2 years instead of every month which is too big 
                   3014:      for the memory).
                   3015:      Model is determined by parameters x and covariates have to be 
                   3016:      included manually here. 
                   3017: 
                   3018:      */
                   3019: 
                   3020:   int i, j, d, h, k;
1.131     brouard  3021:   double **out, cov[NCOVMAX+1];
1.126     brouard  3022:   double **newm;
1.187     brouard  3023:   double agexact;
1.214     brouard  3024:   double agebegin, ageend;
1.126     brouard  3025: 
                   3026:   /* Hstepm could be zero and should return the unit matrix */
                   3027:   for (i=1;i<=nlstate+ndeath;i++)
                   3028:     for (j=1;j<=nlstate+ndeath;j++){
                   3029:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   3030:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   3031:     }
                   3032:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   3033:   for(h=1; h <=nhstepm; h++){
                   3034:     for(d=1; d <=hstepm; d++){
                   3035:       newm=savm;
                   3036:       /* Covariates have to be included here again */
                   3037:       cov[1]=1.;
1.214     brouard  3038:       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187     brouard  3039:       cov[2]=agexact;
                   3040:       if(nagesqr==1)
1.227     brouard  3041:        cov[3]= agexact*agexact;
1.235     brouard  3042:       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                   3043:                        /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                   3044:        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
                   3045:        /* 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)); */
                   3046:       }
                   3047:       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                   3048:        /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
                   3049:        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
                   3050:        /* 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]); */
                   3051:       }
                   3052:       for (k=1; k<=cptcovage;k++){
                   3053:        if(Dummy[Tvar[Tage[k]]]){
                   3054:          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                   3055:        } else{
                   3056:          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
                   3057:        }
                   3058:        /* 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]); */
                   3059:       }
                   3060:       for (k=1; k<=cptcovprod;k++){ /*  */
                   3061:        /* 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]); */
                   3062:        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
                   3063:       }
                   3064:       /* for (k=1; k<=cptcovn;k++)  */
                   3065:       /*       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
                   3066:       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
                   3067:       /*       cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
                   3068:       /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
                   3069:       /*       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227     brouard  3070:       
                   3071:       
1.126     brouard  3072:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   3073:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218     brouard  3074:                        /* right multiplication of oldm by the current matrix */
1.126     brouard  3075:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                   3076:                   pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217     brouard  3077:       /* if((int)age == 70){ */
                   3078:       /*       printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
                   3079:       /*       for(i=1; i<=nlstate+ndeath; i++) { */
                   3080:       /*         printf("%d pmmij ",i); */
                   3081:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3082:       /*           printf("%f ",pmmij[i][j]); */
                   3083:       /*         } */
                   3084:       /*         printf(" oldm "); */
                   3085:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3086:       /*           printf("%f ",oldm[i][j]); */
                   3087:       /*         } */
                   3088:       /*         printf("\n"); */
                   3089:       /*       } */
                   3090:       /* } */
1.126     brouard  3091:       savm=oldm;
                   3092:       oldm=newm;
                   3093:     }
                   3094:     for(i=1; i<=nlstate+ndeath; i++)
                   3095:       for(j=1;j<=nlstate+ndeath;j++) {
1.218     brouard  3096:                                po[i][j][h]=newm[i][j];
                   3097:                                /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126     brouard  3098:       }
1.128     brouard  3099:     /*printf("h=%d ",h);*/
1.126     brouard  3100:   } /* end h */
1.218     brouard  3101:        /*     printf("\n H=%d \n",h); */
1.126     brouard  3102:   return po;
                   3103: }
                   3104: 
1.217     brouard  3105: /************* Higher Back Matrix Product ***************/
1.218     brouard  3106: /* 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 ) */
1.222     brouard  3107: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217     brouard  3108: {
1.218     brouard  3109:   /* Computes the transition matrix starting at age 'age' over
1.217     brouard  3110:      'nhstepm*hstepm*stepm' months (i.e. until
1.218     brouard  3111:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
                   3112:      nhstepm*hstepm matrices.
                   3113:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
                   3114:      (typically every 2 years instead of every month which is too big
1.217     brouard  3115:      for the memory).
1.218     brouard  3116:      Model is determined by parameters x and covariates have to be
                   3117:      included manually here.
1.217     brouard  3118: 
1.222     brouard  3119:   */
1.217     brouard  3120: 
                   3121:   int i, j, d, h, k;
                   3122:   double **out, cov[NCOVMAX+1];
                   3123:   double **newm;
                   3124:   double agexact;
                   3125:   double agebegin, ageend;
1.222     brouard  3126:   double **oldm, **savm;
1.217     brouard  3127: 
1.222     brouard  3128:   oldm=oldms;savm=savms;
1.217     brouard  3129:   /* Hstepm could be zero and should return the unit matrix */
                   3130:   for (i=1;i<=nlstate+ndeath;i++)
                   3131:     for (j=1;j<=nlstate+ndeath;j++){
                   3132:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   3133:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   3134:     }
                   3135:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   3136:   for(h=1; h <=nhstepm; h++){
                   3137:     for(d=1; d <=hstepm; d++){
                   3138:       newm=savm;
                   3139:       /* Covariates have to be included here again */
                   3140:       cov[1]=1.;
                   3141:       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
                   3142:       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
                   3143:       cov[2]=agexact;
                   3144:       if(nagesqr==1)
1.222     brouard  3145:        cov[3]= agexact*agexact;
1.218     brouard  3146:       for (k=1; k<=cptcovn;k++)
1.222     brouard  3147:        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
                   3148:       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217     brouard  3149:       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222     brouard  3150:        /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                   3151:        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                   3152:       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217     brouard  3153:       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222     brouard  3154:        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                   3155:       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.218     brouard  3156:                        
                   3157:                        
1.217     brouard  3158:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   3159:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218     brouard  3160:       /* Careful transposed matrix */
1.222     brouard  3161:       /* age is in cov[2] */
1.218     brouard  3162:       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222     brouard  3163:       /*                                                1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218     brouard  3164:       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222     brouard  3165:                   1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217     brouard  3166:       /* if((int)age == 70){ */
                   3167:       /*       printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
                   3168:       /*       for(i=1; i<=nlstate+ndeath; i++) { */
                   3169:       /*         printf("%d pmmij ",i); */
                   3170:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3171:       /*           printf("%f ",pmmij[i][j]); */
                   3172:       /*         } */
                   3173:       /*         printf(" oldm "); */
                   3174:       /*         for(j=1;j<=nlstate+ndeath;j++) { */
                   3175:       /*           printf("%f ",oldm[i][j]); */
                   3176:       /*         } */
                   3177:       /*         printf("\n"); */
                   3178:       /*       } */
                   3179:       /* } */
                   3180:       savm=oldm;
                   3181:       oldm=newm;
                   3182:     }
                   3183:     for(i=1; i<=nlstate+ndeath; i++)
                   3184:       for(j=1;j<=nlstate+ndeath;j++) {
1.222     brouard  3185:        po[i][j][h]=newm[i][j];
                   3186:        /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217     brouard  3187:       }
                   3188:     /*printf("h=%d ",h);*/
                   3189:   } /* end h */
1.222     brouard  3190:   /*     printf("\n H=%d \n",h); */
1.217     brouard  3191:   return po;
                   3192: }
                   3193: 
                   3194: 
1.162     brouard  3195: #ifdef NLOPT
                   3196:   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
                   3197:   double fret;
                   3198:   double *xt;
                   3199:   int j;
                   3200:   myfunc_data *d2 = (myfunc_data *) pd;
                   3201: /* xt = (p1-1); */
                   3202:   xt=vector(1,n); 
                   3203:   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
                   3204: 
                   3205:   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
                   3206:   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
                   3207:   printf("Function = %.12lf ",fret);
                   3208:   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
                   3209:   printf("\n");
                   3210:  free_vector(xt,1,n);
                   3211:   return fret;
                   3212: }
                   3213: #endif
1.126     brouard  3214: 
                   3215: /*************** log-likelihood *************/
                   3216: double func( double *x)
                   3217: {
1.226     brouard  3218:   int i, ii, j, k, mi, d, kk;
                   3219:   int ioffset=0;
                   3220:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
                   3221:   double **out;
                   3222:   double lli; /* Individual log likelihood */
                   3223:   int s1, s2;
1.228     brouard  3224:   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  3225:   double bbh, survp;
                   3226:   long ipmx;
                   3227:   double agexact;
                   3228:   /*extern weight */
                   3229:   /* We are differentiating ll according to initial status */
                   3230:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   3231:   /*for(i=1;i<imx;i++) 
                   3232:     printf(" %d\n",s[4][i]);
                   3233:   */
1.162     brouard  3234: 
1.226     brouard  3235:   ++countcallfunc;
1.162     brouard  3236: 
1.226     brouard  3237:   cov[1]=1.;
1.126     brouard  3238: 
1.226     brouard  3239:   for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224     brouard  3240:   ioffset=0;
1.226     brouard  3241:   if(mle==1){
                   3242:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3243:       /* Computes the values of the ncovmodel covariates of the model
                   3244:         depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
                   3245:         Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
                   3246:         to be observed in j being in i according to the model.
                   3247:       */
1.243     brouard  3248:       ioffset=2+nagesqr ;
1.233     brouard  3249:    /* Fixed */
1.234     brouard  3250:       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
                   3251:        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)*/
                   3252:       }
1.226     brouard  3253:       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
                   3254:         is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
                   3255:         has been calculated etc */
                   3256:       /* For an individual i, wav[i] gives the number of effective waves */
                   3257:       /* We compute the contribution to Likelihood of each effective transition
                   3258:         mw[mi][i] is real wave of the mi th effectve wave */
                   3259:       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
                   3260:         s2=s[mw[mi+1][i]][i];
                   3261:         And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
                   3262:         But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
                   3263:         meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
                   3264:       */
                   3265:       for(mi=1; mi<= wav[i]-1; mi++){
1.234     brouard  3266:        for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
1.242     brouard  3267:          /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
                   3268:          cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234     brouard  3269:        }
                   3270:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3271:          for (j=1;j<=nlstate+ndeath;j++){
                   3272:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3273:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3274:          }
                   3275:        for(d=0; d<dh[mi][i]; d++){
                   3276:          newm=savm;
                   3277:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3278:          cov[2]=agexact;
                   3279:          if(nagesqr==1)
                   3280:            cov[3]= agexact*agexact;  /* Should be changed here */
                   3281:          for (kk=1; kk<=cptcovage;kk++) {
1.242     brouard  3282:          if(!FixedV[Tvar[Tage[kk]]])
1.234     brouard  3283:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242     brouard  3284:          else
                   3285:            cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234     brouard  3286:          }
                   3287:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3288:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3289:          savm=oldm;
                   3290:          oldm=newm;
                   3291:        } /* end mult */
                   3292:        
                   3293:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   3294:        /* But now since version 0.9 we anticipate for bias at large stepm.
                   3295:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   3296:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   3297:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   3298:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   3299:         * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                   3300:         * probability in order to take into account the bias as a fraction of the way
1.231     brouard  3301:                                 * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                   3302:                                 * -stepm/2 to stepm/2 .
                   3303:                                 * For stepm=1 the results are the same as for previous versions of Imach.
                   3304:                                 * For stepm > 1 the results are less biased than in previous versions. 
                   3305:                                 */
1.234     brouard  3306:        s1=s[mw[mi][i]][i];
                   3307:        s2=s[mw[mi+1][i]][i];
                   3308:        bbh=(double)bh[mi][i]/(double)stepm; 
                   3309:        /* bias bh is positive if real duration
                   3310:         * is higher than the multiple of stepm and negative otherwise.
                   3311:         */
                   3312:        /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                   3313:        if( s2 > nlstate){ 
                   3314:          /* i.e. if s2 is a death state and if the date of death is known 
                   3315:             then the contribution to the likelihood is the probability to 
                   3316:             die between last step unit time and current  step unit time, 
                   3317:             which is also equal to probability to die before dh 
                   3318:             minus probability to die before dh-stepm . 
                   3319:             In version up to 0.92 likelihood was computed
                   3320:             as if date of death was unknown. Death was treated as any other
                   3321:             health state: the date of the interview describes the actual state
                   3322:             and not the date of a change in health state. The former idea was
                   3323:             to consider that at each interview the state was recorded
                   3324:             (healthy, disable or death) and IMaCh was corrected; but when we
                   3325:             introduced the exact date of death then we should have modified
                   3326:             the contribution of an exact death to the likelihood. This new
                   3327:             contribution is smaller and very dependent of the step unit
                   3328:             stepm. It is no more the probability to die between last interview
                   3329:             and month of death but the probability to survive from last
                   3330:             interview up to one month before death multiplied by the
                   3331:             probability to die within a month. Thanks to Chris
                   3332:             Jackson for correcting this bug.  Former versions increased
                   3333:             mortality artificially. The bad side is that we add another loop
                   3334:             which slows down the processing. The difference can be up to 10%
                   3335:             lower mortality.
                   3336:          */
                   3337:          /* If, at the beginning of the maximization mostly, the
                   3338:             cumulative probability or probability to be dead is
                   3339:             constant (ie = 1) over time d, the difference is equal to
                   3340:             0.  out[s1][3] = savm[s1][3]: probability, being at state
                   3341:             s1 at precedent wave, to be dead a month before current
                   3342:             wave is equal to probability, being at state s1 at
                   3343:             precedent wave, to be dead at mont of the current
                   3344:             wave. Then the observed probability (that this person died)
                   3345:             is null according to current estimated parameter. In fact,
                   3346:             it should be very low but not zero otherwise the log go to
                   3347:             infinity.
                   3348:          */
1.183     brouard  3349: /* #ifdef INFINITYORIGINAL */
                   3350: /*         lli=log(out[s1][s2] - savm[s1][s2]); */
                   3351: /* #else */
                   3352: /*       if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
                   3353: /*         lli=log(mytinydouble); */
                   3354: /*       else */
                   3355: /*         lli=log(out[s1][s2] - savm[s1][s2]); */
                   3356: /* #endif */
1.226     brouard  3357:          lli=log(out[s1][s2] - savm[s1][s2]);
1.216     brouard  3358:          
1.226     brouard  3359:        } else if  ( s2==-1 ) { /* alive */
                   3360:          for (j=1,survp=0. ; j<=nlstate; j++) 
                   3361:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   3362:          /*survp += out[s1][j]; */
                   3363:          lli= log(survp);
                   3364:        }
                   3365:        else if  (s2==-4) { 
                   3366:          for (j=3,survp=0. ; j<=nlstate; j++)  
                   3367:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   3368:          lli= log(survp); 
                   3369:        } 
                   3370:        else if  (s2==-5) { 
                   3371:          for (j=1,survp=0. ; j<=2; j++)  
                   3372:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   3373:          lli= log(survp); 
                   3374:        } 
                   3375:        else{
                   3376:          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   3377:          /*  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 */
                   3378:        } 
                   3379:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   3380:        /*if(lli ==000.0)*/
                   3381:        /*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); */
                   3382:        ipmx +=1;
                   3383:        sw += weight[i];
                   3384:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3385:        /* if (lli < log(mytinydouble)){ */
                   3386:        /*   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); */
                   3387:        /*   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]); */
                   3388:        /* } */
                   3389:       } /* end of wave */
                   3390:     } /* end of individual */
                   3391:   }  else if(mle==2){
                   3392:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3393:       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   3394:       for(mi=1; mi<= wav[i]-1; mi++){
                   3395:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3396:          for (j=1;j<=nlstate+ndeath;j++){
                   3397:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3398:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3399:          }
                   3400:        for(d=0; d<=dh[mi][i]; d++){
                   3401:          newm=savm;
                   3402:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3403:          cov[2]=agexact;
                   3404:          if(nagesqr==1)
                   3405:            cov[3]= agexact*agexact;
                   3406:          for (kk=1; kk<=cptcovage;kk++) {
                   3407:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3408:          }
                   3409:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3410:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3411:          savm=oldm;
                   3412:          oldm=newm;
                   3413:        } /* end mult */
                   3414:       
                   3415:        s1=s[mw[mi][i]][i];
                   3416:        s2=s[mw[mi+1][i]][i];
                   3417:        bbh=(double)bh[mi][i]/(double)stepm; 
                   3418:        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 */
                   3419:        ipmx +=1;
                   3420:        sw += weight[i];
                   3421:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3422:       } /* end of wave */
                   3423:     } /* end of individual */
                   3424:   }  else if(mle==3){  /* exponential inter-extrapolation */
                   3425:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3426:       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   3427:       for(mi=1; mi<= wav[i]-1; mi++){
                   3428:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3429:          for (j=1;j<=nlstate+ndeath;j++){
                   3430:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3431:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3432:          }
                   3433:        for(d=0; d<dh[mi][i]; d++){
                   3434:          newm=savm;
                   3435:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3436:          cov[2]=agexact;
                   3437:          if(nagesqr==1)
                   3438:            cov[3]= agexact*agexact;
                   3439:          for (kk=1; kk<=cptcovage;kk++) {
                   3440:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3441:          }
                   3442:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3443:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3444:          savm=oldm;
                   3445:          oldm=newm;
                   3446:        } /* end mult */
                   3447:       
                   3448:        s1=s[mw[mi][i]][i];
                   3449:        s2=s[mw[mi+1][i]][i];
                   3450:        bbh=(double)bh[mi][i]/(double)stepm; 
                   3451:        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 */
                   3452:        ipmx +=1;
                   3453:        sw += weight[i];
                   3454:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3455:       } /* end of wave */
                   3456:     } /* end of individual */
                   3457:   }else if (mle==4){  /* ml=4 no inter-extrapolation */
                   3458:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3459:       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   3460:       for(mi=1; mi<= wav[i]-1; mi++){
                   3461:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3462:          for (j=1;j<=nlstate+ndeath;j++){
                   3463:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3464:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3465:          }
                   3466:        for(d=0; d<dh[mi][i]; d++){
                   3467:          newm=savm;
                   3468:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3469:          cov[2]=agexact;
                   3470:          if(nagesqr==1)
                   3471:            cov[3]= agexact*agexact;
                   3472:          for (kk=1; kk<=cptcovage;kk++) {
                   3473:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3474:          }
1.126     brouard  3475:        
1.226     brouard  3476:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3477:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3478:          savm=oldm;
                   3479:          oldm=newm;
                   3480:        } /* end mult */
                   3481:       
                   3482:        s1=s[mw[mi][i]][i];
                   3483:        s2=s[mw[mi+1][i]][i];
                   3484:        if( s2 > nlstate){ 
                   3485:          lli=log(out[s1][s2] - savm[s1][s2]);
                   3486:        } else if  ( s2==-1 ) { /* alive */
                   3487:          for (j=1,survp=0. ; j<=nlstate; j++) 
                   3488:            survp += out[s1][j];
                   3489:          lli= log(survp);
                   3490:        }else{
                   3491:          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   3492:        }
                   3493:        ipmx +=1;
                   3494:        sw += weight[i];
                   3495:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126     brouard  3496: /*     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  3497:       } /* end of wave */
                   3498:     } /* end of individual */
                   3499:   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                   3500:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   3501:       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                   3502:       for(mi=1; mi<= wav[i]-1; mi++){
                   3503:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   3504:          for (j=1;j<=nlstate+ndeath;j++){
                   3505:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3506:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3507:          }
                   3508:        for(d=0; d<dh[mi][i]; d++){
                   3509:          newm=savm;
                   3510:          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   3511:          cov[2]=agexact;
                   3512:          if(nagesqr==1)
                   3513:            cov[3]= agexact*agexact;
                   3514:          for (kk=1; kk<=cptcovage;kk++) {
                   3515:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3516:          }
1.126     brouard  3517:        
1.226     brouard  3518:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3519:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3520:          savm=oldm;
                   3521:          oldm=newm;
                   3522:        } /* end mult */
                   3523:       
                   3524:        s1=s[mw[mi][i]][i];
                   3525:        s2=s[mw[mi+1][i]][i];
                   3526:        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   3527:        ipmx +=1;
                   3528:        sw += weight[i];
                   3529:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   3530:        /*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]);*/
                   3531:       } /* end of wave */
                   3532:     } /* end of individual */
                   3533:   } /* End of if */
                   3534:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   3535:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   3536:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   3537:   return -l;
1.126     brouard  3538: }
                   3539: 
                   3540: /*************** log-likelihood *************/
                   3541: double funcone( double *x)
                   3542: {
1.228     brouard  3543:   /* Same as func but slower because of a lot of printf and if */
1.126     brouard  3544:   int i, ii, j, k, mi, d, kk;
1.228     brouard  3545:   int ioffset=0;
1.131     brouard  3546:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126     brouard  3547:   double **out;
                   3548:   double lli; /* Individual log likelihood */
                   3549:   double llt;
                   3550:   int s1, s2;
1.228     brouard  3551:   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
                   3552: 
1.126     brouard  3553:   double bbh, survp;
1.187     brouard  3554:   double agexact;
1.214     brouard  3555:   double agebegin, ageend;
1.126     brouard  3556:   /*extern weight */
                   3557:   /* We are differentiating ll according to initial status */
                   3558:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   3559:   /*for(i=1;i<imx;i++) 
                   3560:     printf(" %d\n",s[4][i]);
                   3561:   */
                   3562:   cov[1]=1.;
                   3563: 
                   3564:   for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224     brouard  3565:   ioffset=0;
                   3566:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243     brouard  3567:     /* ioffset=2+nagesqr+cptcovage; */
                   3568:     ioffset=2+nagesqr;
1.232     brouard  3569:     /* Fixed */
1.224     brouard  3570:     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232     brouard  3571:     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
                   3572:     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
                   3573:       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)*/
                   3574: /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
                   3575: /*    cov[2+6]=covar[Tvar[6]][i];  */
                   3576: /*    cov[2+6]=covar[2][i]; V2  */
                   3577: /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
                   3578: /*    cov[2+7]=covar[Tvar[7]][i];  */
                   3579: /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
                   3580: /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
                   3581: /*    cov[2+9]=covar[Tvar[9]][i];  */
                   3582: /*    cov[2+9]=covar[1][i]; V1  */
1.225     brouard  3583:     }
1.232     brouard  3584:     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
                   3585:     /*   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?)*\/ */
                   3586:     /* } */
1.231     brouard  3587:     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
                   3588:     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
                   3589:     /* } */
1.225     brouard  3590:     
1.233     brouard  3591: 
                   3592:     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
1.232     brouard  3593:     /* Wave varying (but not age varying) */
                   3594:       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
1.242     brouard  3595:        /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
                   3596:        cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
                   3597:       }
1.232     brouard  3598:       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242     brouard  3599:       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
                   3600:       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
                   3601:       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
                   3602:       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
                   3603:       /* 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  3604:       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242     brouard  3605:       /*       iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
                   3606:       /*       /\* 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]); *\/ */
                   3607:       /*       cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232     brouard  3608:       /* } */
1.126     brouard  3609:       for (ii=1;ii<=nlstate+ndeath;ii++)
1.242     brouard  3610:        for (j=1;j<=nlstate+ndeath;j++){
                   3611:          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3612:          savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   3613:        }
1.214     brouard  3614:       
                   3615:       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
                   3616:       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
                   3617:       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
1.247     brouard  3618:       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242     brouard  3619:        /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   3620:          and mw[mi+1][i]. dh depends on stepm.*/
                   3621:        newm=savm;
1.247     brouard  3622:        agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
1.242     brouard  3623:        cov[2]=agexact;
                   3624:        if(nagesqr==1)
                   3625:          cov[3]= agexact*agexact;
                   3626:        for (kk=1; kk<=cptcovage;kk++) {
                   3627:          if(!FixedV[Tvar[Tage[kk]]])
                   3628:            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                   3629:          else
                   3630:            cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
                   3631:        }
                   3632:        /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
                   3633:        /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   3634:        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   3635:                     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   3636:        /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                   3637:        /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
                   3638:        savm=oldm;
                   3639:        oldm=newm;
1.126     brouard  3640:       } /* end mult */
                   3641:       
                   3642:       s1=s[mw[mi][i]][i];
                   3643:       s2=s[mw[mi+1][i]][i];
1.217     brouard  3644:       /* if(s2==-1){ */
                   3645:       /*       printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
                   3646:       /*       /\* exit(1); *\/ */
                   3647:       /* } */
1.126     brouard  3648:       bbh=(double)bh[mi][i]/(double)stepm; 
                   3649:       /* bias is positive if real duration
                   3650:        * is higher than the multiple of stepm and negative otherwise.
                   3651:        */
                   3652:       if( s2 > nlstate && (mle <5) ){  /* Jackson */
1.242     brouard  3653:        lli=log(out[s1][s2] - savm[s1][s2]);
1.216     brouard  3654:       } else if  ( s2==-1 ) { /* alive */
1.242     brouard  3655:        for (j=1,survp=0. ; j<=nlstate; j++) 
                   3656:          survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   3657:        lli= log(survp);
1.126     brouard  3658:       }else if (mle==1){
1.242     brouard  3659:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126     brouard  3660:       } else if(mle==2){
1.242     brouard  3661:        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  3662:       } else if(mle==3){  /* exponential inter-extrapolation */
1.242     brouard  3663:        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  3664:       } else if (mle==4){  /* mle=4 no inter-extrapolation */
1.242     brouard  3665:        lli=log(out[s1][s2]); /* Original formula */
1.136     brouard  3666:       } else{  /* mle=0 back to 1 */
1.242     brouard  3667:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   3668:        /*lli=log(out[s1][s2]); */ /* Original formula */
1.126     brouard  3669:       } /* End of if */
                   3670:       ipmx +=1;
                   3671:       sw += weight[i];
                   3672:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132     brouard  3673:       /*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  3674:       if(globpr){
1.246     brouard  3675:        fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126     brouard  3676:  %11.6f %11.6f %11.6f ", \
1.242     brouard  3677:                num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                   3678:                2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                   3679:        for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   3680:          llt +=ll[k]*gipmx/gsw;
                   3681:          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                   3682:        }
                   3683:        fprintf(ficresilk," %10.6f\n", -llt);
1.126     brouard  3684:       }
1.232     brouard  3685:        } /* end of wave */
                   3686: } /* end of individual */
                   3687: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   3688: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   3689: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   3690: if(globpr==0){ /* First time we count the contributions and weights */
                   3691:        gipmx=ipmx;
                   3692:        gsw=sw;
                   3693: }
                   3694: return -l;
1.126     brouard  3695: }
                   3696: 
                   3697: 
                   3698: /*************** function likelione ***********/
                   3699: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
                   3700: {
                   3701:   /* This routine should help understanding what is done with 
                   3702:      the selection of individuals/waves and
                   3703:      to check the exact contribution to the likelihood.
                   3704:      Plotting could be done.
                   3705:    */
                   3706:   int k;
                   3707: 
                   3708:   if(*globpri !=0){ /* Just counts and sums, no printings */
1.201     brouard  3709:     strcpy(fileresilk,"ILK_"); 
1.202     brouard  3710:     strcat(fileresilk,fileresu);
1.126     brouard  3711:     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                   3712:       printf("Problem with resultfile: %s\n", fileresilk);
                   3713:       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
                   3714:     }
1.214     brouard  3715:     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");
                   3716:     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126     brouard  3717:     /*         i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                   3718:     for(k=1; k<=nlstate; k++) 
                   3719:       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                   3720:     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
                   3721:   }
                   3722: 
                   3723:   *fretone=(*funcone)(p);
                   3724:   if(*globpri !=0){
                   3725:     fclose(ficresilk);
1.205     brouard  3726:     if (mle ==0)
                   3727:       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
                   3728:     else if(mle >=1)
                   3729:       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
                   3730:     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));
1.207     brouard  3731:     
1.208     brouard  3732:       
                   3733:     for (k=1; k<= nlstate ; k++) {
1.211     brouard  3734:       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  3735: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
                   3736:     }
1.207     brouard  3737:     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  3738: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207     brouard  3739:     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204     brouard  3740: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207     brouard  3741:     fflush(fichtm);
1.205     brouard  3742:   }
1.126     brouard  3743:   return;
                   3744: }
                   3745: 
                   3746: 
                   3747: /*********** Maximum Likelihood Estimation ***************/
                   3748: 
                   3749: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                   3750: {
1.165     brouard  3751:   int i,j, iter=0;
1.126     brouard  3752:   double **xi;
                   3753:   double fret;
                   3754:   double fretone; /* Only one call to likelihood */
                   3755:   /*  char filerespow[FILENAMELENGTH];*/
1.162     brouard  3756: 
                   3757: #ifdef NLOPT
                   3758:   int creturn;
                   3759:   nlopt_opt opt;
                   3760:   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
                   3761:   double *lb;
                   3762:   double minf; /* the minimum objective value, upon return */
                   3763:   double * p1; /* Shifted parameters from 0 instead of 1 */
                   3764:   myfunc_data dinst, *d = &dinst;
                   3765: #endif
                   3766: 
                   3767: 
1.126     brouard  3768:   xi=matrix(1,npar,1,npar);
                   3769:   for (i=1;i<=npar;i++)
                   3770:     for (j=1;j<=npar;j++)
                   3771:       xi[i][j]=(i==j ? 1.0 : 0.0);
                   3772:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.201     brouard  3773:   strcpy(filerespow,"POW_"); 
1.126     brouard  3774:   strcat(filerespow,fileres);
                   3775:   if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   3776:     printf("Problem with resultfile: %s\n", filerespow);
                   3777:     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   3778:   }
                   3779:   fprintf(ficrespow,"# Powell\n# iter -2*LL");
                   3780:   for (i=1;i<=nlstate;i++)
                   3781:     for(j=1;j<=nlstate+ndeath;j++)
                   3782:       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   3783:   fprintf(ficrespow,"\n");
1.162     brouard  3784: #ifdef POWELL
1.126     brouard  3785:   powell(p,xi,npar,ftol,&iter,&fret,func);
1.162     brouard  3786: #endif
1.126     brouard  3787: 
1.162     brouard  3788: #ifdef NLOPT
                   3789: #ifdef NEWUOA
                   3790:   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
                   3791: #else
                   3792:   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
                   3793: #endif
                   3794:   lb=vector(0,npar-1);
                   3795:   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
                   3796:   nlopt_set_lower_bounds(opt, lb);
                   3797:   nlopt_set_initial_step1(opt, 0.1);
                   3798:   
                   3799:   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
                   3800:   d->function = func;
                   3801:   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
                   3802:   nlopt_set_min_objective(opt, myfunc, d);
                   3803:   nlopt_set_xtol_rel(opt, ftol);
                   3804:   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
                   3805:     printf("nlopt failed! %d\n",creturn); 
                   3806:   }
                   3807:   else {
                   3808:     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
                   3809:     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
                   3810:     iter=1; /* not equal */
                   3811:   }
                   3812:   nlopt_destroy(opt);
                   3813: #endif
1.126     brouard  3814:   free_matrix(xi,1,npar,1,npar);
                   3815:   fclose(ficrespow);
1.203     brouard  3816:   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   3817:   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180     brouard  3818:   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126     brouard  3819: 
                   3820: }
                   3821: 
                   3822: /**** Computes Hessian and covariance matrix ***/
1.203     brouard  3823: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126     brouard  3824: {
                   3825:   double  **a,**y,*x,pd;
1.203     brouard  3826:   /* double **hess; */
1.164     brouard  3827:   int i, j;
1.126     brouard  3828:   int *indx;
                   3829: 
                   3830:   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203     brouard  3831:   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126     brouard  3832:   void lubksb(double **a, int npar, int *indx, double b[]) ;
                   3833:   void ludcmp(double **a, int npar, int *indx, double *d) ;
                   3834:   double gompertz(double p[]);
1.203     brouard  3835:   /* hess=matrix(1,npar,1,npar); */
1.126     brouard  3836: 
                   3837:   printf("\nCalculation of the hessian matrix. Wait...\n");
                   3838:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                   3839:   for (i=1;i<=npar;i++){
1.203     brouard  3840:     printf("%d-",i);fflush(stdout);
                   3841:     fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126     brouard  3842:    
                   3843:      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                   3844:     
                   3845:     /*  printf(" %f ",p[i]);
                   3846:        printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
                   3847:   }
                   3848:   
                   3849:   for (i=1;i<=npar;i++) {
                   3850:     for (j=1;j<=npar;j++)  {
                   3851:       if (j>i) { 
1.203     brouard  3852:        printf(".%d-%d",i,j);fflush(stdout);
                   3853:        fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
                   3854:        hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126     brouard  3855:        
                   3856:        hess[j][i]=hess[i][j];    
                   3857:        /*printf(" %lf ",hess[i][j]);*/
                   3858:       }
                   3859:     }
                   3860:   }
                   3861:   printf("\n");
                   3862:   fprintf(ficlog,"\n");
                   3863: 
                   3864:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
                   3865:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                   3866:   
                   3867:   a=matrix(1,npar,1,npar);
                   3868:   y=matrix(1,npar,1,npar);
                   3869:   x=vector(1,npar);
                   3870:   indx=ivector(1,npar);
                   3871:   for (i=1;i<=npar;i++)
                   3872:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   3873:   ludcmp(a,npar,indx,&pd);
                   3874: 
                   3875:   for (j=1;j<=npar;j++) {
                   3876:     for (i=1;i<=npar;i++) x[i]=0;
                   3877:     x[j]=1;
                   3878:     lubksb(a,npar,indx,x);
                   3879:     for (i=1;i<=npar;i++){ 
                   3880:       matcov[i][j]=x[i];
                   3881:     }
                   3882:   }
                   3883: 
                   3884:   printf("\n#Hessian matrix#\n");
                   3885:   fprintf(ficlog,"\n#Hessian matrix#\n");
                   3886:   for (i=1;i<=npar;i++) { 
                   3887:     for (j=1;j<=npar;j++) { 
1.203     brouard  3888:       printf("%.6e ",hess[i][j]);
                   3889:       fprintf(ficlog,"%.6e ",hess[i][j]);
1.126     brouard  3890:     }
                   3891:     printf("\n");
                   3892:     fprintf(ficlog,"\n");
                   3893:   }
                   3894: 
1.203     brouard  3895:   /* printf("\n#Covariance matrix#\n"); */
                   3896:   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
                   3897:   /* for (i=1;i<=npar;i++) {  */
                   3898:   /*   for (j=1;j<=npar;j++) {  */
                   3899:   /*     printf("%.6e ",matcov[i][j]); */
                   3900:   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
                   3901:   /*   } */
                   3902:   /*   printf("\n"); */
                   3903:   /*   fprintf(ficlog,"\n"); */
                   3904:   /* } */
                   3905: 
1.126     brouard  3906:   /* Recompute Inverse */
1.203     brouard  3907:   /* for (i=1;i<=npar;i++) */
                   3908:   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
                   3909:   /* ludcmp(a,npar,indx,&pd); */
                   3910: 
                   3911:   /*  printf("\n#Hessian matrix recomputed#\n"); */
                   3912: 
                   3913:   /* for (j=1;j<=npar;j++) { */
                   3914:   /*   for (i=1;i<=npar;i++) x[i]=0; */
                   3915:   /*   x[j]=1; */
                   3916:   /*   lubksb(a,npar,indx,x); */
                   3917:   /*   for (i=1;i<=npar;i++){  */
                   3918:   /*     y[i][j]=x[i]; */
                   3919:   /*     printf("%.3e ",y[i][j]); */
                   3920:   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
                   3921:   /*   } */
                   3922:   /*   printf("\n"); */
                   3923:   /*   fprintf(ficlog,"\n"); */
                   3924:   /* } */
                   3925: 
                   3926:   /* Verifying the inverse matrix */
                   3927: #ifdef DEBUGHESS
                   3928:   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126     brouard  3929: 
1.203     brouard  3930:    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
                   3931:    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126     brouard  3932: 
                   3933:   for (j=1;j<=npar;j++) {
                   3934:     for (i=1;i<=npar;i++){ 
1.203     brouard  3935:       printf("%.2f ",y[i][j]);
                   3936:       fprintf(ficlog,"%.2f ",y[i][j]);
1.126     brouard  3937:     }
                   3938:     printf("\n");
                   3939:     fprintf(ficlog,"\n");
                   3940:   }
1.203     brouard  3941: #endif
1.126     brouard  3942: 
                   3943:   free_matrix(a,1,npar,1,npar);
                   3944:   free_matrix(y,1,npar,1,npar);
                   3945:   free_vector(x,1,npar);
                   3946:   free_ivector(indx,1,npar);
1.203     brouard  3947:   /* free_matrix(hess,1,npar,1,npar); */
1.126     brouard  3948: 
                   3949: 
                   3950: }
                   3951: 
                   3952: /*************** hessian matrix ****************/
                   3953: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203     brouard  3954: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126     brouard  3955:   int i;
                   3956:   int l=1, lmax=20;
1.203     brouard  3957:   double k1,k2, res, fx;
1.132     brouard  3958:   double p2[MAXPARM+1]; /* identical to x */
1.126     brouard  3959:   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   3960:   int k=0,kmax=10;
                   3961:   double l1;
                   3962: 
                   3963:   fx=func(x);
                   3964:   for (i=1;i<=npar;i++) p2[i]=x[i];
1.145     brouard  3965:   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
1.126     brouard  3966:     l1=pow(10,l);
                   3967:     delts=delt;
                   3968:     for(k=1 ; k <kmax; k=k+1){
                   3969:       delt = delta*(l1*k);
                   3970:       p2[theta]=x[theta] +delt;
1.145     brouard  3971:       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
1.126     brouard  3972:       p2[theta]=x[theta]-delt;
                   3973:       k2=func(p2)-fx;
                   3974:       /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203     brouard  3975:       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126     brouard  3976:       
1.203     brouard  3977: #ifdef DEBUGHESSII
1.126     brouard  3978:       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);
                   3979:       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);
                   3980: #endif
                   3981:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                   3982:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   3983:        k=kmax;
                   3984:       }
                   3985:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164     brouard  3986:        k=kmax; l=lmax*10;
1.126     brouard  3987:       }
                   3988:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                   3989:        delts=delt;
                   3990:       }
1.203     brouard  3991:     } /* End loop k */
1.126     brouard  3992:   }
                   3993:   delti[theta]=delts;
                   3994:   return res; 
                   3995:   
                   3996: }
                   3997: 
1.203     brouard  3998: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126     brouard  3999: {
                   4000:   int i;
1.164     brouard  4001:   int l=1, lmax=20;
1.126     brouard  4002:   double k1,k2,k3,k4,res,fx;
1.132     brouard  4003:   double p2[MAXPARM+1];
1.203     brouard  4004:   int k, kmax=1;
                   4005:   double v1, v2, cv12, lc1, lc2;
1.208     brouard  4006: 
                   4007:   int firstime=0;
1.203     brouard  4008:   
1.126     brouard  4009:   fx=func(x);
1.203     brouard  4010:   for (k=1; k<=kmax; k=k+10) {
1.126     brouard  4011:     for (i=1;i<=npar;i++) p2[i]=x[i];
1.203     brouard  4012:     p2[thetai]=x[thetai]+delti[thetai]*k;
                   4013:     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126     brouard  4014:     k1=func(p2)-fx;
                   4015:   
1.203     brouard  4016:     p2[thetai]=x[thetai]+delti[thetai]*k;
                   4017:     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126     brouard  4018:     k2=func(p2)-fx;
                   4019:   
1.203     brouard  4020:     p2[thetai]=x[thetai]-delti[thetai]*k;
                   4021:     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126     brouard  4022:     k3=func(p2)-fx;
                   4023:   
1.203     brouard  4024:     p2[thetai]=x[thetai]-delti[thetai]*k;
                   4025:     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126     brouard  4026:     k4=func(p2)-fx;
1.203     brouard  4027:     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
                   4028:     if(k1*k2*k3*k4 <0.){
1.208     brouard  4029:       firstime=1;
1.203     brouard  4030:       kmax=kmax+10;
1.208     brouard  4031:     }
                   4032:     if(kmax >=10 || firstime ==1){
1.246     brouard  4033:       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);
                   4034:       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  4035:       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);
                   4036:       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);
                   4037:     }
                   4038: #ifdef DEBUGHESSIJ
                   4039:     v1=hess[thetai][thetai];
                   4040:     v2=hess[thetaj][thetaj];
                   4041:     cv12=res;
                   4042:     /* Computing eigen value of Hessian matrix */
                   4043:     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   4044:     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   4045:     if ((lc2 <0) || (lc1 <0) ){
                   4046:       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
                   4047:       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
                   4048:       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);
                   4049:       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);
                   4050:     }
1.126     brouard  4051: #endif
                   4052:   }
                   4053:   return res;
                   4054: }
                   4055: 
1.203     brouard  4056:     /* Not done yet: Was supposed to fix if not exactly at the maximum */
                   4057: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
                   4058: /* { */
                   4059: /*   int i; */
                   4060: /*   int l=1, lmax=20; */
                   4061: /*   double k1,k2,k3,k4,res,fx; */
                   4062: /*   double p2[MAXPARM+1]; */
                   4063: /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
                   4064: /*   int k=0,kmax=10; */
                   4065: /*   double l1; */
                   4066:   
                   4067: /*   fx=func(x); */
                   4068: /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
                   4069: /*     l1=pow(10,l); */
                   4070: /*     delts=delt; */
                   4071: /*     for(k=1 ; k <kmax; k=k+1){ */
                   4072: /*       delt = delti*(l1*k); */
                   4073: /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
                   4074: /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
                   4075: /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
                   4076: /*       k1=func(p2)-fx; */
                   4077:       
                   4078: /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
                   4079: /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
                   4080: /*       k2=func(p2)-fx; */
                   4081:       
                   4082: /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
                   4083: /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
                   4084: /*       k3=func(p2)-fx; */
                   4085:       
                   4086: /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
                   4087: /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
                   4088: /*       k4=func(p2)-fx; */
                   4089: /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
                   4090: /* #ifdef DEBUGHESSIJ */
                   4091: /*       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); */
                   4092: /*       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); */
                   4093: /* #endif */
                   4094: /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
                   4095: /*     k=kmax; */
                   4096: /*       } */
                   4097: /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
                   4098: /*     k=kmax; l=lmax*10; */
                   4099: /*       } */
                   4100: /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
                   4101: /*     delts=delt; */
                   4102: /*       } */
                   4103: /*     } /\* End loop k *\/ */
                   4104: /*   } */
                   4105: /*   delti[theta]=delts; */
                   4106: /*   return res;  */
                   4107: /* } */
                   4108: 
                   4109: 
1.126     brouard  4110: /************** Inverse of matrix **************/
                   4111: void ludcmp(double **a, int n, int *indx, double *d) 
                   4112: { 
                   4113:   int i,imax,j,k; 
                   4114:   double big,dum,sum,temp; 
                   4115:   double *vv; 
                   4116:  
                   4117:   vv=vector(1,n); 
                   4118:   *d=1.0; 
                   4119:   for (i=1;i<=n;i++) { 
                   4120:     big=0.0; 
                   4121:     for (j=1;j<=n;j++) 
                   4122:       if ((temp=fabs(a[i][j])) > big) big=temp; 
                   4123:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                   4124:     vv[i]=1.0/big; 
                   4125:   } 
                   4126:   for (j=1;j<=n;j++) { 
                   4127:     for (i=1;i<j;i++) { 
                   4128:       sum=a[i][j]; 
                   4129:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                   4130:       a[i][j]=sum; 
                   4131:     } 
                   4132:     big=0.0; 
                   4133:     for (i=j;i<=n;i++) { 
                   4134:       sum=a[i][j]; 
                   4135:       for (k=1;k<j;k++) 
                   4136:        sum -= a[i][k]*a[k][j]; 
                   4137:       a[i][j]=sum; 
                   4138:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   4139:        big=dum; 
                   4140:        imax=i; 
                   4141:       } 
                   4142:     } 
                   4143:     if (j != imax) { 
                   4144:       for (k=1;k<=n;k++) { 
                   4145:        dum=a[imax][k]; 
                   4146:        a[imax][k]=a[j][k]; 
                   4147:        a[j][k]=dum; 
                   4148:       } 
                   4149:       *d = -(*d); 
                   4150:       vv[imax]=vv[j]; 
                   4151:     } 
                   4152:     indx[j]=imax; 
                   4153:     if (a[j][j] == 0.0) a[j][j]=TINY; 
                   4154:     if (j != n) { 
                   4155:       dum=1.0/(a[j][j]); 
                   4156:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                   4157:     } 
                   4158:   } 
                   4159:   free_vector(vv,1,n);  /* Doesn't work */
                   4160: ;
                   4161: } 
                   4162: 
                   4163: void lubksb(double **a, int n, int *indx, double b[]) 
                   4164: { 
                   4165:   int i,ii=0,ip,j; 
                   4166:   double sum; 
                   4167:  
                   4168:   for (i=1;i<=n;i++) { 
                   4169:     ip=indx[i]; 
                   4170:     sum=b[ip]; 
                   4171:     b[ip]=b[i]; 
                   4172:     if (ii) 
                   4173:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                   4174:     else if (sum) ii=i; 
                   4175:     b[i]=sum; 
                   4176:   } 
                   4177:   for (i=n;i>=1;i--) { 
                   4178:     sum=b[i]; 
                   4179:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   4180:     b[i]=sum/a[i][i]; 
                   4181:   } 
                   4182: } 
                   4183: 
                   4184: void pstamp(FILE *fichier)
                   4185: {
1.196     brouard  4186:   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126     brouard  4187: }
                   4188: 
                   4189: /************ Frequencies ********************/
1.251     brouard  4190: void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226     brouard  4191:                  int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   4192:                  int firstpass,  int lastpass, int stepm, int weightopt, char model[])
1.250     brouard  4193: {  /* Some frequencies as well as proposing some starting values */
1.226     brouard  4194:   
1.250     brouard  4195:   int i, m, jk, j1, bool, z1,j, k, iv, jj=0;
1.226     brouard  4196:   int iind=0, iage=0;
                   4197:   int mi; /* Effective wave */
                   4198:   int first;
                   4199:   double ***freq; /* Frequencies */
                   4200:   double *meanq;
                   4201:   double **meanqt;
                   4202:   double *pp, **prop, *posprop, *pospropt;
                   4203:   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
                   4204:   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
                   4205:   double agebegin, ageend;
                   4206:     
                   4207:   pp=vector(1,nlstate);
1.251     brouard  4208:   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
1.226     brouard  4209:   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
                   4210:   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
                   4211:   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
                   4212:   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
                   4213:   meanqt=matrix(1,lastpass,1,nqtveff);
                   4214:   strcpy(fileresp,"P_");
                   4215:   strcat(fileresp,fileresu);
                   4216:   /*strcat(fileresphtm,fileresu);*/
                   4217:   if((ficresp=fopen(fileresp,"w"))==NULL) {
                   4218:     printf("Problem with prevalence resultfile: %s\n", fileresp);
                   4219:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                   4220:     exit(0);
                   4221:   }
1.240     brouard  4222:   
1.226     brouard  4223:   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
                   4224:   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
                   4225:     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
                   4226:     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
                   4227:     fflush(ficlog);
                   4228:     exit(70); 
                   4229:   }
                   4230:   else{
                   4231:     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240     brouard  4232: <hr size=\"2\" color=\"#EC5E5E\"> \n                                   \
1.214     brouard  4233: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226     brouard  4234:            fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   4235:   }
1.237     brouard  4236:   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
1.240     brouard  4237:   
1.226     brouard  4238:   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
                   4239:   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
                   4240:     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
                   4241:     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
                   4242:     fflush(ficlog);
                   4243:     exit(70); 
1.240     brouard  4244:   } else{
1.226     brouard  4245:     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240     brouard  4246: <hr size=\"2\" color=\"#EC5E5E\"> \n                                   \
1.214     brouard  4247: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226     brouard  4248:            fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   4249:   }
1.240     brouard  4250:   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>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);
                   4251:   
1.251     brouard  4252:   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226     brouard  4253:   j1=0;
1.126     brouard  4254:   
1.227     brouard  4255:   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
                   4256:   j=cptcoveff;  /* Only dummy covariates of the model */
1.226     brouard  4257:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240     brouard  4258:   
                   4259:   
1.226     brouard  4260:   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
                   4261:      reference=low_education V1=0,V2=0
                   4262:      med_educ                V1=1 V2=0, 
                   4263:      high_educ               V1=0 V2=1
                   4264:      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
                   4265:   */
1.249     brouard  4266:   dateintsum=0;
                   4267:   k2cpt=0;
                   4268: 
1.251     brouard  4269:   for (j = 0; j <= cptcoveff; j+=cptcoveff){   /* j= 0 constant model */
                   4270:     first=1;
                   4271:     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
                   4272:       posproptt=0.;
                   4273:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                   4274:        scanf("%d", i);*/
                   4275:       for (i=-5; i<=nlstate+ndeath; i++)  
                   4276:        for (jk=-5; jk<=nlstate+ndeath; jk++)  
                   4277:          for(m=iagemin; m <= iagemax+3; m++)
                   4278:            freq[i][jk][m]=0;
                   4279:       
                   4280:       for (i=1; i<=nlstate; i++)  {
1.240     brouard  4281:        for(m=iagemin; m <= iagemax+3; m++)
1.251     brouard  4282:          prop[i][m]=0;
                   4283:        posprop[i]=0;
                   4284:        pospropt[i]=0;
                   4285:       }
                   4286:       /* for (z1=1; z1<= nqfveff; z1++) {   */
                   4287:       /*   meanq[z1]+=0.; */
                   4288:       /*   for(m=1;m<=lastpass;m++){ */
                   4289:       /*       meanqt[m][z1]=0.; */
                   4290:       /*   } */
                   4291:       /* } */
                   4292:       
                   4293:       /* dateintsum=0; */
                   4294:       /* k2cpt=0; */
                   4295:       
                   4296:       /* For that combination of covariate j1, we count and print the frequencies in one pass */
                   4297:       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
                   4298:        bool=1;
                   4299:        if(j !=0){
                   4300:          if(anyvaryingduminmodel==0){ /* If All fixed covariates */
                   4301:            if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                   4302:              /* for (z1=1; z1<= nqfveff; z1++) {   */
                   4303:              /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
                   4304:              /* } */
                   4305:              for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                   4306:                /* if(Tvaraff[z1] ==-20){ */
                   4307:                /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                   4308:                /* }else  if(Tvaraff[z1] ==-10){ */
                   4309:                /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                   4310:                /* }else  */
                   4311:                if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
                   4312:                  /* Tests if this individual iind responded to combination j1 (V4=1 V3=0) */
                   4313:                  bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
                   4314:                  /* 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", 
                   4315:                     bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                   4316:                     j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                   4317:                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                   4318:                } /* Onlyf fixed */
                   4319:              } /* end z1 */
                   4320:            } /* cptcovn > 0 */
                   4321:          } /* end any */
                   4322:        }/* end j==0 */
                   4323:        if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
                   4324:          /* for(m=firstpass; m<=lastpass; m++){ */
                   4325:          for(mi=1; mi<wav[iind];mi++){ /* For that wave */
                   4326:            m=mw[mi][iind];
                   4327:            if(j!=0){
                   4328:              if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                   4329:                for (z1=1; z1<=cptcoveff; z1++) {
                   4330:                  if( Fixed[Tmodelind[z1]]==1){
                   4331:                    iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                   4332:                    if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's 
                   4333:                                                                                      value is -1, we don't select. It differs from the 
                   4334:                                                                                      constant and age model which counts them. */
                   4335:                      bool=0; /* not selected */
                   4336:                  }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                   4337:                    if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                   4338:                      bool=0;
                   4339:                    }
                   4340:                  }
                   4341:                }
                   4342:              }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
                   4343:            } /* end j==0 */
                   4344:            /* bool =0 we keep that guy which corresponds to the combination of dummy values */
                   4345:            if(bool==1){
                   4346:              /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                   4347:                 and mw[mi+1][iind]. dh depends on stepm. */
                   4348:              agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
                   4349:              ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
                   4350:              if(m >=firstpass && m <=lastpass){
                   4351:                k2=anint[m][iind]+(mint[m][iind]/12.);
                   4352:                /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                   4353:                if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                   4354:                if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                   4355:                if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                   4356:                  prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                   4357:                if (m<lastpass) {
                   4358:                  /* if(s[m][iind]==4 && s[m+1][iind]==4) */
                   4359:                  /*   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]); */
                   4360:                  if(s[m][iind]==-1)
                   4361:                    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.));
                   4362:                  freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                   4363:                  /* if((int)agev[m][iind] == 55) */
                   4364:                  /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
                   4365:                  /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                   4366:                  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  4367:                }
1.251     brouard  4368:              } /* end if between passes */  
                   4369:              if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
                   4370:                dateintsum=dateintsum+k2; /* on all covariates ?*/
                   4371:                k2cpt++;
                   4372:                /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234     brouard  4373:              }
1.251     brouard  4374:            }else{
                   4375:              bool=1;
                   4376:            }/* end bool 2 */
                   4377:          } /* end m */
                   4378:        } /* end bool */
                   4379:       } /* end iind = 1 to imx */
                   4380:       /* prop[s][age] is feeded for any initial and valid live state as well as
                   4381:         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
                   4382:       
                   4383:       
                   4384:       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                   4385:       pstamp(ficresp);
                   4386:       if  (cptcoveff>0 && j!=0){
                   4387:        printf( "\n#********** Variable "); 
                   4388:        fprintf(ficresp, "\n#********** Variable "); 
                   4389:        fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
                   4390:        fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
                   4391:        fprintf(ficlog, "\n#********** Variable "); 
                   4392:        for (z1=1; z1<=cptcoveff; z1++){
                   4393:          if(!FixedV[Tvaraff[z1]]){
                   4394:            printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4395:            fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4396:            fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4397:            fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4398:            fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250     brouard  4399:          }else{
1.251     brouard  4400:            printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4401:            fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4402:            fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4403:            fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4404:            fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   4405:          }
                   4406:        }
                   4407:        printf( "**********\n#");
                   4408:        fprintf(ficresp, "**********\n#");
                   4409:        fprintf(ficresphtm, "**********</h3>\n");
                   4410:        fprintf(ficresphtmfr, "**********</h3>\n");
                   4411:        fprintf(ficlog, "**********\n");
                   4412:       }
                   4413:       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
                   4414:       for(i=1; i<=nlstate;i++) {
                   4415:        fprintf(ficresp, " Age Prev(%d)  N(%d)  N  ",i,i);
                   4416:        fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
                   4417:       }
                   4418:       fprintf(ficresp, "\n");
                   4419:       fprintf(ficresphtm, "\n");
                   4420:       
                   4421:       /* Header of frequency table by age */
                   4422:       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
                   4423:       fprintf(ficresphtmfr,"<th>Age</th> ");
                   4424:       for(jk=-1; jk <=nlstate+ndeath; jk++){
                   4425:        for(m=-1; m <=nlstate+ndeath; m++){
                   4426:          if(jk!=0 && m!=0)
                   4427:            fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
1.240     brouard  4428:        }
1.226     brouard  4429:       }
1.251     brouard  4430:       fprintf(ficresphtmfr, "\n");
                   4431:     
                   4432:       /* For each age */
                   4433:       for(iage=iagemin; iage <= iagemax+3; iage++){
                   4434:        fprintf(ficresphtm,"<tr>");
                   4435:        if(iage==iagemax+1){
                   4436:          fprintf(ficlog,"1");
                   4437:          fprintf(ficresphtmfr,"<tr><th>0</th> ");
                   4438:        }else if(iage==iagemax+2){
                   4439:          fprintf(ficlog,"0");
                   4440:          fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
                   4441:        }else if(iage==iagemax+3){
                   4442:          fprintf(ficlog,"Total");
                   4443:          fprintf(ficresphtmfr,"<tr><th>Total</th> ");
                   4444:        }else{
1.240     brouard  4445:          if(first==1){
1.251     brouard  4446:            first=0;
                   4447:            printf("See log file for details...\n");
                   4448:          }
                   4449:          fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
                   4450:          fprintf(ficlog,"Age %d", iage);
                   4451:        }
                   4452:        for(jk=1; jk <=nlstate ; jk++){
                   4453:          for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                   4454:            pp[jk] += freq[jk][m][iage]; 
                   4455:        }
                   4456:        for(jk=1; jk <=nlstate ; jk++){
                   4457:          for(m=-1, pos=0; m <=0 ; m++)
                   4458:            pos += freq[jk][m][iage];
                   4459:          if(pp[jk]>=1.e-10){
                   4460:            if(first==1){
                   4461:              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   4462:            }
                   4463:            fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   4464:          }else{
                   4465:            if(first==1)
                   4466:              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   4467:            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1.240     brouard  4468:          }
                   4469:        }
                   4470:       
1.251     brouard  4471:        for(jk=1; jk <=nlstate ; jk++){ 
                   4472:          /* posprop[jk]=0; */
                   4473:          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
                   4474:            pp[jk] += freq[jk][m][iage];
                   4475:        }       /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
                   4476:       
                   4477:        for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
                   4478:          pos += pp[jk]; /* pos is the total number of transitions until this age */
                   4479:          posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
                   4480:                                            from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                   4481:          pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
1.240     brouard  4482:                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                   4483:        }
1.251     brouard  4484:        for(jk=1; jk <=nlstate ; jk++){
1.240     brouard  4485:          if(pos>=1.e-5){
1.251     brouard  4486:            if(first==1)
                   4487:              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   4488:            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   4489:          }else{
                   4490:            if(first==1)
                   4491:              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   4492:            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   4493:          }
                   4494:          if( iage <= iagemax){
                   4495:            if(pos>=1.e-5){
                   4496:              fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                   4497:              fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                   4498:              /*probs[iage][jk][j1]= pp[jk]/pos;*/
                   4499:              /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
                   4500:            }
                   4501:            else{
                   4502:              fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
                   4503:              fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
                   4504:            }
1.240     brouard  4505:          }
1.251     brouard  4506:          pospropt[jk] +=posprop[jk];
                   4507:        } /* end loop jk */
                   4508:        /* pospropt=0.; */
                   4509:        for(jk=-1; jk <=nlstate+ndeath; jk++){
                   4510:          for(m=-1; m <=nlstate+ndeath; m++){
                   4511:            if(freq[jk][m][iage] !=0 ) { /* minimizing output */
                   4512:              if(first==1){
                   4513:                printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
                   4514:              }
                   4515:              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
                   4516:            }
                   4517:            if(jk!=0 && m!=0)
                   4518:              fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
1.240     brouard  4519:          }
1.251     brouard  4520:        } /* end loop jk */
                   4521:        posproptt=0.; 
                   4522:        for(jk=1; jk <=nlstate; jk++){
                   4523:          posproptt += pospropt[jk];
                   4524:        }
                   4525:        fprintf(ficresphtmfr,"</tr>\n ");
                   4526:        if(iage <= iagemax){
                   4527:          fprintf(ficresp,"\n");
                   4528:          fprintf(ficresphtm,"</tr>\n");
1.240     brouard  4529:        }
1.251     brouard  4530:        if(first==1)
                   4531:          printf("Others in log...\n");
                   4532:        fprintf(ficlog,"\n");
                   4533:       } /* end loop age iage */
                   4534:       fprintf(ficresphtm,"<tr><th>Tot</th>");
                   4535:       for(jk=1; jk <=nlstate ; jk++){
                   4536:        if(posproptt < 1.e-5){
                   4537:          fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt); 
                   4538:        }else{
                   4539:          fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);  
1.240     brouard  4540:        }
1.226     brouard  4541:       }
1.251     brouard  4542:       fprintf(ficresphtm,"</tr>\n");
                   4543:       fprintf(ficresphtm,"</table>\n");
                   4544:       fprintf(ficresphtmfr,"</table>\n");
1.226     brouard  4545:       if(posproptt < 1.e-5){
1.251     brouard  4546:        fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
                   4547:        fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
                   4548:        fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
                   4549:        invalidvarcomb[j1]=1;
1.226     brouard  4550:       }else{
1.251     brouard  4551:        fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
                   4552:        invalidvarcomb[j1]=0;
1.226     brouard  4553:       }
1.251     brouard  4554:       fprintf(ficresphtmfr,"</table>\n");
                   4555:       fprintf(ficlog,"\n");
                   4556:       if(j!=0){
                   4557:        printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
                   4558:        for(i=1,jk=1; i <=nlstate; i++){
                   4559:          for(k=1; k <=(nlstate+ndeath); k++){
                   4560:            if (k != i) {
                   4561:              for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */
                   4562:                if(jj==1){  /* Constant case */
                   4563:                  if(j1==1){ /* All dummy covariates to zero */
                   4564:                    freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
                   4565:                    freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252   ! brouard  4566:                    printf("%d%d ",i,k);
        !          4567:                    fprintf(ficlog,"%d%d ",i,k);
        !          4568:                    printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[jk],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]));
        !          4569:                    fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
        !          4570:                    pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251     brouard  4571:                  }
1.252   ! brouard  4572:                }else if(jj==2 || nagesqr==1){ /* age or age*age parameter */
        !          4573:                  ;
        !          4574:                }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 */ 
        !          4575:                  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]);
        !          4576:                  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]);
1.251     brouard  4577:                  pstart[jk]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
1.252   ! brouard  4578:                  printf("%d%d ",i,k);
        !          4579:                  fprintf(ficlog,"%d%d ",i,k);
1.251     brouard  4580:                  printf("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],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]));
                   4581:                }else{ /* Other cases, like quantitative fixed or varying covariates */
                   4582:                  ;
                   4583:                }
                   4584:                /* printf("%12.7f )", param[i][jj][k]); */
                   4585:                /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                   4586:                jk++; 
                   4587:              } /* end jj */
                   4588:            } /* end k!= i */
                   4589:          } /* end k */
                   4590:        } /* end i, jk */
                   4591:       } /* end j !=0 */
                   4592:     } /* end selected combination of covariate j1 */
                   4593:     if(j==0){ /* We can estimate starting values from the occurences in each case */
                   4594:       printf("#Freqsummary: Starting values for the constants:\n");
                   4595:       fprintf(ficlog,"\n");
                   4596:       for(i=1,jk=1; i <=nlstate; i++){
                   4597:        for(k=1; k <=(nlstate+ndeath); k++){
                   4598:          if (k != i) {
                   4599:            printf("%d%d ",i,k);
                   4600:            fprintf(ficlog,"%d%d ",i,k);
                   4601:            for(jj=1; jj <=ncovmodel; jj++){
                   4602:              if(jj==1){
                   4603:                printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   4604:                fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   4605:              }
                   4606:              /* printf("%12.7f )", param[i][jj][k]); */
                   4607:              /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                   4608:              jk++; 
1.250     brouard  4609:            }
1.251     brouard  4610:            printf("\n");
                   4611:            fprintf(ficlog,"\n");
1.250     brouard  4612:          }
                   4613:        }
                   4614:       }
1.251     brouard  4615:       printf("#Freqsummary\n");
                   4616:       fprintf(ficlog,"\n");
                   4617:       for(jk=-1; jk <=nlstate+ndeath; jk++){
                   4618:        for(m=-1; m <=nlstate+ndeath; m++){
                   4619:          /* param[i]|j][k]= freq[jk][m][iagemax+3] */
1.250     brouard  4620:          printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
                   4621:          fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
1.251     brouard  4622:          /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */
                   4623:          /*   printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
                   4624:          /*   fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
                   4625:          /* } */
                   4626:        }
                   4627:       } /* end loop jk */
                   4628:       
                   4629:       printf("\n");
                   4630:       fprintf(ficlog,"\n");
                   4631:     } /* end j=0 */
1.249     brouard  4632:   } /* end j */
1.252   ! brouard  4633: 
        !          4634:   if(mle == -2){
        !          4635:     for(i=1, jk=1; i <=nlstate; i++){
        !          4636:       for(j=1; j <=nlstate+ndeath; j++){
        !          4637:        if(j!=i){
        !          4638:          /*ca[0]= k+'a'-1;ca[1]='\0';*/
        !          4639:          printf("%1d%1d",i,j);
        !          4640:          fprintf(ficparo,"%1d%1d",i,j);
        !          4641:          for(k=1; k<=ncovmodel;k++){
        !          4642:            /*    printf(" %lf",param[i][j][k]); */
        !          4643:            /*    fprintf(ficparo," %lf",param[i][j][k]); */
        !          4644:            p[jk]=pstart[jk];
        !          4645:            printf(" %f ",pstart[jk]);
        !          4646:            fprintf(ficparo," %f ",pstart[jk]);
        !          4647:            jk++;
        !          4648:          }
        !          4649:          printf("\n");
        !          4650:          fprintf(ficparo,"\n");
        !          4651:        }
        !          4652:       }
        !          4653:     }
        !          4654:   } /* end mle=-2 */
1.226     brouard  4655:   dateintmean=dateintsum/k2cpt; 
1.240     brouard  4656:   
1.226     brouard  4657:   fclose(ficresp);
                   4658:   fclose(ficresphtm);
                   4659:   fclose(ficresphtmfr);
                   4660:   free_vector(meanq,1,nqfveff);
                   4661:   free_matrix(meanqt,1,lastpass,1,nqtveff);
1.251     brouard  4662:   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226     brouard  4663:   free_vector(pospropt,1,nlstate);
                   4664:   free_vector(posprop,1,nlstate);
1.251     brouard  4665:   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226     brouard  4666:   free_vector(pp,1,nlstate);
                   4667:   /* End of freqsummary */
                   4668: }
1.126     brouard  4669: 
                   4670: /************ Prevalence ********************/
1.227     brouard  4671: 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)
                   4672: {  
                   4673:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   4674:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   4675:      We still use firstpass and lastpass as another selection.
                   4676:   */
1.126     brouard  4677:  
1.227     brouard  4678:   int i, m, jk, j1, bool, z1,j, iv;
                   4679:   int mi; /* Effective wave */
                   4680:   int iage;
                   4681:   double agebegin, ageend;
                   4682: 
                   4683:   double **prop;
                   4684:   double posprop; 
                   4685:   double  y2; /* in fractional years */
                   4686:   int iagemin, iagemax;
                   4687:   int first; /** to stop verbosity which is redirected to log file */
                   4688: 
                   4689:   iagemin= (int) agemin;
                   4690:   iagemax= (int) agemax;
                   4691:   /*pp=vector(1,nlstate);*/
1.251     brouard  4692:   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
1.227     brouard  4693:   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                   4694:   j1=0;
1.222     brouard  4695:   
1.227     brouard  4696:   /*j=cptcoveff;*/
                   4697:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222     brouard  4698:   
1.227     brouard  4699:   first=1;
                   4700:   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
                   4701:     for (i=1; i<=nlstate; i++)  
1.251     brouard  4702:       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227     brouard  4703:        prop[i][iage]=0.0;
                   4704:     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
                   4705:     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
                   4706:     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
                   4707:     
                   4708:     for (i=1; i<=imx; i++) { /* Each individual */
                   4709:       bool=1;
                   4710:       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
                   4711:       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
                   4712:        m=mw[mi][i];
                   4713:        /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
                   4714:        /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
                   4715:        for (z1=1; z1<=cptcoveff; z1++){
                   4716:          if( Fixed[Tmodelind[z1]]==1){
                   4717:            iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                   4718:            if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                   4719:              bool=0;
                   4720:          }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
                   4721:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                   4722:              bool=0;
                   4723:            }
                   4724:        }
                   4725:        if(bool==1){ /* Otherwise we skip that wave/person */
                   4726:          agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
                   4727:          /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                   4728:          if(m >=firstpass && m <=lastpass){
                   4729:            y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   4730:            if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                   4731:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   4732:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251     brouard  4733:              if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227     brouard  4734:                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); 
                   4735:                exit(1);
                   4736:              }
                   4737:              if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   4738:                /*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]]);*/
                   4739:                prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                   4740:                prop[s[m][i]][iagemax+3] += weight[i]; 
                   4741:              } /* end valid statuses */ 
                   4742:            } /* end selection of dates */
                   4743:          } /* end selection of waves */
                   4744:        } /* end bool */
                   4745:       } /* end wave */
                   4746:     } /* end individual */
                   4747:     for(i=iagemin; i <= iagemax+3; i++){  
                   4748:       for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   4749:        posprop += prop[jk][i]; 
                   4750:       } 
                   4751:       
                   4752:       for(jk=1; jk <=nlstate ; jk++){      
                   4753:        if( i <=  iagemax){ 
                   4754:          if(posprop>=1.e-5){ 
                   4755:            probs[i][jk][j1]= prop[jk][i]/posprop;
                   4756:          } else{
                   4757:            if(first==1){
                   4758:              first=0;
                   4759:              printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
                   4760:            }
                   4761:          }
                   4762:        } 
                   4763:       }/* end jk */ 
                   4764:     }/* end i */ 
1.222     brouard  4765:      /*} *//* end i1 */
1.227     brouard  4766:   } /* end j1 */
1.222     brouard  4767:   
1.227     brouard  4768:   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   4769:   /*free_vector(pp,1,nlstate);*/
1.251     brouard  4770:   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227     brouard  4771: }  /* End of prevalence */
1.126     brouard  4772: 
                   4773: /************* Waves Concatenation ***************/
                   4774: 
                   4775: 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)
                   4776: {
                   4777:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   4778:      Death is a valid wave (if date is known).
                   4779:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
                   4780:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   4781:      and mw[mi+1][i]. dh depends on stepm.
1.227     brouard  4782:   */
1.126     brouard  4783: 
1.224     brouard  4784:   int i=0, mi=0, m=0, mli=0;
1.126     brouard  4785:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                   4786:      double sum=0., jmean=0.;*/
1.224     brouard  4787:   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126     brouard  4788:   int j, k=0,jk, ju, jl;
                   4789:   double sum=0.;
                   4790:   first=0;
1.214     brouard  4791:   firstwo=0;
1.217     brouard  4792:   firsthree=0;
1.218     brouard  4793:   firstfour=0;
1.164     brouard  4794:   jmin=100000;
1.126     brouard  4795:   jmax=-1;
                   4796:   jmean=0.;
1.224     brouard  4797: 
                   4798: /* Treating live states */
1.214     brouard  4799:   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
1.224     brouard  4800:     mi=0;  /* First valid wave */
1.227     brouard  4801:     mli=0; /* Last valid wave */
1.126     brouard  4802:     m=firstpass;
1.214     brouard  4803:     while(s[m][i] <= nlstate){  /* a live state */
1.227     brouard  4804:       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 */
                   4805:        mli=m-1;/* mw[++mi][i]=m-1; */
                   4806:       }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 */
                   4807:        mw[++mi][i]=m;
                   4808:        mli=m;
1.224     brouard  4809:       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
                   4810:       if(m < lastpass){ /* m < lastpass, standard case */
1.227     brouard  4811:        m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216     brouard  4812:       }
1.227     brouard  4813:       else{ /* m >= lastpass, eventual special issue with warning */
1.224     brouard  4814: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227     brouard  4815:        break;
1.224     brouard  4816: #else
1.227     brouard  4817:        if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
                   4818:          if(firsthree == 0){
                   4819:            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 pi. .\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);
                   4820:            firsthree=1;
                   4821:          }
                   4822:          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 pi. .\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);
                   4823:          mw[++mi][i]=m;
                   4824:          mli=m;
                   4825:        }
                   4826:        if(s[m][i]==-2){ /* Vital status is really unknown */
                   4827:          nbwarn++;
                   4828:          if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
                   4829:            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);
                   4830:            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);
                   4831:          }
                   4832:          break;
                   4833:        }
                   4834:        break;
1.224     brouard  4835: #endif
1.227     brouard  4836:       }/* End m >= lastpass */
1.126     brouard  4837:     }/* end while */
1.224     brouard  4838: 
1.227     brouard  4839:     /* 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  4840:     /* After last pass */
1.224     brouard  4841: /* Treating death states */
1.214     brouard  4842:     if (s[m][i] > nlstate){  /* In a death state */
1.227     brouard  4843:       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
                   4844:       /* } */
1.126     brouard  4845:       mi++;    /* Death is another wave */
                   4846:       /* if(mi==0)  never been interviewed correctly before death */
1.227     brouard  4847:       /* Only death is a correct wave */
1.126     brouard  4848:       mw[mi][i]=m;
1.224     brouard  4849:     }
                   4850: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227     brouard  4851:     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
1.216     brouard  4852:       /* m++; */
                   4853:       /* mi++; */
                   4854:       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
                   4855:       /* mw[mi][i]=m; */
1.218     brouard  4856:       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227     brouard  4857:        if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
                   4858:          nbwarn++;
                   4859:          if(firstfiv==0){
                   4860:            printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %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 );
                   4861:            firstfiv=1;
                   4862:          }else{
                   4863:            fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %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 );
                   4864:          }
                   4865:        }else{ /* Death occured afer last wave potential bias */
                   4866:          nberr++;
                   4867:          if(firstwo==0){
                   4868:            printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%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], i,m );
                   4869:            firstwo=1;
                   4870:          }
                   4871:          fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%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], i,m );
                   4872:        }
1.218     brouard  4873:       }else{ /* end date of interview is known */
1.227     brouard  4874:        /* death is known but not confirmed by death status at any wave */
                   4875:        if(firstfour==0){
                   4876:          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. 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], i,m );
                   4877:          firstfour=1;
                   4878:        }
                   4879:        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. 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], i,m );
1.214     brouard  4880:       }
1.224     brouard  4881:     } /* end if date of death is known */
                   4882: #endif
                   4883:     wav[i]=mi; /* mi should be the last effective wave (or mli) */
                   4884:     /* wav[i]=mw[mi][i]; */
1.126     brouard  4885:     if(mi==0){
                   4886:       nbwarn++;
                   4887:       if(first==0){
1.227     brouard  4888:        printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                   4889:        first=1;
1.126     brouard  4890:       }
                   4891:       if(first==1){
1.227     brouard  4892:        fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126     brouard  4893:       }
                   4894:     } /* end mi==0 */
                   4895:   } /* End individuals */
1.214     brouard  4896:   /* wav and mw are no more changed */
1.223     brouard  4897:        
1.214     brouard  4898:   
1.126     brouard  4899:   for(i=1; i<=imx; i++){
                   4900:     for(mi=1; mi<wav[i];mi++){
                   4901:       if (stepm <=0)
1.227     brouard  4902:        dh[mi][i]=1;
1.126     brouard  4903:       else{
1.227     brouard  4904:        if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                   4905:          if (agedc[i] < 2*AGESUP) {
                   4906:            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   4907:            if(j==0) j=1;  /* Survives at least one month after exam */
                   4908:            else if(j<0){
                   4909:              nberr++;
                   4910:              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]);
                   4911:              j=1; /* Temporary Dangerous patch */
                   4912:              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);
                   4913:              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]);
                   4914:              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);
                   4915:            }
                   4916:            k=k+1;
                   4917:            if (j >= jmax){
                   4918:              jmax=j;
                   4919:              ijmax=i;
                   4920:            }
                   4921:            if (j <= jmin){
                   4922:              jmin=j;
                   4923:              ijmin=i;
                   4924:            }
                   4925:            sum=sum+j;
                   4926:            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   4927:            /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                   4928:          }
                   4929:        }
                   4930:        else{
                   4931:          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126     brouard  4932: /*       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  4933:                                        
1.227     brouard  4934:          k=k+1;
                   4935:          if (j >= jmax) {
                   4936:            jmax=j;
                   4937:            ijmax=i;
                   4938:          }
                   4939:          else if (j <= jmin){
                   4940:            jmin=j;
                   4941:            ijmin=i;
                   4942:          }
                   4943:          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                   4944:          /*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]);*/
                   4945:          if(j<0){
                   4946:            nberr++;
                   4947:            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]);
                   4948:            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]);
                   4949:          }
                   4950:          sum=sum+j;
                   4951:        }
                   4952:        jk= j/stepm;
                   4953:        jl= j -jk*stepm;
                   4954:        ju= j -(jk+1)*stepm;
                   4955:        if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                   4956:          if(jl==0){
                   4957:            dh[mi][i]=jk;
                   4958:            bh[mi][i]=0;
                   4959:          }else{ /* We want a negative bias in order to only have interpolation ie
                   4960:                  * to avoid the price of an extra matrix product in likelihood */
                   4961:            dh[mi][i]=jk+1;
                   4962:            bh[mi][i]=ju;
                   4963:          }
                   4964:        }else{
                   4965:          if(jl <= -ju){
                   4966:            dh[mi][i]=jk;
                   4967:            bh[mi][i]=jl;       /* bias is positive if real duration
                   4968:                                 * is higher than the multiple of stepm and negative otherwise.
                   4969:                                 */
                   4970:          }
                   4971:          else{
                   4972:            dh[mi][i]=jk+1;
                   4973:            bh[mi][i]=ju;
                   4974:          }
                   4975:          if(dh[mi][i]==0){
                   4976:            dh[mi][i]=1; /* At least one step */
                   4977:            bh[mi][i]=ju; /* At least one step */
                   4978:            /*  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);*/
                   4979:          }
                   4980:        } /* end if mle */
1.126     brouard  4981:       }
                   4982:     } /* end wave */
                   4983:   }
                   4984:   jmean=sum/k;
                   4985:   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  4986:   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  4987: }
1.126     brouard  4988: 
                   4989: /*********** Tricode ****************************/
1.220     brouard  4990:  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242     brouard  4991:  {
                   4992:    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
                   4993:    /*    Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
                   4994:     * Boring subroutine which should only output nbcode[Tvar[j]][k]
                   4995:     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
                   4996:     * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
                   4997:     */
1.130     brouard  4998: 
1.242     brouard  4999:    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
                   5000:    int modmaxcovj=0; /* Modality max of covariates j */
                   5001:    int cptcode=0; /* Modality max of covariates j */
                   5002:    int modmincovj=0; /* Modality min of covariates j */
1.145     brouard  5003: 
                   5004: 
1.242     brouard  5005:    /* cptcoveff=0;  */
                   5006:    /* *cptcov=0; */
1.126     brouard  5007:  
1.242     brouard  5008:    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126     brouard  5009: 
1.242     brouard  5010:    /* Loop on covariates without age and products and no quantitative variable */
                   5011:    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
                   5012:    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
                   5013:      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
                   5014:      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
                   5015:        switch(Fixed[k]) {
                   5016:        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
                   5017:         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*/
                   5018:           ij=(int)(covar[Tvar[k]][i]);
                   5019:           /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                   5020:            * If product of Vn*Vm, still boolean *:
                   5021:            * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                   5022:            * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
                   5023:           /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                   5024:              modality of the nth covariate of individual i. */
                   5025:           if (ij > modmaxcovj)
                   5026:             modmaxcovj=ij; 
                   5027:           else if (ij < modmincovj) 
                   5028:             modmincovj=ij; 
                   5029:           if ((ij < -1) && (ij > NCOVMAX)){
                   5030:             printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                   5031:             exit(1);
                   5032:           }else
                   5033:             Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
                   5034:           /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
                   5035:           /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                   5036:           /* getting the maximum value of the modality of the covariate
                   5037:              (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                   5038:              female ies 1, then modmaxcovj=1.
                   5039:           */
                   5040:         } /* end for loop on individuals i */
                   5041:         printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                   5042:         fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                   5043:         cptcode=modmaxcovj;
                   5044:         /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
                   5045:         /*for (i=0; i<=cptcode; i++) {*/
                   5046:         for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
                   5047:           printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
                   5048:           fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
                   5049:           if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
                   5050:             if( j != -1){
                   5051:               ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
                   5052:                                  covariate for which somebody answered excluding 
                   5053:                                  undefined. Usually 2: 0 and 1. */
                   5054:             }
                   5055:             ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
                   5056:                                     covariate for which somebody answered including 
                   5057:                                     undefined. Usually 3: -1, 0 and 1. */
                   5058:           }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
                   5059:                 * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
                   5060:         } /* Ndum[-1] number of undefined modalities */
1.231     brouard  5061:                        
1.242     brouard  5062:         /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
                   5063:         /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
                   5064:         /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
                   5065:         /* modmincovj=3; modmaxcovj = 7; */
                   5066:         /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
                   5067:         /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
                   5068:         /*              defining two dummy variables: variables V1_1 and V1_2.*/
                   5069:         /* nbcode[Tvar[j]][ij]=k; */
                   5070:         /* nbcode[Tvar[j]][1]=0; */
                   5071:         /* nbcode[Tvar[j]][2]=1; */
                   5072:         /* nbcode[Tvar[j]][3]=2; */
                   5073:         /* To be continued (not working yet). */
                   5074:         ij=0; /* ij is similar to i but can jump over null modalities */
                   5075:         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*/
                   5076:           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
                   5077:             break;
                   5078:           }
                   5079:           ij++;
                   5080:           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*/
                   5081:           cptcode = ij; /* New max modality for covar j */
                   5082:         } /* end of loop on modality i=-1 to 1 or more */
                   5083:         break;
                   5084:        case 1: /* Testing on varying covariate, could be simple and
                   5085:                * should look at waves or product of fixed *
                   5086:                * varying. No time to test -1, assuming 0 and 1 only */
                   5087:         ij=0;
                   5088:         for(i=0; i<=1;i++){
                   5089:           nbcode[Tvar[k]][++ij]=i;
                   5090:         }
                   5091:         break;
                   5092:        default:
                   5093:         break;
                   5094:        } /* end switch */
                   5095:      } /* end dummy test */
                   5096:     
                   5097:      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
                   5098:      /*        /\*recode from 0 *\/ */
                   5099:      /*                                     k is a modality. If we have model=V1+V1*sex  */
                   5100:      /*                                     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                   5101:      /*                                  But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
                   5102:      /*        } */
                   5103:      /*        /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
                   5104:      /*        if (ij > ncodemax[j]) { */
                   5105:      /*          printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
                   5106:      /*          fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
                   5107:      /*          break; */
                   5108:      /*        } */
                   5109:      /*   }  /\* end of loop on modality k *\/ */
                   5110:    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
                   5111:   
                   5112:    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
                   5113:    /* Look at fixed dummy (single or product) covariates to check empty modalities */
                   5114:    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
                   5115:      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
                   5116:      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 */ 
                   5117:      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 */
                   5118:      /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
                   5119:    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
                   5120:   
                   5121:    ij=0;
                   5122:    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
                   5123:    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
                   5124:      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
                   5125:      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
                   5126:      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
                   5127:        /* If product not in single variable we don't print results */
                   5128:        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
                   5129:        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
                   5130:        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*/
                   5131:        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
                   5132:        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 */
                   5133:        if(Fixed[k]!=0)
                   5134:         anyvaryingduminmodel=1;
                   5135:        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
                   5136:        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
                   5137:        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
                   5138:        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
                   5139:        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
                   5140:        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
                   5141:      } 
                   5142:    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
                   5143:    /* ij--; */
                   5144:    /* cptcoveff=ij; /\*Number of total covariates*\/ */
                   5145:    *cptcov=ij; /*Number of total real effective covariates: effective
                   5146:                * because they can be excluded from the model and real
                   5147:                * if in the model but excluded because missing values, but how to get k from ij?*/
                   5148:    for(j=ij+1; j<= cptcovt; j++){
                   5149:      Tvaraff[j]=0;
                   5150:      Tmodelind[j]=0;
                   5151:    }
                   5152:    for(j=ntveff+1; j<= cptcovt; j++){
                   5153:      TmodelInvind[j]=0;
                   5154:    }
                   5155:    /* To be sorted */
                   5156:    ;
                   5157:  }
1.126     brouard  5158: 
1.145     brouard  5159: 
1.126     brouard  5160: /*********** Health Expectancies ****************/
                   5161: 
1.235     brouard  5162:  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  5163: 
                   5164: {
                   5165:   /* Health expectancies, no variances */
1.164     brouard  5166:   int i, j, nhstepm, hstepm, h, nstepm;
1.126     brouard  5167:   int nhstepma, nstepma; /* Decreasing with age */
                   5168:   double age, agelim, hf;
                   5169:   double ***p3mat;
                   5170:   double eip;
                   5171: 
1.238     brouard  5172:   /* pstamp(ficreseij); */
1.126     brouard  5173:   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
                   5174:   fprintf(ficreseij,"# Age");
                   5175:   for(i=1; i<=nlstate;i++){
                   5176:     for(j=1; j<=nlstate;j++){
                   5177:       fprintf(ficreseij," e%1d%1d ",i,j);
                   5178:     }
                   5179:     fprintf(ficreseij," e%1d. ",i);
                   5180:   }
                   5181:   fprintf(ficreseij,"\n");
                   5182: 
                   5183:   
                   5184:   if(estepm < stepm){
                   5185:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   5186:   }
                   5187:   else  hstepm=estepm;   
                   5188:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   5189:    * This is mainly to measure the difference between two models: for example
                   5190:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   5191:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   5192:    * progression in between and thus overestimating or underestimating according
                   5193:    * to the curvature of the survival function. If, for the same date, we 
                   5194:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   5195:    * to compare the new estimate of Life expectancy with the same linear 
                   5196:    * hypothesis. A more precise result, taking into account a more precise
                   5197:    * curvature will be obtained if estepm is as small as stepm. */
                   5198: 
                   5199:   /* For example we decided to compute the life expectancy with the smallest unit */
                   5200:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   5201:      nhstepm is the number of hstepm from age to agelim 
                   5202:      nstepm is the number of stepm from age to agelin. 
                   5203:      Look at hpijx to understand the reason of that which relies in memory size
                   5204:      and note for a fixed period like estepm months */
                   5205:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   5206:      survival function given by stepm (the optimization length). Unfortunately it
                   5207:      means that if the survival funtion is printed only each two years of age and if
                   5208:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   5209:      results. So we changed our mind and took the option of the best precision.
                   5210:   */
                   5211:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   5212: 
                   5213:   agelim=AGESUP;
                   5214:   /* If stepm=6 months */
                   5215:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   5216:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   5217:     
                   5218: /* nhstepm age range expressed in number of stepm */
                   5219:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   5220:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   5221:   /* if (stepm >= YEARM) hstepm=1;*/
                   5222:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   5223:   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5224: 
                   5225:   for (age=bage; age<=fage; age ++){ 
                   5226:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   5227:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   5228:     /* if (stepm >= YEARM) hstepm=1;*/
                   5229:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   5230: 
                   5231:     /* If stepm=6 months */
                   5232:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   5233:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   5234:     
1.235     brouard  5235:     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
1.126     brouard  5236:     
                   5237:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   5238:     
                   5239:     printf("%d|",(int)age);fflush(stdout);
                   5240:     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   5241:     
                   5242:     /* Computing expectancies */
                   5243:     for(i=1; i<=nlstate;i++)
                   5244:       for(j=1; j<=nlstate;j++)
                   5245:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   5246:          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                   5247:          
                   5248:          /* 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]);*/
                   5249: 
                   5250:        }
                   5251: 
                   5252:     fprintf(ficreseij,"%3.0f",age );
                   5253:     for(i=1; i<=nlstate;i++){
                   5254:       eip=0;
                   5255:       for(j=1; j<=nlstate;j++){
                   5256:        eip +=eij[i][j][(int)age];
                   5257:        fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                   5258:       }
                   5259:       fprintf(ficreseij,"%9.4f", eip );
                   5260:     }
                   5261:     fprintf(ficreseij,"\n");
                   5262:     
                   5263:   }
                   5264:   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5265:   printf("\n");
                   5266:   fprintf(ficlog,"\n");
                   5267:   
                   5268: }
                   5269: 
1.235     brouard  5270:  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  5271: 
                   5272: {
                   5273:   /* Covariances of health expectancies eij and of total life expectancies according
1.222     brouard  5274:      to initial status i, ei. .
1.126     brouard  5275:   */
                   5276:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
                   5277:   int nhstepma, nstepma; /* Decreasing with age */
                   5278:   double age, agelim, hf;
                   5279:   double ***p3matp, ***p3matm, ***varhe;
                   5280:   double **dnewm,**doldm;
                   5281:   double *xp, *xm;
                   5282:   double **gp, **gm;
                   5283:   double ***gradg, ***trgradg;
                   5284:   int theta;
                   5285: 
                   5286:   double eip, vip;
                   5287: 
                   5288:   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                   5289:   xp=vector(1,npar);
                   5290:   xm=vector(1,npar);
                   5291:   dnewm=matrix(1,nlstate*nlstate,1,npar);
                   5292:   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
                   5293:   
                   5294:   pstamp(ficresstdeij);
                   5295:   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
                   5296:   fprintf(ficresstdeij,"# Age");
                   5297:   for(i=1; i<=nlstate;i++){
                   5298:     for(j=1; j<=nlstate;j++)
                   5299:       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
                   5300:     fprintf(ficresstdeij," e%1d. ",i);
                   5301:   }
                   5302:   fprintf(ficresstdeij,"\n");
                   5303: 
                   5304:   pstamp(ficrescveij);
                   5305:   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
                   5306:   fprintf(ficrescveij,"# Age");
                   5307:   for(i=1; i<=nlstate;i++)
                   5308:     for(j=1; j<=nlstate;j++){
                   5309:       cptj= (j-1)*nlstate+i;
                   5310:       for(i2=1; i2<=nlstate;i2++)
                   5311:        for(j2=1; j2<=nlstate;j2++){
                   5312:          cptj2= (j2-1)*nlstate+i2;
                   5313:          if(cptj2 <= cptj)
                   5314:            fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
                   5315:        }
                   5316:     }
                   5317:   fprintf(ficrescveij,"\n");
                   5318:   
                   5319:   if(estepm < stepm){
                   5320:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   5321:   }
                   5322:   else  hstepm=estepm;   
                   5323:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   5324:    * This is mainly to measure the difference between two models: for example
                   5325:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   5326:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   5327:    * progression in between and thus overestimating or underestimating according
                   5328:    * to the curvature of the survival function. If, for the same date, we 
                   5329:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   5330:    * to compare the new estimate of Life expectancy with the same linear 
                   5331:    * hypothesis. A more precise result, taking into account a more precise
                   5332:    * curvature will be obtained if estepm is as small as stepm. */
                   5333: 
                   5334:   /* For example we decided to compute the life expectancy with the smallest unit */
                   5335:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   5336:      nhstepm is the number of hstepm from age to agelim 
                   5337:      nstepm is the number of stepm from age to agelin. 
                   5338:      Look at hpijx to understand the reason of that which relies in memory size
                   5339:      and note for a fixed period like estepm months */
                   5340:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   5341:      survival function given by stepm (the optimization length). Unfortunately it
                   5342:      means that if the survival funtion is printed only each two years of age and if
                   5343:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   5344:      results. So we changed our mind and took the option of the best precision.
                   5345:   */
                   5346:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   5347: 
                   5348:   /* If stepm=6 months */
                   5349:   /* nhstepm age range expressed in number of stepm */
                   5350:   agelim=AGESUP;
                   5351:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                   5352:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   5353:   /* if (stepm >= YEARM) hstepm=1;*/
                   5354:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   5355:   
                   5356:   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5357:   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5358:   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                   5359:   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                   5360:   gp=matrix(0,nhstepm,1,nlstate*nlstate);
                   5361:   gm=matrix(0,nhstepm,1,nlstate*nlstate);
                   5362: 
                   5363:   for (age=bage; age<=fage; age ++){ 
                   5364:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   5365:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   5366:     /* if (stepm >= YEARM) hstepm=1;*/
                   5367:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218     brouard  5368:                
1.126     brouard  5369:     /* If stepm=6 months */
                   5370:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   5371:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   5372:     
                   5373:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
1.218     brouard  5374:                
1.126     brouard  5375:     /* Computing  Variances of health expectancies */
                   5376:     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
                   5377:        decrease memory allocation */
                   5378:     for(theta=1; theta <=npar; theta++){
                   5379:       for(i=1; i<=npar; i++){ 
1.222     brouard  5380:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   5381:        xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126     brouard  5382:       }
1.235     brouard  5383:       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);  
                   5384:       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);  
1.218     brouard  5385:                        
1.126     brouard  5386:       for(j=1; j<= nlstate; j++){
1.222     brouard  5387:        for(i=1; i<=nlstate; i++){
                   5388:          for(h=0; h<=nhstepm-1; h++){
                   5389:            gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                   5390:            gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                   5391:          }
                   5392:        }
1.126     brouard  5393:       }
1.218     brouard  5394:                        
1.126     brouard  5395:       for(ij=1; ij<= nlstate*nlstate; ij++)
1.222     brouard  5396:        for(h=0; h<=nhstepm-1; h++){
                   5397:          gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
                   5398:        }
1.126     brouard  5399:     }/* End theta */
                   5400:     
                   5401:     
                   5402:     for(h=0; h<=nhstepm-1; h++)
                   5403:       for(j=1; j<=nlstate*nlstate;j++)
1.222     brouard  5404:        for(theta=1; theta <=npar; theta++)
                   5405:          trgradg[h][j][theta]=gradg[h][theta][j];
1.126     brouard  5406:     
1.218     brouard  5407:                
1.222     brouard  5408:     for(ij=1;ij<=nlstate*nlstate;ij++)
1.126     brouard  5409:       for(ji=1;ji<=nlstate*nlstate;ji++)
1.222     brouard  5410:        varhe[ij][ji][(int)age] =0.;
1.218     brouard  5411:                
1.222     brouard  5412:     printf("%d|",(int)age);fflush(stdout);
                   5413:     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   5414:     for(h=0;h<=nhstepm-1;h++){
1.126     brouard  5415:       for(k=0;k<=nhstepm-1;k++){
1.222     brouard  5416:        matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   5417:        matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                   5418:        for(ij=1;ij<=nlstate*nlstate;ij++)
                   5419:          for(ji=1;ji<=nlstate*nlstate;ji++)
                   5420:            varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126     brouard  5421:       }
                   5422:     }
1.218     brouard  5423:                
1.126     brouard  5424:     /* Computing expectancies */
1.235     brouard  5425:     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);  
1.126     brouard  5426:     for(i=1; i<=nlstate;i++)
                   5427:       for(j=1; j<=nlstate;j++)
1.222     brouard  5428:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   5429:          eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218     brouard  5430:                                        
1.222     brouard  5431:          /* 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  5432:                                        
1.222     brouard  5433:        }
1.218     brouard  5434:                
1.126     brouard  5435:     fprintf(ficresstdeij,"%3.0f",age );
                   5436:     for(i=1; i<=nlstate;i++){
                   5437:       eip=0.;
                   5438:       vip=0.;
                   5439:       for(j=1; j<=nlstate;j++){
1.222     brouard  5440:        eip += eij[i][j][(int)age];
                   5441:        for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                   5442:          vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                   5443:        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  5444:       }
                   5445:       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
                   5446:     }
                   5447:     fprintf(ficresstdeij,"\n");
1.218     brouard  5448:                
1.126     brouard  5449:     fprintf(ficrescveij,"%3.0f",age );
                   5450:     for(i=1; i<=nlstate;i++)
                   5451:       for(j=1; j<=nlstate;j++){
1.222     brouard  5452:        cptj= (j-1)*nlstate+i;
                   5453:        for(i2=1; i2<=nlstate;i2++)
                   5454:          for(j2=1; j2<=nlstate;j2++){
                   5455:            cptj2= (j2-1)*nlstate+i2;
                   5456:            if(cptj2 <= cptj)
                   5457:              fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                   5458:          }
1.126     brouard  5459:       }
                   5460:     fprintf(ficrescveij,"\n");
1.218     brouard  5461:                
1.126     brouard  5462:   }
                   5463:   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   5464:   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   5465:   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   5466:   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                   5467:   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5468:   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5469:   printf("\n");
                   5470:   fprintf(ficlog,"\n");
1.218     brouard  5471:        
1.126     brouard  5472:   free_vector(xm,1,npar);
                   5473:   free_vector(xp,1,npar);
                   5474:   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   5475:   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   5476:   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                   5477: }
1.218     brouard  5478:  
1.126     brouard  5479: /************ Variance ******************/
1.235     brouard  5480:  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  5481:  {
                   5482:    /* Variance of health expectancies */
                   5483:    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                   5484:    /* double **newm;*/
                   5485:    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
                   5486:   
                   5487:    /* int movingaverage(); */
                   5488:    double **dnewm,**doldm;
                   5489:    double **dnewmp,**doldmp;
                   5490:    int i, j, nhstepm, hstepm, h, nstepm ;
                   5491:    int k;
                   5492:    double *xp;
                   5493:    double **gp, **gm;  /* for var eij */
                   5494:    double ***gradg, ***trgradg; /*for var eij */
                   5495:    double **gradgp, **trgradgp; /* for var p point j */
                   5496:    double *gpp, *gmp; /* for var p point j */
                   5497:    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                   5498:    double ***p3mat;
                   5499:    double age,agelim, hf;
                   5500:    /* double ***mobaverage; */
                   5501:    int theta;
                   5502:    char digit[4];
                   5503:    char digitp[25];
                   5504: 
                   5505:    char fileresprobmorprev[FILENAMELENGTH];
                   5506: 
                   5507:    if(popbased==1){
                   5508:      if(mobilav!=0)
                   5509:        strcpy(digitp,"-POPULBASED-MOBILAV_");
                   5510:      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
                   5511:    }
                   5512:    else 
                   5513:      strcpy(digitp,"-STABLBASED_");
1.126     brouard  5514: 
1.218     brouard  5515:    /* if (mobilav!=0) { */
                   5516:    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   5517:    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
                   5518:    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
                   5519:    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
                   5520:    /*   } */
                   5521:    /* } */
                   5522: 
                   5523:    strcpy(fileresprobmorprev,"PRMORPREV-"); 
                   5524:    sprintf(digit,"%-d",ij);
                   5525:    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   5526:    strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   5527:    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   5528:    strcat(fileresprobmorprev,fileresu);
                   5529:    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   5530:      printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   5531:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   5532:    }
                   5533:    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   5534:    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   5535:    pstamp(ficresprobmorprev);
                   5536:    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  5537:    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
                   5538:    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   5539:      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   5540:    }
                   5541:    for(j=1;j<=cptcoveff;j++) 
                   5542:      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
                   5543:    fprintf(ficresprobmorprev,"\n");
                   5544: 
1.218     brouard  5545:    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   5546:    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   5547:      fprintf(ficresprobmorprev," p.%-d SE",j);
                   5548:      for(i=1; i<=nlstate;i++)
                   5549:        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   5550:    }  
                   5551:    fprintf(ficresprobmorprev,"\n");
                   5552:   
                   5553:    fprintf(ficgp,"\n# Routine varevsij");
                   5554:    fprintf(ficgp,"\nunset title \n");
                   5555:    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
                   5556:    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");
                   5557:    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   5558:    /*   } */
                   5559:    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   5560:    pstamp(ficresvij);
                   5561:    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
                   5562:    if(popbased==1)
                   5563:      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);
                   5564:    else
                   5565:      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
                   5566:    fprintf(ficresvij,"# Age");
                   5567:    for(i=1; i<=nlstate;i++)
                   5568:      for(j=1; j<=nlstate;j++)
                   5569:        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
                   5570:    fprintf(ficresvij,"\n");
                   5571: 
                   5572:    xp=vector(1,npar);
                   5573:    dnewm=matrix(1,nlstate,1,npar);
                   5574:    doldm=matrix(1,nlstate,1,nlstate);
                   5575:    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   5576:    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   5577: 
                   5578:    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                   5579:    gpp=vector(nlstate+1,nlstate+ndeath);
                   5580:    gmp=vector(nlstate+1,nlstate+ndeath);
                   5581:    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126     brouard  5582:   
1.218     brouard  5583:    if(estepm < stepm){
                   5584:      printf ("Problem %d lower than %d\n",estepm, stepm);
                   5585:    }
                   5586:    else  hstepm=estepm;   
                   5587:    /* For example we decided to compute the life expectancy with the smallest unit */
                   5588:    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   5589:       nhstepm is the number of hstepm from age to agelim 
                   5590:       nstepm is the number of stepm from age to agelim. 
                   5591:       Look at function hpijx to understand why because of memory size limitations, 
                   5592:       we decided (b) to get a life expectancy respecting the most precise curvature of the
                   5593:       survival function given by stepm (the optimization length). Unfortunately it
                   5594:       means that if the survival funtion is printed every two years of age and if
                   5595:       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   5596:       results. So we changed our mind and took the option of the best precision.
                   5597:    */
                   5598:    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   5599:    agelim = AGESUP;
                   5600:    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   5601:      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   5602:      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   5603:      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5604:      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                   5605:      gp=matrix(0,nhstepm,1,nlstate);
                   5606:      gm=matrix(0,nhstepm,1,nlstate);
                   5607:                
                   5608:                
                   5609:      for(theta=1; theta <=npar; theta++){
                   5610:        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                   5611:         xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   5612:        }
                   5613:                        
1.242     brouard  5614:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218     brouard  5615:                        
                   5616:        if (popbased==1) {
                   5617:         if(mobilav ==0){
                   5618:           for(i=1; i<=nlstate;i++)
                   5619:             prlim[i][i]=probs[(int)age][i][ij];
                   5620:         }else{ /* mobilav */ 
                   5621:           for(i=1; i<=nlstate;i++)
                   5622:             prlim[i][i]=mobaverage[(int)age][i][ij];
                   5623:         }
                   5624:        }
                   5625:                        
1.235     brouard  5626:        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.218     brouard  5627:        for(j=1; j<= nlstate; j++){
                   5628:         for(h=0; h<=nhstepm; h++){
                   5629:           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                   5630:             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   5631:         }
                   5632:        }
                   5633:        /* Next for computing probability of death (h=1 means
                   5634:          computed over hstepm matrices product = hstepm*stepm months) 
                   5635:          as a weighted average of prlim.
                   5636:        */
                   5637:        for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   5638:         for(i=1,gpp[j]=0.; i<= nlstate; i++)
                   5639:           gpp[j] += prlim[i][i]*p3mat[i][j][1];
                   5640:        }    
                   5641:        /* end probability of death */
                   5642:                        
                   5643:        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                   5644:         xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   5645:                        
1.242     brouard  5646:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218     brouard  5647:                        
                   5648:        if (popbased==1) {
                   5649:         if(mobilav ==0){
                   5650:           for(i=1; i<=nlstate;i++)
                   5651:             prlim[i][i]=probs[(int)age][i][ij];
                   5652:         }else{ /* mobilav */ 
                   5653:           for(i=1; i<=nlstate;i++)
                   5654:             prlim[i][i]=mobaverage[(int)age][i][ij];
                   5655:         }
                   5656:        }
                   5657:                        
1.235     brouard  5658:        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  
1.218     brouard  5659:                        
                   5660:        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
                   5661:         for(h=0; h<=nhstepm; h++){
                   5662:           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   5663:             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                   5664:         }
                   5665:        }
                   5666:        /* This for computing probability of death (h=1 means
                   5667:          computed over hstepm matrices product = hstepm*stepm months) 
                   5668:          as a weighted average of prlim.
                   5669:        */
                   5670:        for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   5671:         for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   5672:           gmp[j] += prlim[i][i]*p3mat[i][j][1];
                   5673:        }    
                   5674:        /* end probability of death */
                   5675:                        
                   5676:        for(j=1; j<= nlstate; j++) /* vareij */
                   5677:         for(h=0; h<=nhstepm; h++){
                   5678:           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   5679:         }
                   5680:                        
                   5681:        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                   5682:         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                   5683:        }
                   5684:                        
                   5685:      } /* End theta */
                   5686:                
                   5687:      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   5688:                
                   5689:      for(h=0; h<=nhstepm; h++) /* veij */
                   5690:        for(j=1; j<=nlstate;j++)
                   5691:         for(theta=1; theta <=npar; theta++)
                   5692:           trgradg[h][j][theta]=gradg[h][theta][j];
                   5693:                
                   5694:      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                   5695:        for(theta=1; theta <=npar; theta++)
                   5696:         trgradgp[j][theta]=gradgp[theta][j];
                   5697:                
                   5698:                
                   5699:      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   5700:      for(i=1;i<=nlstate;i++)
                   5701:        for(j=1;j<=nlstate;j++)
                   5702:         vareij[i][j][(int)age] =0.;
                   5703:                
                   5704:      for(h=0;h<=nhstepm;h++){
                   5705:        for(k=0;k<=nhstepm;k++){
                   5706:         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                   5707:         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                   5708:         for(i=1;i<=nlstate;i++)
                   5709:           for(j=1;j<=nlstate;j++)
                   5710:             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                   5711:        }
                   5712:      }
                   5713:                
                   5714:      /* pptj */
                   5715:      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                   5716:      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                   5717:      for(j=nlstate+1;j<=nlstate+ndeath;j++)
                   5718:        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                   5719:         varppt[j][i]=doldmp[j][i];
                   5720:      /* end ppptj */
                   5721:      /*  x centered again */
                   5722:                
1.242     brouard  5723:      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218     brouard  5724:                
                   5725:      if (popbased==1) {
                   5726:        if(mobilav ==0){
                   5727:         for(i=1; i<=nlstate;i++)
                   5728:           prlim[i][i]=probs[(int)age][i][ij];
                   5729:        }else{ /* mobilav */ 
                   5730:         for(i=1; i<=nlstate;i++)
                   5731:           prlim[i][i]=mobaverage[(int)age][i][ij];
                   5732:        }
                   5733:      }
                   5734:                
                   5735:      /* This for computing probability of death (h=1 means
                   5736:        computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   5737:        as a weighted average of prlim.
                   5738:      */
1.235     brouard  5739:      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);  
1.218     brouard  5740:      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   5741:        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                   5742:         gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   5743:      }    
                   5744:      /* end probability of death */
                   5745:                
                   5746:      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   5747:      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   5748:        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                   5749:        for(i=1; i<=nlstate;i++){
                   5750:         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   5751:        }
                   5752:      } 
                   5753:      fprintf(ficresprobmorprev,"\n");
                   5754:                
                   5755:      fprintf(ficresvij,"%.0f ",age );
                   5756:      for(i=1; i<=nlstate;i++)
                   5757:        for(j=1; j<=nlstate;j++){
                   5758:         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                   5759:        }
                   5760:      fprintf(ficresvij,"\n");
                   5761:      free_matrix(gp,0,nhstepm,1,nlstate);
                   5762:      free_matrix(gm,0,nhstepm,1,nlstate);
                   5763:      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                   5764:      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                   5765:      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5766:    } /* End age */
                   5767:    free_vector(gpp,nlstate+1,nlstate+ndeath);
                   5768:    free_vector(gmp,nlstate+1,nlstate+ndeath);
                   5769:    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                   5770:    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   5771:    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
                   5772:    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
                   5773:    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
                   5774:    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
                   5775:    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
                   5776:    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                   5777:    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   5778:    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   5779:    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
                   5780:    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
                   5781:    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
                   5782:    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
                   5783:    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);
                   5784:    /*  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  5785:     */
1.218     brouard  5786:    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
                   5787:    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126     brouard  5788: 
1.218     brouard  5789:    free_vector(xp,1,npar);
                   5790:    free_matrix(doldm,1,nlstate,1,nlstate);
                   5791:    free_matrix(dnewm,1,nlstate,1,npar);
                   5792:    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   5793:    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   5794:    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   5795:    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   5796:    fclose(ficresprobmorprev);
                   5797:    fflush(ficgp);
                   5798:    fflush(fichtm); 
                   5799:  }  /* end varevsij */
1.126     brouard  5800: 
                   5801: /************ Variance of prevlim ******************/
1.235     brouard  5802:  void varprevlim(char fileres[], 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  5803: {
1.205     brouard  5804:   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126     brouard  5805:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164     brouard  5806: 
1.126     brouard  5807:   double **dnewm,**doldm;
                   5808:   int i, j, nhstepm, hstepm;
                   5809:   double *xp;
                   5810:   double *gp, *gm;
                   5811:   double **gradg, **trgradg;
1.208     brouard  5812:   double **mgm, **mgp;
1.126     brouard  5813:   double age,agelim;
                   5814:   int theta;
                   5815:   
                   5816:   pstamp(ficresvpl);
                   5817:   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
1.241     brouard  5818:   fprintf(ficresvpl,"# Age ");
                   5819:   if(nresult >=1)
                   5820:     fprintf(ficresvpl," Result# ");
1.126     brouard  5821:   for(i=1; i<=nlstate;i++)
                   5822:       fprintf(ficresvpl," %1d-%1d",i,i);
                   5823:   fprintf(ficresvpl,"\n");
                   5824: 
                   5825:   xp=vector(1,npar);
                   5826:   dnewm=matrix(1,nlstate,1,npar);
                   5827:   doldm=matrix(1,nlstate,1,nlstate);
                   5828:   
                   5829:   hstepm=1*YEARM; /* Every year of age */
                   5830:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                   5831:   agelim = AGESUP;
                   5832:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   5833:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   5834:     if (stepm >= YEARM) hstepm=1;
                   5835:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   5836:     gradg=matrix(1,npar,1,nlstate);
1.208     brouard  5837:     mgp=matrix(1,npar,1,nlstate);
                   5838:     mgm=matrix(1,npar,1,nlstate);
1.126     brouard  5839:     gp=vector(1,nlstate);
                   5840:     gm=vector(1,nlstate);
                   5841: 
                   5842:     for(theta=1; theta <=npar; theta++){
                   5843:       for(i=1; i<=npar; i++){ /* Computes gradient */
                   5844:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   5845:       }
1.209     brouard  5846:       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235     brouard  5847:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209     brouard  5848:       else
1.235     brouard  5849:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208     brouard  5850:       for(i=1;i<=nlstate;i++){
1.126     brouard  5851:        gp[i] = prlim[i][i];
1.208     brouard  5852:        mgp[theta][i] = prlim[i][i];
                   5853:       }
1.126     brouard  5854:       for(i=1; i<=npar; i++) /* Computes gradient */
                   5855:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209     brouard  5856:       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235     brouard  5857:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209     brouard  5858:       else
1.235     brouard  5859:        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208     brouard  5860:       for(i=1;i<=nlstate;i++){
1.126     brouard  5861:        gm[i] = prlim[i][i];
1.208     brouard  5862:        mgm[theta][i] = prlim[i][i];
                   5863:       }
1.126     brouard  5864:       for(i=1;i<=nlstate;i++)
                   5865:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209     brouard  5866:       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126     brouard  5867:     } /* End theta */
                   5868: 
                   5869:     trgradg =matrix(1,nlstate,1,npar);
                   5870: 
                   5871:     for(j=1; j<=nlstate;j++)
                   5872:       for(theta=1; theta <=npar; theta++)
                   5873:        trgradg[j][theta]=gradg[theta][j];
1.209     brouard  5874:     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
                   5875:     /*   printf("\nmgm mgp %d ",(int)age); */
                   5876:     /*   for(j=1; j<=nlstate;j++){ */
                   5877:     /*         printf(" %d ",j); */
                   5878:     /*         for(theta=1; theta <=npar; theta++) */
                   5879:     /*           printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
                   5880:     /*         printf("\n "); */
                   5881:     /*   } */
                   5882:     /* } */
                   5883:     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
                   5884:     /*   printf("\n gradg %d ",(int)age); */
                   5885:     /*   for(j=1; j<=nlstate;j++){ */
                   5886:     /*         printf("%d ",j); */
                   5887:     /*         for(theta=1; theta <=npar; theta++) */
                   5888:     /*           printf("%d %lf ",theta,gradg[theta][j]); */
                   5889:     /*         printf("\n "); */
                   5890:     /*   } */
                   5891:     /* } */
1.126     brouard  5892: 
                   5893:     for(i=1;i<=nlstate;i++)
                   5894:       varpl[i][(int)age] =0.;
1.209     brouard  5895:     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
1.205     brouard  5896:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   5897:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   5898:     }else{
1.126     brouard  5899:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   5900:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205     brouard  5901:     }
1.126     brouard  5902:     for(i=1;i<=nlstate;i++)
                   5903:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   5904: 
                   5905:     fprintf(ficresvpl,"%.0f ",age );
1.241     brouard  5906:     if(nresult >=1)
                   5907:       fprintf(ficresvpl,"%d ",nres );
1.126     brouard  5908:     for(i=1; i<=nlstate;i++)
                   5909:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                   5910:     fprintf(ficresvpl,"\n");
                   5911:     free_vector(gp,1,nlstate);
                   5912:     free_vector(gm,1,nlstate);
1.208     brouard  5913:     free_matrix(mgm,1,npar,1,nlstate);
                   5914:     free_matrix(mgp,1,npar,1,nlstate);
1.126     brouard  5915:     free_matrix(gradg,1,npar,1,nlstate);
                   5916:     free_matrix(trgradg,1,nlstate,1,npar);
                   5917:   } /* End age */
                   5918: 
                   5919:   free_vector(xp,1,npar);
                   5920:   free_matrix(doldm,1,nlstate,1,npar);
                   5921:   free_matrix(dnewm,1,nlstate,1,nlstate);
                   5922: 
                   5923: }
                   5924: 
                   5925: /************ Variance of one-step probabilities  ******************/
                   5926: 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  5927:  {
                   5928:    int i, j=0,  k1, l1, tj;
                   5929:    int k2, l2, j1,  z1;
                   5930:    int k=0, l;
                   5931:    int first=1, first1, first2;
                   5932:    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                   5933:    double **dnewm,**doldm;
                   5934:    double *xp;
                   5935:    double *gp, *gm;
                   5936:    double **gradg, **trgradg;
                   5937:    double **mu;
                   5938:    double age, cov[NCOVMAX+1];
                   5939:    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   5940:    int theta;
                   5941:    char fileresprob[FILENAMELENGTH];
                   5942:    char fileresprobcov[FILENAMELENGTH];
                   5943:    char fileresprobcor[FILENAMELENGTH];
                   5944:    double ***varpij;
                   5945: 
                   5946:    strcpy(fileresprob,"PROB_"); 
                   5947:    strcat(fileresprob,fileres);
                   5948:    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                   5949:      printf("Problem with resultfile: %s\n", fileresprob);
                   5950:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   5951:    }
                   5952:    strcpy(fileresprobcov,"PROBCOV_"); 
                   5953:    strcat(fileresprobcov,fileresu);
                   5954:    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   5955:      printf("Problem with resultfile: %s\n", fileresprobcov);
                   5956:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   5957:    }
                   5958:    strcpy(fileresprobcor,"PROBCOR_"); 
                   5959:    strcat(fileresprobcor,fileresu);
                   5960:    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                   5961:      printf("Problem with resultfile: %s\n", fileresprobcor);
                   5962:      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   5963:    }
                   5964:    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   5965:    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   5966:    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   5967:    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   5968:    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   5969:    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   5970:    pstamp(ficresprob);
                   5971:    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
                   5972:    fprintf(ficresprob,"# Age");
                   5973:    pstamp(ficresprobcov);
                   5974:    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
                   5975:    fprintf(ficresprobcov,"# Age");
                   5976:    pstamp(ficresprobcor);
                   5977:    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
                   5978:    fprintf(ficresprobcor,"# Age");
1.126     brouard  5979: 
                   5980: 
1.222     brouard  5981:    for(i=1; i<=nlstate;i++)
                   5982:      for(j=1; j<=(nlstate+ndeath);j++){
                   5983:        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                   5984:        fprintf(ficresprobcov," p%1d-%1d ",i,j);
                   5985:        fprintf(ficresprobcor," p%1d-%1d ",i,j);
                   5986:      }  
                   5987:    /* fprintf(ficresprob,"\n");
                   5988:       fprintf(ficresprobcov,"\n");
                   5989:       fprintf(ficresprobcor,"\n");
                   5990:    */
                   5991:    xp=vector(1,npar);
                   5992:    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   5993:    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   5994:    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                   5995:    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                   5996:    first=1;
                   5997:    fprintf(ficgp,"\n# Routine varprob");
                   5998:    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   5999:    fprintf(fichtm,"\n");
                   6000: 
                   6001:    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.</li>\n",optionfilehtmcov);
                   6002:    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);
                   6003:    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126     brouard  6004: and drawn. It helps understanding how is the covariance between two incidences.\
                   6005:  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222     brouard  6006:    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  6007: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
                   6008: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
                   6009: standard deviations wide on each axis. <br>\
                   6010:  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
                   6011:  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
                   6012: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
                   6013: 
1.222     brouard  6014:    cov[1]=1;
                   6015:    /* tj=cptcoveff; */
1.225     brouard  6016:    tj = (int) pow(2,cptcoveff);
1.222     brouard  6017:    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   6018:    j1=0;
1.224     brouard  6019:    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
1.222     brouard  6020:      if  (cptcovn>0) {
                   6021:        fprintf(ficresprob, "\n#********** Variable "); 
1.225     brouard  6022:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6023:        fprintf(ficresprob, "**********\n#\n");
                   6024:        fprintf(ficresprobcov, "\n#********** Variable "); 
1.225     brouard  6025:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6026:        fprintf(ficresprobcov, "**********\n#\n");
1.220     brouard  6027:                        
1.222     brouard  6028:        fprintf(ficgp, "\n#********** Variable "); 
1.225     brouard  6029:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6030:        fprintf(ficgp, "**********\n#\n");
1.220     brouard  6031:                        
                   6032:                        
1.222     brouard  6033:        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
1.225     brouard  6034:        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6035:        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220     brouard  6036:                        
1.222     brouard  6037:        fprintf(ficresprobcor, "\n#********** Variable ");    
1.225     brouard  6038:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222     brouard  6039:        fprintf(ficresprobcor, "**********\n#");    
                   6040:        if(invalidvarcomb[j1]){
                   6041:         fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
                   6042:         fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
                   6043:         continue;
                   6044:        }
                   6045:      }
                   6046:      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                   6047:      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   6048:      gp=vector(1,(nlstate)*(nlstate+ndeath));
                   6049:      gm=vector(1,(nlstate)*(nlstate+ndeath));
                   6050:      for (age=bage; age<=fage; age ++){ 
                   6051:        cov[2]=age;
                   6052:        if(nagesqr==1)
                   6053:         cov[3]= age*age;
                   6054:        for (k=1; k<=cptcovn;k++) {
                   6055:         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
                   6056:         /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                   6057:                                                                    * 1  1 1 1 1
                   6058:                                                                    * 2  2 1 1 1
                   6059:                                                                    * 3  1 2 1 1
                   6060:                                                                    */
                   6061:         /* nbcode[1][1]=0 nbcode[1][2]=1;*/
                   6062:        }
                   6063:        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                   6064:        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                   6065:        for (k=1; k<=cptcovprod;k++)
                   6066:         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220     brouard  6067:                        
                   6068:                        
1.222     brouard  6069:        for(theta=1; theta <=npar; theta++){
                   6070:         for(i=1; i<=npar; i++)
                   6071:           xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220     brouard  6072:                                
1.222     brouard  6073:         pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220     brouard  6074:                                
1.222     brouard  6075:         k=0;
                   6076:         for(i=1; i<= (nlstate); i++){
                   6077:           for(j=1; j<=(nlstate+ndeath);j++){
                   6078:             k=k+1;
                   6079:             gp[k]=pmmij[i][j];
                   6080:           }
                   6081:         }
1.220     brouard  6082:                                
1.222     brouard  6083:         for(i=1; i<=npar; i++)
                   6084:           xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220     brouard  6085:                                
1.222     brouard  6086:         pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   6087:         k=0;
                   6088:         for(i=1; i<=(nlstate); i++){
                   6089:           for(j=1; j<=(nlstate+ndeath);j++){
                   6090:             k=k+1;
                   6091:             gm[k]=pmmij[i][j];
                   6092:           }
                   6093:         }
1.220     brouard  6094:                                
1.222     brouard  6095:         for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                   6096:           gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
                   6097:        }
1.126     brouard  6098: 
1.222     brouard  6099:        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   6100:         for(theta=1; theta <=npar; theta++)
                   6101:           trgradg[j][theta]=gradg[theta][j];
1.220     brouard  6102:                        
1.222     brouard  6103:        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   6104:        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220     brouard  6105:                        
1.222     brouard  6106:        pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220     brouard  6107:                        
1.222     brouard  6108:        k=0;
                   6109:        for(i=1; i<=(nlstate); i++){
                   6110:         for(j=1; j<=(nlstate+ndeath);j++){
                   6111:           k=k+1;
                   6112:           mu[k][(int) age]=pmmij[i][j];
                   6113:         }
                   6114:        }
                   6115:        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                   6116:         for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   6117:           varpij[i][j][(int)age] = doldm[i][j];
1.220     brouard  6118:                        
1.222     brouard  6119:        /*printf("\n%d ",(int)age);
                   6120:         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   6121:         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   6122:         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   6123:         }*/
1.220     brouard  6124:                        
1.222     brouard  6125:        fprintf(ficresprob,"\n%d ",(int)age);
                   6126:        fprintf(ficresprobcov,"\n%d ",(int)age);
                   6127:        fprintf(ficresprobcor,"\n%d ",(int)age);
1.220     brouard  6128:                        
1.222     brouard  6129:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   6130:         fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                   6131:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   6132:         fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                   6133:         fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                   6134:        }
                   6135:        i=0;
                   6136:        for (k=1; k<=(nlstate);k++){
                   6137:         for (l=1; l<=(nlstate+ndeath);l++){ 
                   6138:           i++;
                   6139:           fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   6140:           fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                   6141:           for (j=1; j<=i;j++){
                   6142:             /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                   6143:             fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                   6144:             fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   6145:           }
                   6146:         }
                   6147:        }/* end of loop for state */
                   6148:      } /* end of loop for age */
                   6149:      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                   6150:      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                   6151:      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   6152:      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   6153:     
                   6154:      /* Confidence intervalle of pij  */
                   6155:      /*
                   6156:        fprintf(ficgp,"\nunset parametric;unset label");
                   6157:        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                   6158:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                   6159:        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);
                   6160:        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                   6161:        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                   6162:        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                   6163:      */
                   6164:                
                   6165:      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                   6166:      first1=1;first2=2;
                   6167:      for (k2=1; k2<=(nlstate);k2++){
                   6168:        for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                   6169:         if(l2==k2) continue;
                   6170:         j=(k2-1)*(nlstate+ndeath)+l2;
                   6171:         for (k1=1; k1<=(nlstate);k1++){
                   6172:           for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                   6173:             if(l1==k1) continue;
                   6174:             i=(k1-1)*(nlstate+ndeath)+l1;
                   6175:             if(i<=j) continue;
                   6176:             for (age=bage; age<=fage; age ++){ 
                   6177:               if ((int)age %5==0){
                   6178:                 v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                   6179:                 v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   6180:                 cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   6181:                 mu1=mu[i][(int) age]/stepm*YEARM ;
                   6182:                 mu2=mu[j][(int) age]/stepm*YEARM;
                   6183:                 c12=cv12/sqrt(v1*v2);
                   6184:                 /* Computing eigen value of matrix of covariance */
                   6185:                 lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   6186:                 lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   6187:                 if ((lc2 <0) || (lc1 <0) ){
                   6188:                   if(first2==1){
                   6189:                     first1=0;
                   6190:                     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);
                   6191:                   }
                   6192:                   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);
                   6193:                   /* lc1=fabs(lc1); */ /* If we want to have them positive */
                   6194:                   /* lc2=fabs(lc2); */
                   6195:                 }
1.220     brouard  6196:                                                                
1.222     brouard  6197:                 /* Eigen vectors */
                   6198:                 v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   6199:                 /*v21=sqrt(1.-v11*v11); *//* error */
                   6200:                 v21=(lc1-v1)/cv12*v11;
                   6201:                 v12=-v21;
                   6202:                 v22=v11;
                   6203:                 tnalp=v21/v11;
                   6204:                 if(first1==1){
                   6205:                   first1=0;
                   6206:                   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);
                   6207:                 }
                   6208:                 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);
                   6209:                 /*printf(fignu*/
                   6210:                 /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                   6211:                 /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   6212:                 if(first==1){
                   6213:                   first=0;
                   6214:                   fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                   6215:                   fprintf(ficgp,"\nset parametric;unset label");
                   6216:                   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);
                   6217:                   fprintf(ficgp,"\nset ter svg size 640, 480");
                   6218:                   fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220     brouard  6219:  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                          \
1.201     brouard  6220: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222     brouard  6221:                           subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
                   6222:                           subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   6223:                   fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   6224:                   fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                   6225:                   fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   6226:                   fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   6227:                   fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   6228:                   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",      \
                   6229:                           mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
                   6230:                           mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   6231:                 }else{
                   6232:                   first=0;
                   6233:                   fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                   6234:                   fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   6235:                   fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   6236:                   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", \
                   6237:                           mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
                   6238:                           mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   6239:                 }/* if first */
                   6240:               } /* age mod 5 */
                   6241:             } /* end loop age */
                   6242:             fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                   6243:             first=1;
                   6244:           } /*l12 */
                   6245:         } /* k12 */
                   6246:        } /*l1 */
                   6247:      }/* k1 */
                   6248:    }  /* loop on combination of covariates j1 */
                   6249:    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
                   6250:    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
                   6251:    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   6252:    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
                   6253:    free_vector(xp,1,npar);
                   6254:    fclose(ficresprob);
                   6255:    fclose(ficresprobcov);
                   6256:    fclose(ficresprobcor);
                   6257:    fflush(ficgp);
                   6258:    fflush(fichtmcov);
                   6259:  }
1.126     brouard  6260: 
                   6261: 
                   6262: /******************* Printing html file ***********/
1.201     brouard  6263: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126     brouard  6264:                  int lastpass, int stepm, int weightopt, char model[],\
                   6265:                  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217     brouard  6266:                  int popforecast, int prevfcast, int backcast, int estepm , \
1.213     brouard  6267:                  double jprev1, double mprev1,double anprev1, double dateprev1, \
                   6268:                  double jprev2, double mprev2,double anprev2, double dateprev2){
1.237     brouard  6269:   int jj1, k1, i1, cpt, k4, nres;
1.126     brouard  6270: 
                   6271:    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
                   6272:    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
                   6273: </ul>");
1.237     brouard  6274:    fprintf(fichtm,"<ul><li> model=1+age+%s\n \
                   6275: </ul>", model);
1.214     brouard  6276:    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
                   6277:    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",
                   6278:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
                   6279:    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  6280:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
                   6281:    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126     brouard  6282:    fprintf(fichtm,"\
                   6283:  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201     brouard  6284:           stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126     brouard  6285:    fprintf(fichtm,"\
1.217     brouard  6286:  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
                   6287:           stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
                   6288:    fprintf(fichtm,"\
1.126     brouard  6289:  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201     brouard  6290:           subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126     brouard  6291:    fprintf(fichtm,"\
1.217     brouard  6292:  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
                   6293:           subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
                   6294:    fprintf(fichtm,"\
1.211     brouard  6295:  - (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  6296:    <a href=\"%s\">%s</a> <br>\n",
1.201     brouard  6297:           estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211     brouard  6298:    if(prevfcast==1){
                   6299:      fprintf(fichtm,"\
                   6300:  - Prevalence projections by age and states:                           \
1.201     brouard  6301:    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211     brouard  6302:    }
1.126     brouard  6303: 
1.222     brouard  6304:    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126     brouard  6305: 
1.225     brouard  6306:    m=pow(2,cptcoveff);
1.222     brouard  6307:    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126     brouard  6308: 
1.222     brouard  6309:    jj1=0;
1.237     brouard  6310: 
                   6311:    for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241     brouard  6312:    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.237     brouard  6313:      if(TKresult[nres]!= k1)
                   6314:        continue;
1.220     brouard  6315: 
1.222     brouard  6316:      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
                   6317:      jj1++;
                   6318:      if (cptcovn > 0) {
                   6319:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225     brouard  6320:        for (cpt=1; cpt<=cptcoveff;cpt++){ 
1.237     brouard  6321:         fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
                   6322:         printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
                   6323:         /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
                   6324:         /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222     brouard  6325:        }
1.237     brouard  6326:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6327:        fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6328:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
                   6329:       }
                   6330:        
1.230     brouard  6331:        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222     brouard  6332:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   6333:        if(invalidvarcomb[k1]){
                   6334:         fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
                   6335:         printf("\nCombination (%d) ignored because no cases \n",k1); 
                   6336:         continue;
                   6337:        }
                   6338:      }
                   6339:      /* aij, bij */
1.241     brouard  6340:      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
                   6341: <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  6342:      /* Pij */
1.241     brouard  6343:      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> \
                   6344: <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  6345:      /* Quasi-incidences */
                   6346:      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  6347:  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211     brouard  6348:  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  6349: 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> \
                   6350: <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  6351:      /* Survival functions (period) in state j */
                   6352:      for(cpt=1; cpt<=nlstate;cpt++){
1.241     brouard  6353:        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive 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> \
                   6354: <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  6355:      }
                   6356:      /* State specific survival functions (period) */
                   6357:      for(cpt=1; cpt<=nlstate;cpt++){
                   6358:        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220     brouard  6359:  Or probability to survive in various states (1 to %d) being in state %d at different ages.    \
1.241     brouard  6360:  <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  6361:      }
                   6362:      /* Period (stable) prevalence in each health state */
                   6363:      for(cpt=1; cpt<=nlstate;cpt++){
1.241     brouard  6364:        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be 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> \
                   6365: <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.222     brouard  6366:      }
                   6367:      if(backcast==1){
                   6368:        /* Period (stable) back prevalence in each health state */
                   6369:        for(cpt=1; cpt<=nlstate;cpt++){
1.241     brouard  6370:         fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be 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> \
                   6371: <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  6372:        }
1.217     brouard  6373:      }
1.222     brouard  6374:      if(prevfcast==1){
                   6375:        /* Projection of prevalence up to period (stable) prevalence in each health state */
                   6376:        for(cpt=1; cpt<=nlstate;cpt++){
1.241     brouard  6377:         fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be 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> \
                   6378: <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222     brouard  6379:        }
                   6380:      }
1.220     brouard  6381:         
1.222     brouard  6382:      for(cpt=1; cpt<=nlstate;cpt++) {
1.241     brouard  6383:        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> <br> \
                   6384: <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.222     brouard  6385:      }
                   6386:      /* } /\* end i1 *\/ */
                   6387:    }/* End k1 */
                   6388:    fprintf(fichtm,"</ul>");
1.126     brouard  6389: 
1.222     brouard  6390:    fprintf(fichtm,"\
1.126     brouard  6391: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193     brouard  6392:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203     brouard  6393:  - 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  6394: But because parameters are usually highly correlated (a higher incidence of disability \
                   6395: and a higher incidence of recovery can give very close observed transition) it might \
                   6396: be very useful to look not only at linear confidence intervals estimated from the \
                   6397: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
                   6398: (parameters) of the logistic regression, it might be more meaningful to visualize the \
                   6399: covariance matrix of the one-step probabilities. \
                   6400: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126     brouard  6401: 
1.222     brouard  6402:    fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   6403:           subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
                   6404:    fprintf(fichtm,"\
1.126     brouard  6405:  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222     brouard  6406:           subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126     brouard  6407: 
1.222     brouard  6408:    fprintf(fichtm,"\
1.126     brouard  6409:  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222     brouard  6410:           subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
                   6411:    fprintf(fichtm,"\
1.126     brouard  6412:  - 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): \
                   6413:    <a href=\"%s\">%s</a> <br>\n</li>",
1.201     brouard  6414:           estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222     brouard  6415:    fprintf(fichtm,"\
1.126     brouard  6416:  - (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): \
                   6417:    <a href=\"%s\">%s</a> <br>\n</li>",
1.201     brouard  6418:           estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222     brouard  6419:    fprintf(fichtm,"\
1.128     brouard  6420:  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the 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  6421:           estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
                   6422:    fprintf(fichtm,"\
1.128     brouard  6423:  - 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  6424:           estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
                   6425:    fprintf(fichtm,"\
1.126     brouard  6426:  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222     brouard  6427:           subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126     brouard  6428: 
                   6429: /*  if(popforecast==1) fprintf(fichtm,"\n */
                   6430: /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                   6431: /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                   6432: /*     <br>",fileres,fileres,fileres,fileres); */
                   6433: /*  else  */
                   6434: /*    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  6435:    fflush(fichtm);
                   6436:    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126     brouard  6437: 
1.225     brouard  6438:    m=pow(2,cptcoveff);
1.222     brouard  6439:    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126     brouard  6440: 
1.222     brouard  6441:    jj1=0;
1.237     brouard  6442: 
1.241     brouard  6443:    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222     brouard  6444:    for(k1=1; k1<=m;k1++){
1.237     brouard  6445:      if(TKresult[nres]!= k1)
                   6446:        continue;
1.222     brouard  6447:      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
                   6448:      jj1++;
1.126     brouard  6449:      if (cptcovn > 0) {
                   6450:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225     brouard  6451:        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
1.237     brouard  6452:         fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
                   6453:         /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
                   6454:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6455:        fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6456:       }
                   6457: 
1.126     brouard  6458:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220     brouard  6459: 
1.222     brouard  6460:        if(invalidvarcomb[k1]){
                   6461:         fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
                   6462:         continue;
                   6463:        }
1.126     brouard  6464:      }
                   6465:      for(cpt=1; cpt<=nlstate;cpt++) {
1.218     brouard  6466:        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
1.241     brouard  6467: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
                   6468: <img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  
1.126     brouard  6469:      }
                   6470:      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128     brouard  6471: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
                   6472: true period expectancies (those weighted with period prevalences are also\
                   6473:  drawn in addition to the population based expectancies computed using\
1.241     brouard  6474:  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
                   6475: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222     brouard  6476:      /* } /\* end i1 *\/ */
                   6477:    }/* End k1 */
1.241     brouard  6478:   }/* End nres */
1.222     brouard  6479:    fprintf(fichtm,"</ul>");
                   6480:    fflush(fichtm);
1.126     brouard  6481: }
                   6482: 
                   6483: /******************* Gnuplot file **************/
1.223     brouard  6484: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126     brouard  6485: 
                   6486:   char dirfileres[132],optfileres[132];
1.223     brouard  6487:   char gplotcondition[132];
1.237     brouard  6488:   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  6489:   int lv=0, vlv=0, kl=0;
1.130     brouard  6490:   int ng=0;
1.201     brouard  6491:   int vpopbased;
1.223     brouard  6492:   int ioffset; /* variable offset for columns */
1.235     brouard  6493:   int nres=0; /* Index of resultline */
1.219     brouard  6494: 
1.126     brouard  6495: /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
                   6496: /*     printf("Problem with file %s",optionfilegnuplot); */
                   6497: /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
                   6498: /*   } */
                   6499: 
                   6500:   /*#ifdef windows */
                   6501:   fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223     brouard  6502:   /*#endif */
1.225     brouard  6503:   m=pow(2,cptcoveff);
1.126     brouard  6504: 
1.202     brouard  6505:   /* Contribution to likelihood */
                   6506:   /* Plot the probability implied in the likelihood */
1.223     brouard  6507:   fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
                   6508:   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
                   6509:   /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
                   6510:   fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204     brouard  6511: /* nice for mle=4 plot by number of matrix products.
1.202     brouard  6512:    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
                   6513: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
1.223     brouard  6514:   /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
                   6515:   fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
                   6516:   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));
                   6517:   fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
                   6518:   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));
                   6519:   for (i=1; i<= nlstate ; i ++) {
                   6520:     fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
                   6521:     fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
                   6522:     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);
                   6523:     for (j=2; j<= nlstate+ndeath ; j ++) {
                   6524:       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);
                   6525:     }
                   6526:     fprintf(ficgp,";\nset out; unset ylabel;\n"); 
                   6527:   }
                   6528:   /* 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 */               
                   6529:   /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
                   6530:   /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
                   6531:   fprintf(ficgp,"\nset out;unset log\n");
                   6532:   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202     brouard  6533: 
1.126     brouard  6534:   strcpy(dirfileres,optionfilefiname);
                   6535:   strcpy(optfileres,"vpl");
1.223     brouard  6536:   /* 1eme*/
1.238     brouard  6537:   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
                   6538:     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236     brouard  6539:       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238     brouard  6540:        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
                   6541:        if(TKresult[nres]!= k1)
                   6542:          continue;
                   6543:        /* We are interested in selected combination by the resultline */
1.246     brouard  6544:        /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.238     brouard  6545:        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
                   6546:        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
                   6547:          lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
                   6548:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6549:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6550:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6551:          vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
                   6552:          /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246     brouard  6553:          /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238     brouard  6554:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   6555:        }
                   6556:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246     brouard  6557:          /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238     brouard  6558:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6559:        }       
1.246     brouard  6560:        /* printf("\n#\n"); */
1.238     brouard  6561:        fprintf(ficgp,"\n#\n");
                   6562:        if(invalidvarcomb[k1]){
                   6563:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6564:          continue;
                   6565:        }
1.235     brouard  6566:       
1.241     brouard  6567:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
                   6568:        fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
                   6569:        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);
1.235     brouard  6570:       
1.238     brouard  6571:        for (i=1; i<= nlstate ; i ++) {
                   6572:          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   6573:          else        fprintf(ficgp," %%*lf (%%*lf)");
                   6574:        }
1.242     brouard  6575:        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
1.238     brouard  6576:        for (i=1; i<= nlstate ; i ++) {
                   6577:          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   6578:          else fprintf(ficgp," %%*lf (%%*lf)");
                   6579:        } 
1.242     brouard  6580:        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); 
1.238     brouard  6581:        for (i=1; i<= nlstate ; i ++) {
                   6582:          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   6583:          else fprintf(ficgp," %%*lf (%%*lf)");
                   6584:        }  
                   6585:        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
                   6586:        if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
                   6587:          /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242     brouard  6588:          fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238     brouard  6589:          if(cptcoveff ==0){
1.245     brouard  6590:            fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
1.238     brouard  6591:          }else{
                   6592:            kl=0;
                   6593:            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                   6594:              lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                   6595:              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6596:              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6597:              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6598:              vlv= nbcode[Tvaraff[k]][lv];
1.223     brouard  6599:              kl++;
1.238     brouard  6600:              /* 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 *\/ */
                   6601:              /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                   6602:              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                   6603:              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                   6604:              if(k==cptcoveff){
1.245     brouard  6605:                fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242     brouard  6606:                        2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
1.238     brouard  6607:              }else{
                   6608:                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                   6609:                kl++;
                   6610:              }
                   6611:            } /* end covariate */
                   6612:          } /* end if no covariate */
                   6613:        } /* end if backcast */
                   6614:        fprintf(ficgp,"\nset out \n");
                   6615:       } /* nres */
1.201     brouard  6616:     } /* k1 */
                   6617:   } /* cpt */
1.235     brouard  6618: 
                   6619:   
1.126     brouard  6620:   /*2 eme*/
1.238     brouard  6621:   for (k1=1; k1<= m ; k1 ++){  
                   6622:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   6623:       if(TKresult[nres]!= k1)
                   6624:        continue;
                   6625:       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
                   6626:       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
1.225     brouard  6627:        lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223     brouard  6628:        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6629:        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6630:        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6631:        vlv= nbcode[Tvaraff[k]][lv];
                   6632:        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211     brouard  6633:       }
1.237     brouard  6634:       /* for(k=1; k <= ncovds; k++){ */
1.236     brouard  6635:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238     brouard  6636:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236     brouard  6637:        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238     brouard  6638:       }
1.211     brouard  6639:       fprintf(ficgp,"\n#\n");
1.223     brouard  6640:       if(invalidvarcomb[k1]){
                   6641:        fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6642:        continue;
                   6643:       }
1.219     brouard  6644:                        
1.241     brouard  6645:       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238     brouard  6646:       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
                   6647:        if(vpopbased==0)
                   6648:          fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
                   6649:        else
                   6650:          fprintf(ficgp,"\nreplot ");
                   6651:        for (i=1; i<= nlstate+1 ; i ++) {
                   6652:          k=2*i;
                   6653:          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
                   6654:          for (j=1; j<= nlstate+1 ; j ++) {
                   6655:            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   6656:            else fprintf(ficgp," %%*lf (%%*lf)");
                   6657:          }   
                   6658:          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
                   6659:          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
                   6660:          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
                   6661:          for (j=1; j<= nlstate+1 ; j ++) {
                   6662:            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   6663:            else fprintf(ficgp," %%*lf (%%*lf)");
                   6664:          }   
                   6665:          fprintf(ficgp,"\" t\"\" w l lt 0,");
                   6666:          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
                   6667:          for (j=1; j<= nlstate+1 ; j ++) {
                   6668:            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   6669:            else fprintf(ficgp," %%*lf (%%*lf)");
                   6670:          }   
                   6671:          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
                   6672:          else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
                   6673:        } /* state */
                   6674:       } /* vpopbased */
1.244     brouard  6675:       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
1.238     brouard  6676:     } /* end nres */
                   6677:   } /* k1 end 2 eme*/
                   6678:        
                   6679:        
                   6680:   /*3eme*/
                   6681:   for (k1=1; k1<= m ; k1 ++){
                   6682:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.240     brouard  6683:       if(TKresult[nres]!= k1)
1.238     brouard  6684:        continue;
                   6685: 
                   6686:       for (cpt=1; cpt<= nlstate ; cpt ++) {
                   6687:        fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
                   6688:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   6689:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   6690:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6691:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6692:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6693:          vlv= nbcode[Tvaraff[k]][lv];
                   6694:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   6695:        }
                   6696:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6697:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6698:        }       
                   6699:        fprintf(ficgp,"\n#\n");
                   6700:        if(invalidvarcomb[k1]){
                   6701:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6702:          continue;
                   6703:        }
                   6704:                        
                   6705:        /*       k=2+nlstate*(2*cpt-2); */
                   6706:        k=2+(nlstate+1)*(cpt-1);
1.241     brouard  6707:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.238     brouard  6708:        fprintf(ficgp,"set ter svg size 640, 480\n\
1.201     brouard  6709: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.238     brouard  6710:        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   6711:          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   6712:          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   6713:          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   6714:          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   6715:          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219     brouard  6716:                                
1.238     brouard  6717:        */
                   6718:        for (i=1; i< nlstate ; i ++) {
                   6719:          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
                   6720:          /*    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  6721:                                
1.238     brouard  6722:        } 
                   6723:        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
                   6724:       }
                   6725:     } /* end nres */
                   6726:   } /* end kl 3eme */
1.126     brouard  6727:   
1.223     brouard  6728:   /* 4eme */
1.201     brouard  6729:   /* Survival functions (period) from state i in state j by initial state i */
1.238     brouard  6730:   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
                   6731:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   6732:       if(TKresult[nres]!= k1)
1.223     brouard  6733:        continue;
1.238     brouard  6734:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
                   6735:        fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
                   6736:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   6737:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   6738:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6739:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6740:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6741:          vlv= nbcode[Tvaraff[k]][lv];
                   6742:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   6743:        }
                   6744:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6745:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6746:        }       
                   6747:        fprintf(ficgp,"\n#\n");
                   6748:        if(invalidvarcomb[k1]){
                   6749:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6750:          continue;
1.223     brouard  6751:        }
1.238     brouard  6752:       
1.241     brouard  6753:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.238     brouard  6754:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
                   6755: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                   6756:        k=3;
                   6757:        for (i=1; i<= nlstate ; i ++){
                   6758:          if(i==1){
                   6759:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                   6760:          }else{
                   6761:            fprintf(ficgp,", '' ");
                   6762:          }
                   6763:          l=(nlstate+ndeath)*(i-1)+1;
                   6764:          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
                   6765:          for (j=2; j<= nlstate+ndeath ; j ++)
                   6766:            fprintf(ficgp,"+$%d",k+l+j-1);
                   6767:          fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
                   6768:        } /* nlstate */
                   6769:        fprintf(ficgp,"\nset out\n");
                   6770:       } /* end cpt state*/ 
                   6771:     } /* end nres */
                   6772:   } /* end covariate k1 */  
                   6773: 
1.220     brouard  6774: /* 5eme */
1.201     brouard  6775:   /* Survival functions (period) from state i in state j by final state j */
1.238     brouard  6776:   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
                   6777:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   6778:       if(TKresult[nres]!= k1)
1.227     brouard  6779:        continue;
1.238     brouard  6780:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
                   6781:        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);
                   6782:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   6783:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   6784:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6785:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6786:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6787:          vlv= nbcode[Tvaraff[k]][lv];
                   6788:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   6789:        }
                   6790:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6791:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6792:        }       
                   6793:        fprintf(ficgp,"\n#\n");
                   6794:        if(invalidvarcomb[k1]){
                   6795:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6796:          continue;
                   6797:        }
1.227     brouard  6798:       
1.241     brouard  6799:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.238     brouard  6800:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
                   6801: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                   6802:        k=3;
                   6803:        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
                   6804:          if(j==1)
                   6805:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                   6806:          else
                   6807:            fprintf(ficgp,", '' ");
                   6808:          l=(nlstate+ndeath)*(cpt-1) +j;
                   6809:          fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
                   6810:          /* for (i=2; i<= nlstate+ndeath ; i ++) */
                   6811:          /*   fprintf(ficgp,"+$%d",k+l+i-1); */
                   6812:          fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
                   6813:        } /* nlstate */
                   6814:        fprintf(ficgp,", '' ");
                   6815:        fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
                   6816:        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
                   6817:          l=(nlstate+ndeath)*(cpt-1) +j;
                   6818:          if(j < nlstate)
                   6819:            fprintf(ficgp,"$%d +",k+l);
                   6820:          else
                   6821:            fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
                   6822:        }
                   6823:        fprintf(ficgp,"\nset out\n");
                   6824:       } /* end cpt state*/ 
                   6825:     } /* end covariate */  
                   6826:   } /* end nres */
1.227     brouard  6827:   
1.220     brouard  6828: /* 6eme */
1.202     brouard  6829:   /* CV preval stable (period) for each covariate */
1.237     brouard  6830:   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
                   6831:   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   6832:     if(TKresult[nres]!= k1)
                   6833:       continue;
1.153     brouard  6834:     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227     brouard  6835:       
1.211     brouard  6836:       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225     brouard  6837:       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
1.227     brouard  6838:        lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   6839:        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6840:        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6841:        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6842:        vlv= nbcode[Tvaraff[k]][lv];
                   6843:        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211     brouard  6844:       }
1.237     brouard  6845:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6846:        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6847:       }        
1.211     brouard  6848:       fprintf(ficgp,"\n#\n");
1.223     brouard  6849:       if(invalidvarcomb[k1]){
1.227     brouard  6850:        fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6851:        continue;
1.223     brouard  6852:       }
1.227     brouard  6853:       
1.241     brouard  6854:       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.126     brouard  6855:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238     brouard  6856: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
1.211     brouard  6857:       k=3; /* Offset */
1.153     brouard  6858:       for (i=1; i<= nlstate ; i ++){
1.227     brouard  6859:        if(i==1)
                   6860:          fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                   6861:        else
                   6862:          fprintf(ficgp,", '' ");
                   6863:        l=(nlstate+ndeath)*(i-1)+1;
                   6864:        fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
                   6865:        for (j=2; j<= nlstate ; j ++)
                   6866:          fprintf(ficgp,"+$%d",k+l+j-1);
                   6867:        fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153     brouard  6868:       } /* nlstate */
1.201     brouard  6869:       fprintf(ficgp,"\nset out\n");
1.153     brouard  6870:     } /* end cpt state*/ 
                   6871:   } /* end covariate */  
1.227     brouard  6872:   
                   6873:   
1.220     brouard  6874: /* 7eme */
1.218     brouard  6875:   if(backcast == 1){
1.217     brouard  6876:     /* CV back preval stable (period) for each covariate */
1.237     brouard  6877:     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
                   6878:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   6879:       if(TKresult[nres]!= k1)
                   6880:        continue;
1.218     brouard  6881:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227     brouard  6882:        fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
                   6883:        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                   6884:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                   6885:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6886:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
1.223     brouard  6887:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
1.227     brouard  6888:          vlv= nbcode[Tvaraff[k]][lv];
                   6889:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   6890:        }
1.237     brouard  6891:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6892:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6893:        }       
1.227     brouard  6894:        fprintf(ficgp,"\n#\n");
                   6895:        if(invalidvarcomb[k1]){
                   6896:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6897:          continue;
                   6898:        }
                   6899:        
1.241     brouard  6900:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.227     brouard  6901:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238     brouard  6902: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
1.227     brouard  6903:        k=3; /* Offset */
                   6904:        for (i=1; i<= nlstate ; i ++){
                   6905:          if(i==1)
                   6906:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
                   6907:          else
                   6908:            fprintf(ficgp,", '' ");
                   6909:          /* l=(nlstate+ndeath)*(i-1)+1; */
                   6910:          l=(nlstate+ndeath)*(cpt-1)+1;
                   6911:          /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
                   6912:          /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
                   6913:          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
                   6914:          /* for (j=2; j<= nlstate ; j ++) */
                   6915:          /*    fprintf(ficgp,"+$%d",k+l+j-1); */
                   6916:          /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
                   6917:          fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
                   6918:        } /* nlstate */
                   6919:        fprintf(ficgp,"\nset out\n");
1.218     brouard  6920:       } /* end cpt state*/ 
                   6921:     } /* end covariate */  
                   6922:   } /* End if backcast */
                   6923:   
1.223     brouard  6924:   /* 8eme */
1.218     brouard  6925:   if(prevfcast==1){
                   6926:     /* Projection from cross-sectional to stable (period) for each covariate */
                   6927:     
1.237     brouard  6928:     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
                   6929:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   6930:       if(TKresult[nres]!= k1)
                   6931:        continue;
1.211     brouard  6932:       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227     brouard  6933:        fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
                   6934:        for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
                   6935:          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                   6936:          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6937:          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6938:          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6939:          vlv= nbcode[Tvaraff[k]][lv];
                   6940:          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                   6941:        }
1.237     brouard  6942:        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   6943:          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   6944:        }       
1.227     brouard  6945:        fprintf(ficgp,"\n#\n");
                   6946:        if(invalidvarcomb[k1]){
                   6947:          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                   6948:          continue;
                   6949:        }
                   6950:        
                   6951:        fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241     brouard  6952:        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.227     brouard  6953:        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238     brouard  6954: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
1.227     brouard  6955:        for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                   6956:          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   6957:          /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                   6958:          /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   6959:          /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                   6960:          if(i==1){
                   6961:            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
                   6962:          }else{
                   6963:            fprintf(ficgp,",\\\n '' ");
                   6964:          }
                   6965:          if(cptcoveff ==0){ /* No covariate */
                   6966:            ioffset=2; /* Age is in 2 */
                   6967:            /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                   6968:            /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                   6969:            /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                   6970:            /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                   6971:            fprintf(ficgp," u %d:(", ioffset); 
                   6972:            if(i==nlstate+1)
                   6973:              fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
                   6974:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                   6975:            else
                   6976:              fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                   6977:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                   6978:          }else{ /* more than 2 covariates */
                   6979:            if(cptcoveff ==1){
                   6980:              ioffset=4; /* Age is in 4 */
                   6981:            }else{
                   6982:              ioffset=6; /* Age is in 6 */
                   6983:              /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                   6984:              /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                   6985:            }   
                   6986:            fprintf(ficgp," u %d:(",ioffset); 
                   6987:            kl=0;
                   6988:            strcpy(gplotcondition,"(");
                   6989:            for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                   6990:              lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                   6991:              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                   6992:              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                   6993:              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                   6994:              vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                   6995:              kl++;
                   6996:              sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                   6997:              kl++;
                   6998:              if(k <cptcoveff && cptcoveff>1)
                   6999:                sprintf(gplotcondition+strlen(gplotcondition)," && ");
                   7000:            }
                   7001:            strcpy(gplotcondition+strlen(gplotcondition),")");
                   7002:            /* 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 *\/ */
                   7003:            /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                   7004:            /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                   7005:            /* ''  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*/
                   7006:            if(i==nlstate+1){
                   7007:              fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
                   7008:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                   7009:            }else{
                   7010:              fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                   7011:                      ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                   7012:            }
                   7013:          } /* end if covariate */
                   7014:        } /* nlstate */
                   7015:        fprintf(ficgp,"\nset out\n");
1.223     brouard  7016:       } /* end cpt state*/
                   7017:     } /* end covariate */
                   7018:   } /* End if prevfcast */
1.227     brouard  7019:   
                   7020:   
1.238     brouard  7021:   /* 9eme writing MLE parameters */
                   7022:   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126     brouard  7023:   for(i=1,jk=1; i <=nlstate; i++){
1.187     brouard  7024:     fprintf(ficgp,"# initial state %d\n",i);
1.126     brouard  7025:     for(k=1; k <=(nlstate+ndeath); k++){
                   7026:       if (k != i) {
1.227     brouard  7027:        fprintf(ficgp,"#   current state %d\n",k);
                   7028:        for(j=1; j <=ncovmodel; j++){
                   7029:          fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
                   7030:          jk++; 
                   7031:        }
                   7032:        fprintf(ficgp,"\n");
1.126     brouard  7033:       }
                   7034:     }
1.223     brouard  7035:   }
1.187     brouard  7036:   fprintf(ficgp,"##############\n#\n");
1.227     brouard  7037:   
1.145     brouard  7038:   /*goto avoid;*/
1.238     brouard  7039:   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
                   7040:   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187     brouard  7041:   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
                   7042:   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
                   7043:   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
                   7044:   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
                   7045:   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
                   7046:   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
                   7047:   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
                   7048:   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
                   7049:   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
                   7050:   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
                   7051:   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
                   7052:   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
                   7053:   fprintf(ficgp,"#\n");
1.223     brouard  7054:   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238     brouard  7055:     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237     brouard  7056:     fprintf(ficgp,"#model=%s \n",model);
1.238     brouard  7057:     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.237     brouard  7058:     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
                   7059:     for(jk=1; jk <=m; jk++)  /* For each combination of covariate */
                   7060:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   7061:       if(TKresult[nres]!= jk)
                   7062:        continue;
                   7063:       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
                   7064:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   7065:        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   7066:       }        
                   7067:       fprintf(ficgp,"\n#\n");
1.241     brouard  7068:       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);
1.223     brouard  7069:       fprintf(ficgp,"\nset ter svg size 640, 480 ");
                   7070:       if (ng==1){
                   7071:        fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
                   7072:        fprintf(ficgp,"\nunset log y");
                   7073:       }else if (ng==2){
                   7074:        fprintf(ficgp,"\nset ylabel \"Probability\"\n");
                   7075:        fprintf(ficgp,"\nset log y");
                   7076:       }else if (ng==3){
                   7077:        fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
                   7078:        fprintf(ficgp,"\nset log y");
                   7079:       }else
                   7080:        fprintf(ficgp,"\nunset title ");
                   7081:       fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                   7082:       i=1;
                   7083:       for(k2=1; k2<=nlstate; k2++) {
                   7084:        k3=i;
                   7085:        for(k=1; k<=(nlstate+ndeath); k++) {
                   7086:          if (k != k2){
                   7087:            switch( ng) {
                   7088:            case 1:
                   7089:              if(nagesqr==0)
                   7090:                fprintf(ficgp," p%d+p%d*x",i,i+1);
                   7091:              else /* nagesqr =1 */
                   7092:                fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                   7093:              break;
                   7094:            case 2: /* ng=2 */
                   7095:              if(nagesqr==0)
                   7096:                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                   7097:              else /* nagesqr =1 */
                   7098:                fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                   7099:              break;
                   7100:            case 3:
                   7101:              if(nagesqr==0)
                   7102:                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                   7103:              else /* nagesqr =1 */
                   7104:                fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                   7105:              break;
                   7106:            }
                   7107:            ij=1;/* To be checked else nbcode[0][0] wrong */
1.237     brouard  7108:            ijp=1; /* product no age */
                   7109:            /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
                   7110:            for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223     brouard  7111:              /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.237     brouard  7112:              if(j==Tage[ij]) { /* Product by age */
                   7113:                if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
1.238     brouard  7114:                  if(DummyV[j]==0){
1.237     brouard  7115:                    fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                   7116:                  }else{ /* quantitative */
                   7117:                    fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                   7118:                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                   7119:                  }
                   7120:                  ij++;
                   7121:                }
                   7122:              }else if(j==Tprod[ijp]) { /* */ 
                   7123:                /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                   7124:                if(ijp <=cptcovprod) { /* Product */
1.238     brouard  7125:                  if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                   7126:                    if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
1.237     brouard  7127:                      /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
                   7128:                      fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                   7129:                    }else{ /* Vn is dummy and Vm is quanti */
                   7130:                      /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                   7131:                      fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                   7132:                    }
                   7133:                  }else{ /* Vn*Vm Vn is quanti */
1.238     brouard  7134:                    if(DummyV[Tvard[ijp][2]]==0){
1.237     brouard  7135:                      fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                   7136:                    }else{ /* Both quanti */
                   7137:                      fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                   7138:                    }
                   7139:                  }
1.238     brouard  7140:                  ijp++;
1.237     brouard  7141:                }
                   7142:              } else{  /* simple covariate */
                   7143:                /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */
                   7144:                if(Dummy[j]==0){
                   7145:                  fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
                   7146:                }else{ /* quantitative */
                   7147:                  fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.223     brouard  7148:                  /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                   7149:                }
1.237     brouard  7150:              } /* end simple */
                   7151:            } /* end j */
1.223     brouard  7152:          }else{
                   7153:            i=i-ncovmodel;
                   7154:            if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                   7155:              fprintf(ficgp," (1.");
                   7156:          }
1.227     brouard  7157:          
1.223     brouard  7158:          if(ng != 1){
                   7159:            fprintf(ficgp,")/(1");
1.227     brouard  7160:            
1.223     brouard  7161:            for(k1=1; k1 <=nlstate; k1++){ 
                   7162:              if(nagesqr==0)
                   7163:                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   7164:              else /* nagesqr =1 */
                   7165:                fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
1.217     brouard  7166:               
1.223     brouard  7167:              ij=1;
                   7168:              for(j=3; j <=ncovmodel-nagesqr; j++){
1.237     brouard  7169:                if((j-2)==Tage[ij]) { /* Bug valgrind */
                   7170:                  if(ij <=cptcovage) { /* Bug valgrind */
1.223     brouard  7171:                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                   7172:                    /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                   7173:                    ij++;
                   7174:                  }
                   7175:                }
                   7176:                else
1.225     brouard  7177:                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
1.223     brouard  7178:              }
                   7179:              fprintf(ficgp,")");
                   7180:            }
                   7181:            fprintf(ficgp,")");
                   7182:            if(ng ==2)
                   7183:              fprintf(ficgp," t \"p%d%d\" ", k2,k);
                   7184:            else /* ng= 3 */
                   7185:              fprintf(ficgp," t \"i%d%d\" ", k2,k);
                   7186:          }else{ /* end ng <> 1 */
                   7187:            if( k !=k2) /* logit p11 is hard to draw */
                   7188:              fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
                   7189:          }
                   7190:          if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
                   7191:            fprintf(ficgp,",");
                   7192:          if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
                   7193:            fprintf(ficgp,",");
                   7194:          i=i+ncovmodel;
                   7195:        } /* end k */
                   7196:       } /* end k2 */
                   7197:       fprintf(ficgp,"\n set out\n");
                   7198:     } /* end jk */
                   7199:   } /* end ng */
                   7200:   /* avoid: */
                   7201:   fflush(ficgp); 
1.126     brouard  7202: }  /* end gnuplot */
                   7203: 
                   7204: 
                   7205: /*************** Moving average **************/
1.219     brouard  7206: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222     brouard  7207:  int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218     brouard  7208:    
1.222     brouard  7209:    int i, cpt, cptcod;
                   7210:    int modcovmax =1;
                   7211:    int mobilavrange, mob;
                   7212:    int iage=0;
                   7213: 
                   7214:    double sum=0.;
                   7215:    double age;
                   7216:    double *sumnewp, *sumnewm;
                   7217:    double *agemingood, *agemaxgood; /* Currently identical for all covariates */
                   7218:   
                   7219:   
1.225     brouard  7220:    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
1.222     brouard  7221:    /*             a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
                   7222: 
                   7223:    sumnewp = vector(1,ncovcombmax);
                   7224:    sumnewm = vector(1,ncovcombmax);
                   7225:    agemingood = vector(1,ncovcombmax); 
                   7226:    agemaxgood = vector(1,ncovcombmax);
                   7227: 
                   7228:    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                   7229:      sumnewm[cptcod]=0.;
                   7230:      sumnewp[cptcod]=0.;
                   7231:      agemingood[cptcod]=0;
                   7232:      agemaxgood[cptcod]=0;
                   7233:    }
                   7234:    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
                   7235:   
                   7236:    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
                   7237:      if(mobilav==1) mobilavrange=5; /* default */
                   7238:      else mobilavrange=mobilav;
                   7239:      for (age=bage; age<=fage; age++)
                   7240:        for (i=1; i<=nlstate;i++)
                   7241:         for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
                   7242:           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   7243:      /* We keep the original values on the extreme ages bage, fage and for 
                   7244:        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
                   7245:        we use a 5 terms etc. until the borders are no more concerned. 
                   7246:      */ 
                   7247:      for (mob=3;mob <=mobilavrange;mob=mob+2){
                   7248:        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                   7249:         for (i=1; i<=nlstate;i++){
                   7250:           for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                   7251:             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                   7252:             for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   7253:               mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   7254:               mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                   7255:             }
                   7256:             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                   7257:           }
                   7258:         }
                   7259:        }/* end age */
                   7260:      }/* end mob */
                   7261:    }else
                   7262:      return -1;
                   7263:    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                   7264:      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
                   7265:      if(invalidvarcomb[cptcod]){
                   7266:        printf("\nCombination (%d) ignored because no cases \n",cptcod); 
                   7267:        continue;
                   7268:      }
1.219     brouard  7269: 
1.222     brouard  7270:      agemingood[cptcod]=fage-(mob-1)/2;
                   7271:      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
                   7272:        sumnewm[cptcod]=0.;
                   7273:        for (i=1; i<=nlstate;i++){
                   7274:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                   7275:        }
                   7276:        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
                   7277:         agemingood[cptcod]=age;
                   7278:        }else{ /* bad */
                   7279:         for (i=1; i<=nlstate;i++){
                   7280:           mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
                   7281:         } /* i */
                   7282:        } /* end bad */
                   7283:      }/* age */
                   7284:      sum=0.;
                   7285:      for (i=1; i<=nlstate;i++){
                   7286:        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
                   7287:      }
                   7288:      if(fabs(sum - 1.) > 1.e-3) { /* bad */
                   7289:        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
                   7290:        /* for (i=1; i<=nlstate;i++){ */
                   7291:        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
                   7292:        /* } /\* i *\/ */
                   7293:      } /* end bad */
                   7294:      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
                   7295:      /* From youngest, finding the oldest wrong */
                   7296:      agemaxgood[cptcod]=bage+(mob-1)/2;
                   7297:      for (age=bage+(mob-1)/2; age<=fage; age++){
                   7298:        sumnewm[cptcod]=0.;
                   7299:        for (i=1; i<=nlstate;i++){
                   7300:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                   7301:        }
                   7302:        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
                   7303:         agemaxgood[cptcod]=age;
                   7304:        }else{ /* bad */
                   7305:         for (i=1; i<=nlstate;i++){
                   7306:           mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                   7307:         } /* i */
                   7308:        } /* end bad */
                   7309:      }/* age */
                   7310:      sum=0.;
                   7311:      for (i=1; i<=nlstate;i++){
                   7312:        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                   7313:      }
                   7314:      if(fabs(sum - 1.) > 1.e-3) { /* bad */
                   7315:        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
                   7316:        /* for (i=1; i<=nlstate;i++){ */
                   7317:        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
                   7318:        /* } /\* i *\/ */
                   7319:      } /* end bad */
                   7320:                
                   7321:      for (age=bage; age<=fage; age++){
1.235     brouard  7322:        /* printf("%d %d ", cptcod, (int)age); */
1.222     brouard  7323:        sumnewp[cptcod]=0.;
                   7324:        sumnewm[cptcod]=0.;
                   7325:        for (i=1; i<=nlstate;i++){
                   7326:         sumnewp[cptcod]+=probs[(int)age][i][cptcod];
                   7327:         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                   7328:         /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
                   7329:        }
                   7330:        /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
                   7331:      }
                   7332:      /* printf("\n"); */
                   7333:      /* } */
                   7334:      /* brutal averaging */
                   7335:      for (i=1; i<=nlstate;i++){
                   7336:        for (age=1; age<=bage; age++){
                   7337:         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
                   7338:         /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
                   7339:        }       
                   7340:        for (age=fage; age<=AGESUP; age++){
                   7341:         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                   7342:         /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
                   7343:        }
                   7344:      } /* end i status */
                   7345:      for (i=nlstate+1; i<=nlstate+ndeath;i++){
                   7346:        for (age=1; age<=AGESUP; age++){
                   7347:         /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
                   7348:         mobaverage[(int)age][i][cptcod]=0.;
                   7349:        }
                   7350:      }
                   7351:    }/* end cptcod */
                   7352:    free_vector(sumnewm,1, ncovcombmax);
                   7353:    free_vector(sumnewp,1, ncovcombmax);
                   7354:    free_vector(agemaxgood,1, ncovcombmax);
                   7355:    free_vector(agemingood,1, ncovcombmax);
                   7356:    return 0;
                   7357:  }/* End movingaverage */
1.218     brouard  7358:  
1.126     brouard  7359: 
                   7360: /************** Forecasting ******************/
1.235     brouard  7361:  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.126     brouard  7362:   /* proj1, year, month, day of starting projection 
                   7363:      agemin, agemax range of age
                   7364:      dateprev1 dateprev2 range of dates during which prevalence is computed
                   7365:      anproj2 year of en of projection (same day and month as proj1).
                   7366:   */
1.235     brouard  7367:    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126     brouard  7368:   double agec; /* generic age */
                   7369:   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
                   7370:   double *popeffectif,*popcount;
                   7371:   double ***p3mat;
1.218     brouard  7372:   /* double ***mobaverage; */
1.126     brouard  7373:   char fileresf[FILENAMELENGTH];
                   7374: 
                   7375:   agelim=AGESUP;
1.211     brouard  7376:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   7377:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   7378:      We still use firstpass and lastpass as another selection.
                   7379:   */
1.214     brouard  7380:   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
                   7381:   /*         firstpass, lastpass,  stepm,  weightopt, model); */
1.126     brouard  7382:  
1.201     brouard  7383:   strcpy(fileresf,"F_"); 
                   7384:   strcat(fileresf,fileresu);
1.126     brouard  7385:   if((ficresf=fopen(fileresf,"w"))==NULL) {
                   7386:     printf("Problem with forecast resultfile: %s\n", fileresf);
                   7387:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
                   7388:   }
1.235     brouard  7389:   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
                   7390:   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126     brouard  7391: 
1.225     brouard  7392:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126     brouard  7393: 
                   7394: 
                   7395:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   7396:   if (stepm<=12) stepsize=1;
                   7397:   if(estepm < stepm){
                   7398:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   7399:   }
                   7400:   else  hstepm=estepm;   
                   7401: 
                   7402:   hstepm=hstepm/stepm; 
                   7403:   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                   7404:                                fractional in yp1 */
                   7405:   anprojmean=yp;
                   7406:   yp2=modf((yp1*12),&yp);
                   7407:   mprojmean=yp;
                   7408:   yp1=modf((yp2*30.5),&yp);
                   7409:   jprojmean=yp;
                   7410:   if(jprojmean==0) jprojmean=1;
                   7411:   if(mprojmean==0) jprojmean=1;
                   7412: 
1.227     brouard  7413:   i1=pow(2,cptcoveff);
1.126     brouard  7414:   if (cptcovn < 1){i1=1;}
                   7415:   
                   7416:   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
                   7417:   
                   7418:   fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227     brouard  7419:   
1.126     brouard  7420: /*           if (h==(int)(YEARM*yearp)){ */
1.235     brouard  7421:   for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   7422:   for(k=1; k<=i1;k++){
                   7423:     if(TKresult[nres]!= k)
                   7424:       continue;
1.227     brouard  7425:     if(invalidvarcomb[k]){
                   7426:       printf("\nCombination (%d) projection ignored because no cases \n",k); 
                   7427:       continue;
                   7428:     }
                   7429:     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
                   7430:     for(j=1;j<=cptcoveff;j++) {
                   7431:       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   7432:     }
1.235     brouard  7433:     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238     brouard  7434:       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235     brouard  7435:     }
1.227     brouard  7436:     fprintf(ficresf," yearproj age");
                   7437:     for(j=1; j<=nlstate+ndeath;j++){ 
                   7438:       for(i=1; i<=nlstate;i++)               
                   7439:        fprintf(ficresf," p%d%d",i,j);
                   7440:       fprintf(ficresf," wp.%d",j);
                   7441:     }
                   7442:     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
                   7443:       fprintf(ficresf,"\n");
                   7444:       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
                   7445:       for (agec=fage; agec>=(ageminpar-1); agec--){ 
                   7446:        nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                   7447:        nhstepm = nhstepm/hstepm; 
                   7448:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   7449:        oldm=oldms;savm=savms;
1.235     brouard  7450:        hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.227     brouard  7451:        
                   7452:        for (h=0; h<=nhstepm; h++){
                   7453:          if (h*hstepm/YEARM*stepm ==yearp) {
                   7454:            fprintf(ficresf,"\n");
                   7455:            for(j=1;j<=cptcoveff;j++) 
                   7456:              fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   7457:            fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                   7458:          } 
                   7459:          for(j=1; j<=nlstate+ndeath;j++) {
                   7460:            ppij=0.;
                   7461:            for(i=1; i<=nlstate;i++) {
                   7462:              if (mobilav==1) 
                   7463:                ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
                   7464:              else {
                   7465:                ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
                   7466:              }
                   7467:              if (h*hstepm/YEARM*stepm== yearp) {
                   7468:                fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   7469:              }
                   7470:            } /* end i */
                   7471:            if (h*hstepm/YEARM*stepm==yearp) {
                   7472:              fprintf(ficresf," %.3f", ppij);
                   7473:            }
                   7474:          }/* end j */
                   7475:        } /* end h */
                   7476:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   7477:       } /* end agec */
                   7478:     } /* end yearp */
                   7479:   } /* end  k */
1.219     brouard  7480:        
1.126     brouard  7481:   fclose(ficresf);
1.215     brouard  7482:   printf("End of Computing forecasting \n");
                   7483:   fprintf(ficlog,"End of Computing forecasting\n");
                   7484: 
1.126     brouard  7485: }
                   7486: 
1.218     brouard  7487: /* /\************** Back Forecasting ******************\/ */
1.225     brouard  7488: /* void prevbackforecast(char fileres[], 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){ */
1.218     brouard  7489: /*   /\* back1, year, month, day of starting backection  */
                   7490: /*      agemin, agemax range of age */
                   7491: /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
                   7492: /*      anback2 year of en of backection (same day and month as back1). */
                   7493: /*   *\/ */
                   7494: /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
                   7495: /*   double agec; /\* generic age *\/ */
                   7496: /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
                   7497: /*   double *popeffectif,*popcount; */
                   7498: /*   double ***p3mat; */
                   7499: /*   /\* double ***mobaverage; *\/ */
                   7500: /*   char fileresfb[FILENAMELENGTH]; */
                   7501:        
                   7502: /*   agelim=AGESUP; */
                   7503: /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
                   7504: /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
                   7505: /*      We still use firstpass and lastpass as another selection. */
                   7506: /*   *\/ */
                   7507: /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
                   7508: /*   /\*             firstpass, lastpass,  stepm,  weightopt, model); *\/ */
                   7509: /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
                   7510:        
                   7511: /*   strcpy(fileresfb,"FB_");  */
                   7512: /*   strcat(fileresfb,fileresu); */
                   7513: /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
                   7514: /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
                   7515: /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
                   7516: /*   } */
                   7517: /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
                   7518: /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
                   7519:        
1.225     brouard  7520: /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218     brouard  7521:        
                   7522: /*   /\* if (mobilav!=0) { *\/ */
                   7523: /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
                   7524: /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
                   7525: /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
                   7526: /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
                   7527: /*   /\*   } *\/ */
                   7528: /*   /\* } *\/ */
                   7529:        
                   7530: /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
                   7531: /*   if (stepm<=12) stepsize=1; */
                   7532: /*   if(estepm < stepm){ */
                   7533: /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
                   7534: /*   } */
                   7535: /*   else  hstepm=estepm;    */
                   7536:        
                   7537: /*   hstepm=hstepm/stepm;  */
                   7538: /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                   7539: /*                                fractional in yp1 *\/ */
                   7540: /*   anprojmean=yp; */
                   7541: /*   yp2=modf((yp1*12),&yp); */
                   7542: /*   mprojmean=yp; */
                   7543: /*   yp1=modf((yp2*30.5),&yp); */
                   7544: /*   jprojmean=yp; */
                   7545: /*   if(jprojmean==0) jprojmean=1; */
                   7546: /*   if(mprojmean==0) jprojmean=1; */
                   7547:        
1.225     brouard  7548: /*   i1=cptcoveff; */
1.218     brouard  7549: /*   if (cptcovn < 1){i1=1;} */
1.217     brouard  7550:   
1.218     brouard  7551: /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
1.217     brouard  7552:   
1.218     brouard  7553: /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
                   7554:        
                   7555: /*     /\*           if (h==(int)(YEARM*yearp)){ *\/ */
                   7556: /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225     brouard  7557: /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218     brouard  7558: /*       k=k+1; */
                   7559: /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225     brouard  7560: /*       for(j=1;j<=cptcoveff;j++) { */
1.218     brouard  7561: /*                             fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
                   7562: /*       } */
                   7563: /*       fprintf(ficresfb," yearbproj age"); */
                   7564: /*       for(j=1; j<=nlstate+ndeath;j++){  */
                   7565: /*                             for(i=1; i<=nlstate;i++)               */
                   7566: /*           fprintf(ficresfb," p%d%d",i,j); */
                   7567: /*                             fprintf(ficresfb," p.%d",j); */
                   7568: /*       } */
                   7569: /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
                   7570: /*                             /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
                   7571: /*                             fprintf(ficresfb,"\n"); */
                   7572: /*                             fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
                   7573: /*                             for (agec=fage; agec>=(ageminpar-1); agec--){  */
                   7574: /*                                     nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
                   7575: /*                                     nhstepm = nhstepm/hstepm;  */
                   7576: /*                                     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   7577: /*                                     oldm=oldms;savm=savms; */
                   7578: /*                                     hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
                   7579: /*                                     for (h=0; h<=nhstepm; h++){ */
                   7580: /*                                             if (h*hstepm/YEARM*stepm ==yearp) { */
                   7581: /*               fprintf(ficresfb,"\n"); */
1.225     brouard  7582: /*               for(j=1;j<=cptcoveff;j++)  */
1.218     brouard  7583: /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
                   7584: /*                                                     fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
                   7585: /*                                             }  */
                   7586: /*                                             for(j=1; j<=nlstate+ndeath;j++) { */
                   7587: /*                                                     ppij=0.; */
                   7588: /*                                                     for(i=1; i<=nlstate;i++) { */
                   7589: /*                                                             if (mobilav==1)  */
                   7590: /*                                                                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
                   7591: /*                                                             else { */
                   7592: /*                                                                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
                   7593: /*                                                             } */
                   7594: /*                                                             if (h*hstepm/YEARM*stepm== yearp) { */
                   7595: /*                                                                     fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
                   7596: /*                                                             } */
                   7597: /*                                                     } /\* end i *\/ */
                   7598: /*                                                     if (h*hstepm/YEARM*stepm==yearp) { */
                   7599: /*                                                             fprintf(ficresfb," %.3f", ppij); */
                   7600: /*                                                     } */
                   7601: /*                                             }/\* end j *\/ */
                   7602: /*                                     } /\* end h *\/ */
                   7603: /*                                     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   7604: /*                             } /\* end agec *\/ */
                   7605: /*       } /\* end yearp *\/ */
                   7606: /*     } /\* end cptcod *\/ */
                   7607: /*   } /\* end  cptcov *\/ */
                   7608:        
                   7609: /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
                   7610:        
                   7611: /*   fclose(ficresfb); */
                   7612: /*   printf("End of Computing Back forecasting \n"); */
                   7613: /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217     brouard  7614:        
1.218     brouard  7615: /* } */
1.217     brouard  7616: 
1.126     brouard  7617: /************** Forecasting *****not tested NB*************/
1.227     brouard  7618: /* 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  7619:   
1.227     brouard  7620: /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
                   7621: /*   int *popage; */
                   7622: /*   double calagedatem, agelim, kk1, kk2; */
                   7623: /*   double *popeffectif,*popcount; */
                   7624: /*   double ***p3mat,***tabpop,***tabpopprev; */
                   7625: /*   /\* double ***mobaverage; *\/ */
                   7626: /*   char filerespop[FILENAMELENGTH]; */
1.126     brouard  7627: 
1.227     brouard  7628: /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   7629: /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   7630: /*   agelim=AGESUP; */
                   7631: /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126     brouard  7632:   
1.227     brouard  7633: /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126     brouard  7634:   
                   7635:   
1.227     brouard  7636: /*   strcpy(filerespop,"POP_");  */
                   7637: /*   strcat(filerespop,fileresu); */
                   7638: /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
                   7639: /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
                   7640: /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
                   7641: /*   } */
                   7642: /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
                   7643: /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126     brouard  7644: 
1.227     brouard  7645: /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126     brouard  7646: 
1.227     brouard  7647: /*   /\* if (mobilav!=0) { *\/ */
                   7648: /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
                   7649: /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
                   7650: /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
                   7651: /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
                   7652: /*   /\*   } *\/ */
                   7653: /*   /\* } *\/ */
1.126     brouard  7654: 
1.227     brouard  7655: /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
                   7656: /*   if (stepm<=12) stepsize=1; */
1.126     brouard  7657:   
1.227     brouard  7658: /*   agelim=AGESUP; */
1.126     brouard  7659:   
1.227     brouard  7660: /*   hstepm=1; */
                   7661: /*   hstepm=hstepm/stepm;  */
1.218     brouard  7662:        
1.227     brouard  7663: /*   if (popforecast==1) { */
                   7664: /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
                   7665: /*       printf("Problem with population file : %s\n",popfile);exit(0); */
                   7666: /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
                   7667: /*     }  */
                   7668: /*     popage=ivector(0,AGESUP); */
                   7669: /*     popeffectif=vector(0,AGESUP); */
                   7670: /*     popcount=vector(0,AGESUP); */
1.126     brouard  7671:     
1.227     brouard  7672: /*     i=1;    */
                   7673: /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218     brouard  7674:     
1.227     brouard  7675: /*     imx=i; */
                   7676: /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
                   7677: /*   } */
1.218     brouard  7678:   
1.227     brouard  7679: /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
                   7680: /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
                   7681: /*       k=k+1; */
                   7682: /*       fprintf(ficrespop,"\n#******"); */
                   7683: /*       for(j=1;j<=cptcoveff;j++) { */
                   7684: /*     fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
                   7685: /*       } */
                   7686: /*       fprintf(ficrespop,"******\n"); */
                   7687: /*       fprintf(ficrespop,"# Age"); */
                   7688: /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
                   7689: /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
1.126     brouard  7690:       
1.227     brouard  7691: /*       for (cpt=0; cpt<=0;cpt++) {  */
                   7692: /*     fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
1.126     brouard  7693:        
1.227     brouard  7694: /*     for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
                   7695: /*       nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
                   7696: /*       nhstepm = nhstepm/hstepm;  */
1.126     brouard  7697:          
1.227     brouard  7698: /*       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   7699: /*       oldm=oldms;savm=savms; */
                   7700: /*       hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
1.218     brouard  7701:          
1.227     brouard  7702: /*       for (h=0; h<=nhstepm; h++){ */
                   7703: /*         if (h==(int) (calagedatem+YEARM*cpt)) { */
                   7704: /*           fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
                   7705: /*         }  */
                   7706: /*         for(j=1; j<=nlstate+ndeath;j++) { */
                   7707: /*           kk1=0.;kk2=0; */
                   7708: /*           for(i=1; i<=nlstate;i++) {               */
                   7709: /*             if (mobilav==1)  */
                   7710: /*               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
                   7711: /*             else { */
                   7712: /*               kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
                   7713: /*             } */
                   7714: /*           } */
                   7715: /*           if (h==(int)(calagedatem+12*cpt)){ */
                   7716: /*             tabpop[(int)(agedeb)][j][cptcod]=kk1; */
                   7717: /*             /\*fprintf(ficrespop," %.3f", kk1); */
                   7718: /*               if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
                   7719: /*           } */
                   7720: /*         } */
                   7721: /*         for(i=1; i<=nlstate;i++){ */
                   7722: /*           kk1=0.; */
                   7723: /*           for(j=1; j<=nlstate;j++){ */
                   7724: /*             kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
                   7725: /*           } */
                   7726: /*           tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
                   7727: /*         } */
1.218     brouard  7728:            
1.227     brouard  7729: /*         if (h==(int)(calagedatem+12*cpt)) */
                   7730: /*           for(j=1; j<=nlstate;j++)  */
                   7731: /*             fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
                   7732: /*       } */
                   7733: /*       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   7734: /*     } */
                   7735: /*       } */
1.218     brouard  7736:       
1.227     brouard  7737: /*       /\******\/ */
1.218     brouard  7738:       
1.227     brouard  7739: /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
                   7740: /*     fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
                   7741: /*     for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
                   7742: /*       nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
                   7743: /*       nhstepm = nhstepm/hstepm;  */
1.126     brouard  7744:          
1.227     brouard  7745: /*       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   7746: /*       oldm=oldms;savm=savms; */
                   7747: /*       hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
                   7748: /*       for (h=0; h<=nhstepm; h++){ */
                   7749: /*         if (h==(int) (calagedatem+YEARM*cpt)) { */
                   7750: /*           fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
                   7751: /*         }  */
                   7752: /*         for(j=1; j<=nlstate+ndeath;j++) { */
                   7753: /*           kk1=0.;kk2=0; */
                   7754: /*           for(i=1; i<=nlstate;i++) {               */
                   7755: /*             kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
                   7756: /*           } */
                   7757: /*           if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
                   7758: /*         } */
                   7759: /*       } */
                   7760: /*       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
                   7761: /*     } */
                   7762: /*       } */
                   7763: /*     }  */
                   7764: /*   } */
1.218     brouard  7765:   
1.227     brouard  7766: /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218     brouard  7767:   
1.227     brouard  7768: /*   if (popforecast==1) { */
                   7769: /*     free_ivector(popage,0,AGESUP); */
                   7770: /*     free_vector(popeffectif,0,AGESUP); */
                   7771: /*     free_vector(popcount,0,AGESUP); */
                   7772: /*   } */
                   7773: /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   7774: /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
                   7775: /*   fclose(ficrespop); */
                   7776: /* } /\* End of popforecast *\/ */
1.218     brouard  7777:  
1.126     brouard  7778: int fileappend(FILE *fichier, char *optionfich)
                   7779: {
                   7780:   if((fichier=fopen(optionfich,"a"))==NULL) {
                   7781:     printf("Problem with file: %s\n", optionfich);
                   7782:     fprintf(ficlog,"Problem with file: %s\n", optionfich);
                   7783:     return (0);
                   7784:   }
                   7785:   fflush(fichier);
                   7786:   return (1);
                   7787: }
                   7788: 
                   7789: 
                   7790: /**************** function prwizard **********************/
                   7791: void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
                   7792: {
                   7793: 
                   7794:   /* Wizard to print covariance matrix template */
                   7795: 
1.164     brouard  7796:   char ca[32], cb[32];
                   7797:   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126     brouard  7798:   int numlinepar;
                   7799: 
                   7800:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   7801:   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   7802:   for(i=1; i <=nlstate; i++){
                   7803:     jj=0;
                   7804:     for(j=1; j <=nlstate+ndeath; j++){
                   7805:       if(j==i) continue;
                   7806:       jj++;
                   7807:       /*ca[0]= k+'a'-1;ca[1]='\0';*/
                   7808:       printf("%1d%1d",i,j);
                   7809:       fprintf(ficparo,"%1d%1d",i,j);
                   7810:       for(k=1; k<=ncovmodel;k++){
                   7811:        /*        printf(" %lf",param[i][j][k]); */
                   7812:        /*        fprintf(ficparo," %lf",param[i][j][k]); */
                   7813:        printf(" 0.");
                   7814:        fprintf(ficparo," 0.");
                   7815:       }
                   7816:       printf("\n");
                   7817:       fprintf(ficparo,"\n");
                   7818:     }
                   7819:   }
                   7820:   printf("# Scales (for hessian or gradient estimation)\n");
                   7821:   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
                   7822:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
                   7823:   for(i=1; i <=nlstate; i++){
                   7824:     jj=0;
                   7825:     for(j=1; j <=nlstate+ndeath; j++){
                   7826:       if(j==i) continue;
                   7827:       jj++;
                   7828:       fprintf(ficparo,"%1d%1d",i,j);
                   7829:       printf("%1d%1d",i,j);
                   7830:       fflush(stdout);
                   7831:       for(k=1; k<=ncovmodel;k++){
                   7832:        /*      printf(" %le",delti3[i][j][k]); */
                   7833:        /*      fprintf(ficparo," %le",delti3[i][j][k]); */
                   7834:        printf(" 0.");
                   7835:        fprintf(ficparo," 0.");
                   7836:       }
                   7837:       numlinepar++;
                   7838:       printf("\n");
                   7839:       fprintf(ficparo,"\n");
                   7840:     }
                   7841:   }
                   7842:   printf("# Covariance matrix\n");
                   7843: /* # 121 Var(a12)\n\ */
                   7844: /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   7845: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   7846: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   7847: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   7848: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   7849: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   7850: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   7851:   fflush(stdout);
                   7852:   fprintf(ficparo,"# Covariance matrix\n");
                   7853:   /* # 121 Var(a12)\n\ */
                   7854:   /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   7855:   /* #   ...\n\ */
                   7856:   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
                   7857:   
                   7858:   for(itimes=1;itimes<=2;itimes++){
                   7859:     jj=0;
                   7860:     for(i=1; i <=nlstate; i++){
                   7861:       for(j=1; j <=nlstate+ndeath; j++){
                   7862:        if(j==i) continue;
                   7863:        for(k=1; k<=ncovmodel;k++){
                   7864:          jj++;
                   7865:          ca[0]= k+'a'-1;ca[1]='\0';
                   7866:          if(itimes==1){
                   7867:            printf("#%1d%1d%d",i,j,k);
                   7868:            fprintf(ficparo,"#%1d%1d%d",i,j,k);
                   7869:          }else{
                   7870:            printf("%1d%1d%d",i,j,k);
                   7871:            fprintf(ficparo,"%1d%1d%d",i,j,k);
                   7872:            /*  printf(" %.5le",matcov[i][j]); */
                   7873:          }
                   7874:          ll=0;
                   7875:          for(li=1;li <=nlstate; li++){
                   7876:            for(lj=1;lj <=nlstate+ndeath; lj++){
                   7877:              if(lj==li) continue;
                   7878:              for(lk=1;lk<=ncovmodel;lk++){
                   7879:                ll++;
                   7880:                if(ll<=jj){
                   7881:                  cb[0]= lk +'a'-1;cb[1]='\0';
                   7882:                  if(ll<jj){
                   7883:                    if(itimes==1){
                   7884:                      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   7885:                      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   7886:                    }else{
                   7887:                      printf(" 0.");
                   7888:                      fprintf(ficparo," 0.");
                   7889:                    }
                   7890:                  }else{
                   7891:                    if(itimes==1){
                   7892:                      printf(" Var(%s%1d%1d)",ca,i,j);
                   7893:                      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                   7894:                    }else{
                   7895:                      printf(" 0.");
                   7896:                      fprintf(ficparo," 0.");
                   7897:                    }
                   7898:                  }
                   7899:                }
                   7900:              } /* end lk */
                   7901:            } /* end lj */
                   7902:          } /* end li */
                   7903:          printf("\n");
                   7904:          fprintf(ficparo,"\n");
                   7905:          numlinepar++;
                   7906:        } /* end k*/
                   7907:       } /*end j */
                   7908:     } /* end i */
                   7909:   } /* end itimes */
                   7910: 
                   7911: } /* end of prwizard */
                   7912: /******************* Gompertz Likelihood ******************************/
                   7913: double gompertz(double x[])
                   7914: { 
                   7915:   double A,B,L=0.0,sump=0.,num=0.;
                   7916:   int i,n=0; /* n is the size of the sample */
                   7917: 
1.220     brouard  7918:   for (i=1;i<=imx ; i++) {
1.126     brouard  7919:     sump=sump+weight[i];
                   7920:     /*    sump=sump+1;*/
                   7921:     num=num+1;
                   7922:   }
                   7923:  
                   7924:  
                   7925:   /* for (i=0; i<=imx; i++) 
                   7926:      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]);*/
                   7927: 
                   7928:   for (i=1;i<=imx ; i++)
                   7929:     {
                   7930:       if (cens[i] == 1 && wav[i]>1)
                   7931:        A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
                   7932:       
                   7933:       if (cens[i] == 0 && wav[i]>1)
                   7934:        A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                   7935:             +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
                   7936:       
                   7937:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
                   7938:       if (wav[i] > 1 ) { /* ??? */
                   7939:        L=L+A*weight[i];
                   7940:        /*      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]);*/
                   7941:       }
                   7942:     }
                   7943: 
                   7944:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
                   7945:  
                   7946:   return -2*L*num/sump;
                   7947: }
                   7948: 
1.136     brouard  7949: #ifdef GSL
                   7950: /******************* Gompertz_f Likelihood ******************************/
                   7951: double gompertz_f(const gsl_vector *v, void *params)
                   7952: { 
                   7953:   double A,B,LL=0.0,sump=0.,num=0.;
                   7954:   double *x= (double *) v->data;
                   7955:   int i,n=0; /* n is the size of the sample */
                   7956: 
                   7957:   for (i=0;i<=imx-1 ; i++) {
                   7958:     sump=sump+weight[i];
                   7959:     /*    sump=sump+1;*/
                   7960:     num=num+1;
                   7961:   }
                   7962:  
                   7963:  
                   7964:   /* for (i=0; i<=imx; i++) 
                   7965:      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]);*/
                   7966:   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
                   7967:   for (i=1;i<=imx ; i++)
                   7968:     {
                   7969:       if (cens[i] == 1 && wav[i]>1)
                   7970:        A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
                   7971:       
                   7972:       if (cens[i] == 0 && wav[i]>1)
                   7973:        A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                   7974:             +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
                   7975:       
                   7976:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
                   7977:       if (wav[i] > 1 ) { /* ??? */
                   7978:        LL=LL+A*weight[i];
                   7979:        /*      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]);*/
                   7980:       }
                   7981:     }
                   7982: 
                   7983:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
                   7984:   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
                   7985:  
                   7986:   return -2*LL*num/sump;
                   7987: }
                   7988: #endif
                   7989: 
1.126     brouard  7990: /******************* Printing html file ***********/
1.201     brouard  7991: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126     brouard  7992:                  int lastpass, int stepm, int weightopt, char model[],\
                   7993:                  int imx,  double p[],double **matcov,double agemortsup){
                   7994:   int i,k;
                   7995: 
                   7996:   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
                   7997:   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
                   7998:   for (i=1;i<=2;i++) 
                   7999:     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  8000:   fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126     brouard  8001:   fprintf(fichtm,"</ul>");
                   8002: 
                   8003: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
                   8004: 
                   8005:  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>");
                   8006: 
                   8007:  for (k=agegomp;k<(agemortsup-2);k++) 
                   8008:    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]);
                   8009: 
                   8010:  
                   8011:   fflush(fichtm);
                   8012: }
                   8013: 
                   8014: /******************* Gnuplot file **************/
1.201     brouard  8015: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126     brouard  8016: 
                   8017:   char dirfileres[132],optfileres[132];
1.164     brouard  8018: 
1.126     brouard  8019:   int ng;
                   8020: 
                   8021: 
                   8022:   /*#ifdef windows */
                   8023:   fprintf(ficgp,"cd \"%s\" \n",pathc);
                   8024:     /*#endif */
                   8025: 
                   8026: 
                   8027:   strcpy(dirfileres,optionfilefiname);
                   8028:   strcpy(optfileres,"vpl");
1.199     brouard  8029:   fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
1.126     brouard  8030:   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
1.199     brouard  8031:   fprintf(ficgp, "set ter svg size 640, 480\n set log y\n"); 
1.145     brouard  8032:   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126     brouard  8033:   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
                   8034: 
                   8035: } 
                   8036: 
1.136     brouard  8037: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
                   8038: {
1.126     brouard  8039: 
1.136     brouard  8040:   /*-------- data file ----------*/
                   8041:   FILE *fic;
                   8042:   char dummy[]="                         ";
1.240     brouard  8043:   int i=0, j=0, n=0, iv=0, v;
1.223     brouard  8044:   int lstra;
1.136     brouard  8045:   int linei, month, year,iout;
                   8046:   char line[MAXLINE], linetmp[MAXLINE];
1.164     brouard  8047:   char stra[MAXLINE], strb[MAXLINE];
1.136     brouard  8048:   char *stratrunc;
1.223     brouard  8049: 
1.240     brouard  8050:   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
                   8051:   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126     brouard  8052: 
1.240     brouard  8053:   for(v=1; v <=ncovcol;v++){
                   8054:     DummyV[v]=0;
                   8055:     FixedV[v]=0;
                   8056:   }
                   8057:   for(v=ncovcol+1; v <=ncovcol+nqv;v++){
                   8058:     DummyV[v]=1;
                   8059:     FixedV[v]=0;
                   8060:   }
                   8061:   for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
                   8062:     DummyV[v]=0;
                   8063:     FixedV[v]=1;
                   8064:   }
                   8065:   for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
                   8066:     DummyV[v]=1;
                   8067:     FixedV[v]=1;
                   8068:   }
                   8069:   for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
                   8070:     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
                   8071:     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]);
                   8072:   }
1.126     brouard  8073: 
1.136     brouard  8074:   if((fic=fopen(datafile,"r"))==NULL)    {
1.218     brouard  8075:     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
                   8076:     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136     brouard  8077:   }
1.126     brouard  8078: 
1.136     brouard  8079:   i=1;
                   8080:   linei=0;
                   8081:   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
                   8082:     linei=linei+1;
                   8083:     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
                   8084:       if(line[j] == '\t')
                   8085:        line[j] = ' ';
                   8086:     }
                   8087:     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
                   8088:       ;
                   8089:     };
                   8090:     line[j+1]=0;  /* Trims blanks at end of line */
                   8091:     if(line[0]=='#'){
                   8092:       fprintf(ficlog,"Comment line\n%s\n",line);
                   8093:       printf("Comment line\n%s\n",line);
                   8094:       continue;
                   8095:     }
                   8096:     trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164     brouard  8097:     strcpy(line, linetmp);
1.223     brouard  8098:     
                   8099:     /* Loops on waves */
                   8100:     for (j=maxwav;j>=1;j--){
                   8101:       for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
1.238     brouard  8102:        cutv(stra, strb, line, ' '); 
                   8103:        if(strb[0]=='.') { /* Missing value */
                   8104:          lval=-1;
                   8105:          cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
                   8106:          cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
                   8107:          if(isalpha(strb[1])) { /* .m or .d Really Missing value */
                   8108:            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);
                   8109:            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);
                   8110:            return 1;
                   8111:          }
                   8112:        }else{
                   8113:          errno=0;
                   8114:          /* what_kind_of_number(strb); */
                   8115:          dval=strtod(strb,&endptr); 
                   8116:          /* if( strb[0]=='\0' || (*endptr != '\0')){ */
                   8117:          /* if(strb != endptr && *endptr == '\0') */
                   8118:          /*    dval=dlval; */
                   8119:          /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                   8120:          if( strb[0]=='\0' || (*endptr != '\0')){
                   8121:            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);
                   8122:            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);
                   8123:            return 1;
                   8124:          }
                   8125:          cotqvar[j][iv][i]=dval; 
                   8126:          cotvar[j][ntv+iv][i]=dval; 
                   8127:        }
                   8128:        strcpy(line,stra);
1.223     brouard  8129:       }/* end loop ntqv */
1.225     brouard  8130:       
1.223     brouard  8131:       for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
1.238     brouard  8132:        cutv(stra, strb, line, ' '); 
                   8133:        if(strb[0]=='.') { /* Missing value */
                   8134:          lval=-1;
                   8135:        }else{
                   8136:          errno=0;
                   8137:          lval=strtol(strb,&endptr,10); 
                   8138:          /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                   8139:          if( strb[0]=='\0' || (*endptr != '\0')){
                   8140:            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);
                   8141:            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);
                   8142:            return 1;
                   8143:          }
                   8144:        }
                   8145:        if(lval <-1 || lval >1){
                   8146:          printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223     brouard  8147:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   8148:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238     brouard  8149:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   8150:  build V1=0 V2=0 for the reference value (1),\n                                \
                   8151:         V1=1 V2=0 for (2) \n                                           \
1.223     brouard  8152:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238     brouard  8153:  output of IMaCh is often meaningless.\n                               \
1.223     brouard  8154:  Exiting.\n",lval,linei, i,line,j);
1.238     brouard  8155:          fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223     brouard  8156:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   8157:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238     brouard  8158:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   8159:  build V1=0 V2=0 for the reference value (1),\n                                \
                   8160:         V1=1 V2=0 for (2) \n                                           \
1.223     brouard  8161:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238     brouard  8162:  output of IMaCh is often meaningless.\n                               \
1.223     brouard  8163:  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238     brouard  8164:          return 1;
                   8165:        }
                   8166:        cotvar[j][iv][i]=(double)(lval);
                   8167:        strcpy(line,stra);
1.223     brouard  8168:       }/* end loop ntv */
1.225     brouard  8169:       
1.223     brouard  8170:       /* Statuses  at wave */
1.137     brouard  8171:       cutv(stra, strb, line, ' '); 
1.223     brouard  8172:       if(strb[0]=='.') { /* Missing value */
1.238     brouard  8173:        lval=-1;
1.136     brouard  8174:       }else{
1.238     brouard  8175:        errno=0;
                   8176:        lval=strtol(strb,&endptr,10); 
                   8177:        /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                   8178:        if( strb[0]=='\0' || (*endptr != '\0')){
                   8179:          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);
                   8180:          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);
                   8181:          return 1;
                   8182:        }
1.136     brouard  8183:       }
1.225     brouard  8184:       
1.136     brouard  8185:       s[j][i]=lval;
1.225     brouard  8186:       
1.223     brouard  8187:       /* Date of Interview */
1.136     brouard  8188:       strcpy(line,stra);
                   8189:       cutv(stra, strb,line,' ');
1.169     brouard  8190:       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  8191:       }
1.169     brouard  8192:       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225     brouard  8193:        month=99;
                   8194:        year=9999;
1.136     brouard  8195:       }else{
1.225     brouard  8196:        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);
                   8197:        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);
                   8198:        return 1;
1.136     brouard  8199:       }
                   8200:       anint[j][i]= (double) year; 
                   8201:       mint[j][i]= (double)month; 
                   8202:       strcpy(line,stra);
1.223     brouard  8203:     } /* End loop on waves */
1.225     brouard  8204:     
1.223     brouard  8205:     /* Date of death */
1.136     brouard  8206:     cutv(stra, strb,line,' '); 
1.169     brouard  8207:     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  8208:     }
1.169     brouard  8209:     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136     brouard  8210:       month=99;
                   8211:       year=9999;
                   8212:     }else{
1.141     brouard  8213:       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  8214:       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);
                   8215:       return 1;
1.136     brouard  8216:     }
                   8217:     andc[i]=(double) year; 
                   8218:     moisdc[i]=(double) month; 
                   8219:     strcpy(line,stra);
                   8220:     
1.223     brouard  8221:     /* Date of birth */
1.136     brouard  8222:     cutv(stra, strb,line,' '); 
1.169     brouard  8223:     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  8224:     }
1.169     brouard  8225:     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136     brouard  8226:       month=99;
                   8227:       year=9999;
                   8228:     }else{
1.141     brouard  8229:       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);
                   8230:       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  8231:       return 1;
1.136     brouard  8232:     }
                   8233:     if (year==9999) {
1.141     brouard  8234:       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);
                   8235:       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  8236:       return 1;
                   8237:       
1.136     brouard  8238:     }
                   8239:     annais[i]=(double)(year);
                   8240:     moisnais[i]=(double)(month); 
                   8241:     strcpy(line,stra);
1.225     brouard  8242:     
1.223     brouard  8243:     /* Sample weight */
1.136     brouard  8244:     cutv(stra, strb,line,' '); 
                   8245:     errno=0;
                   8246:     dval=strtod(strb,&endptr); 
                   8247:     if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  8248:       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
                   8249:       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  8250:       fflush(ficlog);
                   8251:       return 1;
                   8252:     }
                   8253:     weight[i]=dval; 
                   8254:     strcpy(line,stra);
1.225     brouard  8255:     
1.223     brouard  8256:     for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
                   8257:       cutv(stra, strb, line, ' '); 
                   8258:       if(strb[0]=='.') { /* Missing value */
1.225     brouard  8259:        lval=-1;
1.223     brouard  8260:       }else{
1.225     brouard  8261:        errno=0;
                   8262:        /* what_kind_of_number(strb); */
                   8263:        dval=strtod(strb,&endptr);
                   8264:        /* if(strb != endptr && *endptr == '\0') */
                   8265:        /*   dval=dlval; */
                   8266:        /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                   8267:        if( strb[0]=='\0' || (*endptr != '\0')){
                   8268:          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);
                   8269:          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);
                   8270:          return 1;
                   8271:        }
                   8272:        coqvar[iv][i]=dval; 
1.226     brouard  8273:        covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ 
1.223     brouard  8274:       }
                   8275:       strcpy(line,stra);
                   8276:     }/* end loop nqv */
1.136     brouard  8277:     
1.223     brouard  8278:     /* Covariate values */
1.136     brouard  8279:     for (j=ncovcol;j>=1;j--){
                   8280:       cutv(stra, strb,line,' '); 
1.223     brouard  8281:       if(strb[0]=='.') { /* Missing covariate value */
1.225     brouard  8282:        lval=-1;
1.136     brouard  8283:       }else{
1.225     brouard  8284:        errno=0;
                   8285:        lval=strtol(strb,&endptr,10); 
                   8286:        if( strb[0]=='\0' || (*endptr != '\0')){
                   8287:          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);
                   8288:          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);
                   8289:          return 1;
                   8290:        }
1.136     brouard  8291:       }
                   8292:       if(lval <-1 || lval >1){
1.225     brouard  8293:        printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  8294:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   8295:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225     brouard  8296:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   8297:  build V1=0 V2=0 for the reference value (1),\n                                \
                   8298:         V1=1 V2=0 for (2) \n                                           \
1.136     brouard  8299:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225     brouard  8300:  output of IMaCh is often meaningless.\n                               \
1.136     brouard  8301:  Exiting.\n",lval,linei, i,line,j);
1.225     brouard  8302:        fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  8303:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   8304:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225     brouard  8305:  For example, for multinomial values like 1, 2 and 3,\n                        \
                   8306:  build V1=0 V2=0 for the reference value (1),\n                                \
                   8307:         V1=1 V2=0 for (2) \n                                           \
1.136     brouard  8308:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225     brouard  8309:  output of IMaCh is often meaningless.\n                               \
1.136     brouard  8310:  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225     brouard  8311:        return 1;
1.136     brouard  8312:       }
                   8313:       covar[j][i]=(double)(lval);
                   8314:       strcpy(line,stra);
                   8315:     }  
                   8316:     lstra=strlen(stra);
1.225     brouard  8317:     
1.136     brouard  8318:     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
                   8319:       stratrunc = &(stra[lstra-9]);
                   8320:       num[i]=atol(stratrunc);
                   8321:     }
                   8322:     else
                   8323:       num[i]=atol(stra);
                   8324:     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
                   8325:       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;}*/
                   8326:     
                   8327:     i=i+1;
                   8328:   } /* End loop reading  data */
1.225     brouard  8329:   
1.136     brouard  8330:   *imax=i-1; /* Number of individuals */
                   8331:   fclose(fic);
1.225     brouard  8332:   
1.136     brouard  8333:   return (0);
1.164     brouard  8334:   /* endread: */
1.225     brouard  8335:   printf("Exiting readdata: ");
                   8336:   fclose(fic);
                   8337:   return (1);
1.223     brouard  8338: }
1.126     brouard  8339: 
1.234     brouard  8340: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230     brouard  8341:   char *p1 = *stri, *p2 = *stri;
1.235     brouard  8342:   while (*p2 == ' ')
1.234     brouard  8343:     p2++; 
                   8344:   /* while ((*p1++ = *p2++) !=0) */
                   8345:   /*   ; */
                   8346:   /* do */
                   8347:   /*   while (*p2 == ' ') */
                   8348:   /*     p2++; */
                   8349:   /* while (*p1++ == *p2++); */
                   8350:   *stri=p2; 
1.145     brouard  8351: }
                   8352: 
1.235     brouard  8353: int decoderesult ( char resultline[], int nres)
1.230     brouard  8354: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
                   8355: {
1.235     brouard  8356:   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230     brouard  8357:   char resultsav[MAXLINE];
1.234     brouard  8358:   int resultmodel[MAXLINE];
                   8359:   int modelresult[MAXLINE];
1.230     brouard  8360:   char stra[80], strb[80], strc[80], strd[80],stre[80];
                   8361: 
1.234     brouard  8362:   removefirstspace(&resultline);
1.233     brouard  8363:   printf("decoderesult:%s\n",resultline);
1.230     brouard  8364: 
                   8365:   if (strstr(resultline,"v") !=0){
                   8366:     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
                   8367:     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
                   8368:     return 1;
                   8369:   }
                   8370:   trimbb(resultsav, resultline);
                   8371:   if (strlen(resultsav) >1){
                   8372:     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
                   8373:   }
1.234     brouard  8374:   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
                   8375:     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
                   8376:     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
                   8377:   }
                   8378:   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
                   8379:     if(nbocc(resultsav,'=') >1){
                   8380:        cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' 
                   8381:                                      resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
                   8382:        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
                   8383:     }else
                   8384:       cutl(strc,strd,resultsav,'=');
1.230     brouard  8385:     Tvalsel[k]=atof(strc); /* 1 */
1.234     brouard  8386:     
1.230     brouard  8387:     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
                   8388:     Tvarsel[k]=atoi(strc);
                   8389:     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
                   8390:     /* cptcovsel++;     */
                   8391:     if (nbocc(stra,'=') >0)
                   8392:       strcpy(resultsav,stra); /* and analyzes it */
                   8393:   }
1.235     brouard  8394:   /* Checking for missing or useless values in comparison of current model needs */
1.236     brouard  8395:   for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   8396:     if(Typevar[k1]==0){ /* Single covariate in model */
1.234     brouard  8397:       match=0;
1.236     brouard  8398:       for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
1.237     brouard  8399:        if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
1.236     brouard  8400:          modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
1.234     brouard  8401:          match=1;
                   8402:          break;
                   8403:        }
                   8404:       }
                   8405:       if(match == 0){
                   8406:        printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
                   8407:       }
                   8408:     }
                   8409:   }
1.235     brouard  8410:   /* Checking for missing or useless values in comparison of current model needs */
                   8411:   for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
1.234     brouard  8412:     match=0;
1.235     brouard  8413:     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   8414:       if(Typevar[k1]==0){ /* Single */
1.237     brouard  8415:        if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
1.235     brouard  8416:          resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
1.234     brouard  8417:          ++match;
                   8418:        }
                   8419:       }
                   8420:     }
                   8421:     if(match == 0){
                   8422:       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
                   8423:     }else if(match > 1){
                   8424:       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
                   8425:     }
                   8426:   }
1.235     brouard  8427:       
1.234     brouard  8428:   /* We need to deduce which combination number is chosen and save quantitative values */
1.235     brouard  8429:   /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   8430:   /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
                   8431:   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
                   8432:   /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
                   8433:   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
                   8434:   /*    1 0 0 0 */
                   8435:   /*    2 1 0 0 */
                   8436:   /*    3 0 1 0 */ 
                   8437:   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
                   8438:   /*    5 0 0 1 */
                   8439:   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
                   8440:   /*    7 0 1 1 */
                   8441:   /*    8 1 1 1 */
1.237     brouard  8442:   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
                   8443:   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
                   8444:   /* V5*age V5 known which value for nres?  */
                   8445:   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
1.235     brouard  8446:   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
                   8447:     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237     brouard  8448:       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235     brouard  8449:       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
                   8450:       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
1.237     brouard  8451:       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
                   8452:       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
                   8453:       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235     brouard  8454:       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
                   8455:       k4++;;
                   8456:     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
                   8457:       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
                   8458:       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237     brouard  8459:       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
                   8460:       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
                   8461:       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235     brouard  8462:       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
                   8463:       k4q++;;
                   8464:     }
                   8465:   }
1.234     brouard  8466:   
1.235     brouard  8467:   TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230     brouard  8468:   return (0);
                   8469: }
1.235     brouard  8470: 
1.230     brouard  8471: int decodemodel( char model[], int lastobs)
                   8472:  /**< This routine decodes the model and returns:
1.224     brouard  8473:        * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
                   8474:        * - nagesqr = 1 if age*age in the model, otherwise 0.
                   8475:        * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
                   8476:        * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
                   8477:        * - cptcovage number of covariates with age*products =2
                   8478:        * - cptcovs number of simple covariates
                   8479:        * - 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
                   8480:        *     which is a new column after the 9 (ncovcol) variables. 
                   8481:        * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
                   8482:        * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
                   8483:        *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
                   8484:        * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
                   8485:        */
1.136     brouard  8486: {
1.238     brouard  8487:   int i, j, k, ks, v;
1.227     brouard  8488:   int  j1, k1, k2, k3, k4;
1.136     brouard  8489:   char modelsav[80];
1.145     brouard  8490:   char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187     brouard  8491:   char *strpt;
1.136     brouard  8492: 
1.145     brouard  8493:   /*removespace(model);*/
1.136     brouard  8494:   if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145     brouard  8495:     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137     brouard  8496:     if (strstr(model,"AGE") !=0){
1.192     brouard  8497:       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
                   8498:       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136     brouard  8499:       return 1;
                   8500:     }
1.141     brouard  8501:     if (strstr(model,"v") !=0){
                   8502:       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
                   8503:       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
                   8504:       return 1;
                   8505:     }
1.187     brouard  8506:     strcpy(modelsav,model); 
                   8507:     if ((strpt=strstr(model,"age*age")) !=0){
                   8508:       printf(" strpt=%s, model=%s\n",strpt, model);
                   8509:       if(strpt != model){
1.234     brouard  8510:        printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192     brouard  8511:  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187     brouard  8512:  corresponding column of parameters.\n",model);
1.234     brouard  8513:        fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192     brouard  8514:  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187     brouard  8515:  corresponding column of parameters.\n",model); fflush(ficlog);
1.234     brouard  8516:        return 1;
1.225     brouard  8517:       }
1.187     brouard  8518:       nagesqr=1;
                   8519:       if (strstr(model,"+age*age") !=0)
1.234     brouard  8520:        substrchaine(modelsav, model, "+age*age");
1.187     brouard  8521:       else if (strstr(model,"age*age+") !=0)
1.234     brouard  8522:        substrchaine(modelsav, model, "age*age+");
1.187     brouard  8523:       else 
1.234     brouard  8524:        substrchaine(modelsav, model, "age*age");
1.187     brouard  8525:     }else
                   8526:       nagesqr=0;
                   8527:     if (strlen(modelsav) >1){
                   8528:       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
                   8529:       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224     brouard  8530:       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
1.187     brouard  8531:       cptcovt= j+1; /* Number of total covariates in the model, not including
1.225     brouard  8532:                     * cst, age and age*age 
                   8533:                     * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
                   8534:       /* including age products which are counted in cptcovage.
                   8535:        * but the covariates which are products must be treated 
                   8536:        * separately: ncovn=4- 2=2 (V1+V3). */
1.187     brouard  8537:       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
                   8538:       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
1.225     brouard  8539:       
                   8540:       
1.187     brouard  8541:       /*   Design
                   8542:        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
                   8543:        *  <          ncovcol=8                >
                   8544:        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
                   8545:        *   k=  1    2      3       4     5       6      7        8
                   8546:        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
                   8547:        *  covar[k,i], value of kth covariate if not including age for individual i:
1.224     brouard  8548:        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
                   8549:        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187     brouard  8550:        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
                   8551:        *  Tage[++cptcovage]=k
                   8552:        *       if products, new covar are created after ncovcol with k1
                   8553:        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
                   8554:        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
                   8555:        *  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
                   8556:        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
                   8557:        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
                   8558:        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
                   8559:        *  <          ncovcol=8                >
                   8560:        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
                   8561:        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
                   8562:        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
                   8563:        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
                   8564:        * p Tprod[1]@2={                         6, 5}
                   8565:        *p Tvard[1][1]@4= {7, 8, 5, 6}
                   8566:        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
                   8567:        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   8568:        *How to reorganize?
                   8569:        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
                   8570:        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
                   8571:        *       {2,   1,     4,      8,    5,      6,     3,       7}
                   8572:        * Struct []
                   8573:        */
1.225     brouard  8574:       
1.187     brouard  8575:       /* This loop fills the array Tvar from the string 'model'.*/
                   8576:       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
                   8577:       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
                   8578:       /*       k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
                   8579:       /*       k=3 V4 Tvar[k=3]= 4 (from V4) */
                   8580:       /*       k=2 V1 Tvar[k=2]= 1 (from V1) */
                   8581:       /*       k=1 Tvar[1]=2 (from V2) */
                   8582:       /*       k=5 Tvar[5] */
                   8583:       /* for (k=1; k<=cptcovn;k++) { */
1.198     brouard  8584:       /*       cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187     brouard  8585:       /*       } */
1.198     brouard  8586:       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187     brouard  8587:       /*
                   8588:        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227     brouard  8589:       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
                   8590:         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
                   8591:       }
1.187     brouard  8592:       cptcovage=0;
                   8593:       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234     brouard  8594:        cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
1.225     brouard  8595:                                         modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
1.234     brouard  8596:        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
                   8597:        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
                   8598:        /*scanf("%d",i);*/
                   8599:        if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
                   8600:          cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
                   8601:          if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
                   8602:            /* covar is not filled and then is empty */
                   8603:            cptcovprod--;
                   8604:            cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
                   8605:            Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
                   8606:            Typevar[k]=1;  /* 1 for age product */
                   8607:            cptcovage++; /* Sums the number of covariates which include age as a product */
                   8608:            Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
                   8609:            /*printf("stre=%s ", stre);*/
                   8610:          } else if (strcmp(strd,"age")==0) { /* or age*Vn */
                   8611:            cptcovprod--;
                   8612:            cutl(stre,strb,strc,'V');
                   8613:            Tvar[k]=atoi(stre);
                   8614:            Typevar[k]=1;  /* 1 for age product */
                   8615:            cptcovage++;
                   8616:            Tage[cptcovage]=k;
                   8617:          } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
                   8618:            /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
                   8619:            cptcovn++;
                   8620:            cptcovprodnoage++;k1++;
                   8621:            cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
                   8622:            Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                   8623:                                                because this model-covariate is a construction we invent a new column
                   8624:                                                which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                   8625:                                                If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                   8626:                                                Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
                   8627:            Typevar[k]=2;  /* 2 for double fixed dummy covariates */
                   8628:            cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
                   8629:            Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
                   8630:            Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
                   8631:            Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
                   8632:            Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
                   8633:            k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
                   8634:            /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
                   8635:            /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225     brouard  8636:             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234     brouard  8637:            /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
                   8638:            for (i=1; i<=lastobs;i++){
                   8639:              /* Computes the new covariate which is a product of
                   8640:                 covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                   8641:              covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
                   8642:            }
                   8643:          } /* End age is not in the model */
                   8644:        } /* End if model includes a product */
                   8645:        else { /* no more sum */
                   8646:          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
                   8647:          /*  scanf("%d",i);*/
                   8648:          cutl(strd,strc,strb,'V');
                   8649:          ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
                   8650:          cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
                   8651:          Tvar[k]=atoi(strd);
                   8652:          Typevar[k]=0;  /* 0 for simple covariates */
                   8653:        }
                   8654:        strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
1.223     brouard  8655:                                /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225     brouard  8656:                                  scanf("%d",i);*/
1.187     brouard  8657:       } /* end of loop + on total covariates */
                   8658:     } /* end if strlen(modelsave == 0) age*age might exist */
                   8659:   } /* end if strlen(model == 0) */
1.136     brouard  8660:   
                   8661:   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
                   8662:     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225     brouard  8663:   
1.136     brouard  8664:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225     brouard  8665:      printf("cptcovprod=%d ", cptcovprod);
                   8666:      fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
                   8667:      scanf("%d ",i);*/
                   8668: 
                   8669: 
1.230     brouard  8670: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
                   8671:    of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226     brouard  8672: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
                   8673:    model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
                   8674:    k =           1    2   3     4       5       6      7      8        9
                   8675:    Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
                   8676:    Typevar[k]=   0    0   0     2       1       0      2      1        1
1.227     brouard  8677:    Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
                   8678:    Dummy[k]      1    0   0     0       3       1      1      2        3
                   8679:          Tmodelind[combination of covar]=k;
1.225     brouard  8680: */  
                   8681: /* Dispatching between quantitative and time varying covariates */
1.226     brouard  8682:   /* If Tvar[k] >ncovcol it is a product */
1.225     brouard  8683:   /* 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  8684:        /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227     brouard  8685:   printf("Model=%s\n\
                   8686: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
                   8687: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
                   8688: 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);
                   8689:   fprintf(ficlog,"Model=%s\n\
                   8690: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
                   8691: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
                   8692: 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);
1.240     brouard  8693:   for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234     brouard  8694:   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 */
                   8695:     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227     brouard  8696:       Fixed[k]= 0;
                   8697:       Dummy[k]= 0;
1.225     brouard  8698:       ncoveff++;
1.232     brouard  8699:       ncovf++;
1.234     brouard  8700:       nsd++;
                   8701:       modell[k].maintype= FTYPE;
                   8702:       TvarsD[nsd]=Tvar[k];
                   8703:       TvarsDind[nsd]=k;
                   8704:       TvarF[ncovf]=Tvar[k];
                   8705:       TvarFind[ncovf]=k;
                   8706:       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   8707:       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
                   8708:     }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
                   8709:       Fixed[k]= 0;
                   8710:       Dummy[k]= 0;
                   8711:       ncoveff++;
                   8712:       ncovf++;
                   8713:       modell[k].maintype= FTYPE;
                   8714:       TvarF[ncovf]=Tvar[k];
                   8715:       TvarFind[ncovf]=k;
1.230     brouard  8716:       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231     brouard  8717:       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240     brouard  8718:     }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  8719:       Fixed[k]= 0;
                   8720:       Dummy[k]= 1;
1.230     brouard  8721:       nqfveff++;
1.234     brouard  8722:       modell[k].maintype= FTYPE;
                   8723:       modell[k].subtype= FQ;
                   8724:       nsq++;
                   8725:       TvarsQ[nsq]=Tvar[k];
                   8726:       TvarsQind[nsq]=k;
1.232     brouard  8727:       ncovf++;
1.234     brouard  8728:       TvarF[ncovf]=Tvar[k];
                   8729:       TvarFind[ncovf]=k;
1.231     brouard  8730:       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  8731:       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  8732:     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227     brouard  8733:       Fixed[k]= 1;
                   8734:       Dummy[k]= 0;
1.225     brouard  8735:       ntveff++; /* Only simple time varying dummy variable */
1.234     brouard  8736:       modell[k].maintype= VTYPE;
                   8737:       modell[k].subtype= VD;
                   8738:       nsd++;
                   8739:       TvarsD[nsd]=Tvar[k];
                   8740:       TvarsDind[nsd]=k;
                   8741:       ncovv++; /* Only simple time varying variables */
                   8742:       TvarV[ncovv]=Tvar[k];
1.242     brouard  8743:       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  8744:       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 */
                   8745:       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  8746:       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);
                   8747:       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231     brouard  8748:     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234     brouard  8749:       Fixed[k]= 1;
                   8750:       Dummy[k]= 1;
                   8751:       nqtveff++;
                   8752:       modell[k].maintype= VTYPE;
                   8753:       modell[k].subtype= VQ;
                   8754:       ncovv++; /* Only simple time varying variables */
                   8755:       nsq++;
                   8756:       TvarsQ[nsq]=Tvar[k];
                   8757:       TvarsQind[nsq]=k;
                   8758:       TvarV[ncovv]=Tvar[k];
1.242     brouard  8759:       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  8760:       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 */
                   8761:       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  8762:       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
                   8763:       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
                   8764:       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  8765:       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227     brouard  8766:     }else if (Typevar[k] == 1) {  /* product with age */
1.234     brouard  8767:       ncova++;
                   8768:       TvarA[ncova]=Tvar[k];
                   8769:       TvarAind[ncova]=k;
1.231     brouard  8770:       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240     brouard  8771:        Fixed[k]= 2;
                   8772:        Dummy[k]= 2;
                   8773:        modell[k].maintype= ATYPE;
                   8774:        modell[k].subtype= APFD;
                   8775:        /* ncoveff++; */
1.227     brouard  8776:       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240     brouard  8777:        Fixed[k]= 2;
                   8778:        Dummy[k]= 3;
                   8779:        modell[k].maintype= ATYPE;
                   8780:        modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
                   8781:        /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
1.227     brouard  8782:       }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240     brouard  8783:        Fixed[k]= 3;
                   8784:        Dummy[k]= 2;
                   8785:        modell[k].maintype= ATYPE;
                   8786:        modell[k].subtype= APVD;                /*      Product age * varying dummy */
                   8787:        /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227     brouard  8788:       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240     brouard  8789:        Fixed[k]= 3;
                   8790:        Dummy[k]= 3;
                   8791:        modell[k].maintype= ATYPE;
                   8792:        modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
                   8793:        /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227     brouard  8794:       }
                   8795:     }else if (Typevar[k] == 2) {  /* product without age */
                   8796:       k1=Tposprod[k];
                   8797:       if(Tvard[k1][1] <=ncovcol){
1.240     brouard  8798:        if(Tvard[k1][2] <=ncovcol){
                   8799:          Fixed[k]= 1;
                   8800:          Dummy[k]= 0;
                   8801:          modell[k].maintype= FTYPE;
                   8802:          modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
                   8803:          ncovf++; /* Fixed variables without age */
                   8804:          TvarF[ncovf]=Tvar[k];
                   8805:          TvarFind[ncovf]=k;
                   8806:        }else if(Tvard[k1][2] <=ncovcol+nqv){
                   8807:          Fixed[k]= 0;  /* or 2 ?*/
                   8808:          Dummy[k]= 1;
                   8809:          modell[k].maintype= FTYPE;
                   8810:          modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
                   8811:          ncovf++; /* Varying variables without age */
                   8812:          TvarF[ncovf]=Tvar[k];
                   8813:          TvarFind[ncovf]=k;
                   8814:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   8815:          Fixed[k]= 1;
                   8816:          Dummy[k]= 0;
                   8817:          modell[k].maintype= VTYPE;
                   8818:          modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
                   8819:          ncovv++; /* Varying variables without age */
                   8820:          TvarV[ncovv]=Tvar[k];
                   8821:          TvarVind[ncovv]=k;
                   8822:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   8823:          Fixed[k]= 1;
                   8824:          Dummy[k]= 1;
                   8825:          modell[k].maintype= VTYPE;
                   8826:          modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
                   8827:          ncovv++; /* Varying variables without age */
                   8828:          TvarV[ncovv]=Tvar[k];
                   8829:          TvarVind[ncovv]=k;
                   8830:        }
1.227     brouard  8831:       }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240     brouard  8832:        if(Tvard[k1][2] <=ncovcol){
                   8833:          Fixed[k]= 0;  /* or 2 ?*/
                   8834:          Dummy[k]= 1;
                   8835:          modell[k].maintype= FTYPE;
                   8836:          modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
                   8837:          ncovf++; /* Fixed variables without age */
                   8838:          TvarF[ncovf]=Tvar[k];
                   8839:          TvarFind[ncovf]=k;
                   8840:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   8841:          Fixed[k]= 1;
                   8842:          Dummy[k]= 1;
                   8843:          modell[k].maintype= VTYPE;
                   8844:          modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
                   8845:          ncovv++; /* Varying variables without age */
                   8846:          TvarV[ncovv]=Tvar[k];
                   8847:          TvarVind[ncovv]=k;
                   8848:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   8849:          Fixed[k]= 1;
                   8850:          Dummy[k]= 1;
                   8851:          modell[k].maintype= VTYPE;
                   8852:          modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
                   8853:          ncovv++; /* Varying variables without age */
                   8854:          TvarV[ncovv]=Tvar[k];
                   8855:          TvarVind[ncovv]=k;
                   8856:          ncovv++; /* Varying variables without age */
                   8857:          TvarV[ncovv]=Tvar[k];
                   8858:          TvarVind[ncovv]=k;
                   8859:        }
1.227     brouard  8860:       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240     brouard  8861:        if(Tvard[k1][2] <=ncovcol){
                   8862:          Fixed[k]= 1;
                   8863:          Dummy[k]= 1;
                   8864:          modell[k].maintype= VTYPE;
                   8865:          modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
                   8866:          ncovv++; /* Varying variables without age */
                   8867:          TvarV[ncovv]=Tvar[k];
                   8868:          TvarVind[ncovv]=k;
                   8869:        }else if(Tvard[k1][2] <=ncovcol+nqv){
                   8870:          Fixed[k]= 1;
                   8871:          Dummy[k]= 1;
                   8872:          modell[k].maintype= VTYPE;
                   8873:          modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
                   8874:          ncovv++; /* Varying variables without age */
                   8875:          TvarV[ncovv]=Tvar[k];
                   8876:          TvarVind[ncovv]=k;
                   8877:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   8878:          Fixed[k]= 1;
                   8879:          Dummy[k]= 0;
                   8880:          modell[k].maintype= VTYPE;
                   8881:          modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
                   8882:          ncovv++; /* Varying variables without age */
                   8883:          TvarV[ncovv]=Tvar[k];
                   8884:          TvarVind[ncovv]=k;
                   8885:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   8886:          Fixed[k]= 1;
                   8887:          Dummy[k]= 1;
                   8888:          modell[k].maintype= VTYPE;
                   8889:          modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
                   8890:          ncovv++; /* Varying variables without age */
                   8891:          TvarV[ncovv]=Tvar[k];
                   8892:          TvarVind[ncovv]=k;
                   8893:        }
1.227     brouard  8894:       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240     brouard  8895:        if(Tvard[k1][2] <=ncovcol){
                   8896:          Fixed[k]= 1;
                   8897:          Dummy[k]= 1;
                   8898:          modell[k].maintype= VTYPE;
                   8899:          modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
                   8900:          ncovv++; /* Varying variables without age */
                   8901:          TvarV[ncovv]=Tvar[k];
                   8902:          TvarVind[ncovv]=k;
                   8903:        }else if(Tvard[k1][2] <=ncovcol+nqv){
                   8904:          Fixed[k]= 1;
                   8905:          Dummy[k]= 1;
                   8906:          modell[k].maintype= VTYPE;
                   8907:          modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
                   8908:          ncovv++; /* Varying variables without age */
                   8909:          TvarV[ncovv]=Tvar[k];
                   8910:          TvarVind[ncovv]=k;
                   8911:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                   8912:          Fixed[k]= 1;
                   8913:          Dummy[k]= 1;
                   8914:          modell[k].maintype= VTYPE;
                   8915:          modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
                   8916:          ncovv++; /* Varying variables without age */
                   8917:          TvarV[ncovv]=Tvar[k];
                   8918:          TvarVind[ncovv]=k;
                   8919:        }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
                   8920:          Fixed[k]= 1;
                   8921:          Dummy[k]= 1;
                   8922:          modell[k].maintype= VTYPE;
                   8923:          modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
                   8924:          ncovv++; /* Varying variables without age */
                   8925:          TvarV[ncovv]=Tvar[k];
                   8926:          TvarVind[ncovv]=k;
                   8927:        }
1.227     brouard  8928:       }else{
1.240     brouard  8929:        printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
                   8930:        fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
                   8931:       } /*end k1*/
1.225     brouard  8932:     }else{
1.226     brouard  8933:       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
                   8934:       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  8935:     }
1.227     brouard  8936:     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  8937:     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227     brouard  8938:     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]);
                   8939:   }
                   8940:   /* Searching for doublons in the model */
                   8941:   for(k1=1; k1<= cptcovt;k1++){
                   8942:     for(k2=1; k2 <k1;k2++){
                   8943:       if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
1.234     brouard  8944:        if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
                   8945:          if(Tvar[k1]==Tvar[k2]){
                   8946:            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[Tvar[k1]],Dummy[Tvar[k1]]);
                   8947:            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[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
                   8948:            return(1);
                   8949:          }
                   8950:        }else if (Typevar[k1] ==2){
                   8951:          k3=Tposprod[k1];
                   8952:          k4=Tposprod[k2];
                   8953:          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])) ){
                   8954:            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]]);
                   8955:            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);
                   8956:            return(1);
                   8957:          }
                   8958:        }
1.227     brouard  8959:       }
                   8960:     }
1.225     brouard  8961:   }
                   8962:   printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
                   8963:   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234     brouard  8964:   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
                   8965:   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137     brouard  8966:   return (0); /* with covar[new additional covariate if product] and Tage if age */ 
1.164     brouard  8967:   /*endread:*/
1.225     brouard  8968:   printf("Exiting decodemodel: ");
                   8969:   return (1);
1.136     brouard  8970: }
                   8971: 
1.169     brouard  8972: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248     brouard  8973: {/* Check ages at death */
1.136     brouard  8974:   int i, m;
1.218     brouard  8975:   int firstone=0;
                   8976:   
1.136     brouard  8977:   for (i=1; i<=imx; i++) {
                   8978:     for(m=2; (m<= maxwav); m++) {
                   8979:       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
                   8980:        anint[m][i]=9999;
1.216     brouard  8981:        if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
                   8982:          s[m][i]=-1;
1.136     brouard  8983:       }
                   8984:       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169     brouard  8985:        *nberr = *nberr + 1;
1.218     brouard  8986:        if(firstone == 0){
                   8987:          firstone=1;
                   8988:        printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
                   8989:        }
                   8990:        fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
1.136     brouard  8991:        s[m][i]=-1;
                   8992:       }
                   8993:       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169     brouard  8994:        (*nberr)++;
1.136     brouard  8995:        printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
                   8996:        fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
                   8997:        s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
                   8998:       }
                   8999:     }
                   9000:   }
                   9001: 
                   9002:   for (i=1; i<=imx; i++)  {
                   9003:     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
                   9004:     for(m=firstpass; (m<= lastpass); m++){
1.214     brouard  9005:       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  9006:        if (s[m][i] >= nlstate+1) {
1.169     brouard  9007:          if(agedc[i]>0){
                   9008:            if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136     brouard  9009:              agev[m][i]=agedc[i];
1.214     brouard  9010:              /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169     brouard  9011:            }else {
1.136     brouard  9012:              if ((int)andc[i]!=9999){
                   9013:                nbwarn++;
                   9014:                printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   9015:                fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   9016:                agev[m][i]=-1;
                   9017:              }
                   9018:            }
1.169     brouard  9019:          } /* agedc > 0 */
1.214     brouard  9020:        } /* end if */
1.136     brouard  9021:        else if(s[m][i] !=9){ /* Standard case, age in fractional
                   9022:                                 years but with the precision of a month */
                   9023:          agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
                   9024:          if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
                   9025:            agev[m][i]=1;
                   9026:          else if(agev[m][i] < *agemin){ 
                   9027:            *agemin=agev[m][i];
                   9028:            printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
                   9029:          }
                   9030:          else if(agev[m][i] >*agemax){
                   9031:            *agemax=agev[m][i];
1.156     brouard  9032:            /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136     brouard  9033:          }
                   9034:          /*agev[m][i]=anint[m][i]-annais[i];*/
                   9035:          /*     agev[m][i] = age[i]+2*m;*/
1.214     brouard  9036:        } /* en if 9*/
1.136     brouard  9037:        else { /* =9 */
1.214     brouard  9038:          /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136     brouard  9039:          agev[m][i]=1;
                   9040:          s[m][i]=-1;
                   9041:        }
                   9042:       }
1.214     brouard  9043:       else if(s[m][i]==0) /*= 0 Unknown */
1.136     brouard  9044:        agev[m][i]=1;
1.214     brouard  9045:       else{
                   9046:        printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
                   9047:        fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
                   9048:        agev[m][i]=0;
                   9049:       }
                   9050:     } /* End for lastpass */
                   9051:   }
1.136     brouard  9052:     
                   9053:   for (i=1; i<=imx; i++)  {
                   9054:     for(m=firstpass; (m<=lastpass); m++){
                   9055:       if (s[m][i] > (nlstate+ndeath)) {
1.169     brouard  9056:        (*nberr)++;
1.136     brouard  9057:        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);     
                   9058:        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);     
                   9059:        return 1;
                   9060:       }
                   9061:     }
                   9062:   }
                   9063: 
                   9064:   /*for (i=1; i<=imx; i++){
                   9065:   for (m=firstpass; (m<lastpass); m++){
                   9066:      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
                   9067: }
                   9068: 
                   9069: }*/
                   9070: 
                   9071: 
1.139     brouard  9072:   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
                   9073:   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
1.136     brouard  9074: 
                   9075:   return (0);
1.164     brouard  9076:  /* endread:*/
1.136     brouard  9077:     printf("Exiting calandcheckages: ");
                   9078:     return (1);
                   9079: }
                   9080: 
1.172     brouard  9081: #if defined(_MSC_VER)
                   9082: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
                   9083: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
                   9084: //#include "stdafx.h"
                   9085: //#include <stdio.h>
                   9086: //#include <tchar.h>
                   9087: //#include <windows.h>
                   9088: //#include <iostream>
                   9089: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
                   9090: 
                   9091: LPFN_ISWOW64PROCESS fnIsWow64Process;
                   9092: 
                   9093: BOOL IsWow64()
                   9094: {
                   9095:        BOOL bIsWow64 = FALSE;
                   9096: 
                   9097:        //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
                   9098:        //  (HANDLE, PBOOL);
                   9099: 
                   9100:        //LPFN_ISWOW64PROCESS fnIsWow64Process;
                   9101: 
                   9102:        HMODULE module = GetModuleHandle(_T("kernel32"));
                   9103:        const char funcName[] = "IsWow64Process";
                   9104:        fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   9105:                GetProcAddress(module, funcName);
                   9106: 
                   9107:        if (NULL != fnIsWow64Process)
                   9108:        {
                   9109:                if (!fnIsWow64Process(GetCurrentProcess(),
                   9110:                        &bIsWow64))
                   9111:                        //throw std::exception("Unknown error");
                   9112:                        printf("Unknown error\n");
                   9113:        }
                   9114:        return bIsWow64 != FALSE;
                   9115: }
                   9116: #endif
1.177     brouard  9117: 
1.191     brouard  9118: void syscompilerinfo(int logged)
1.167     brouard  9119:  {
                   9120:    /* #include "syscompilerinfo.h"*/
1.185     brouard  9121:    /* command line Intel compiler 32bit windows, XP compatible:*/
                   9122:    /* /GS /W3 /Gy
                   9123:       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
                   9124:       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
                   9125:       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186     brouard  9126:       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
                   9127:    */ 
                   9128:    /* 64 bits */
1.185     brouard  9129:    /*
                   9130:      /GS /W3 /Gy
                   9131:      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
                   9132:      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
                   9133:      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
                   9134:      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
                   9135:    /* Optimization are useless and O3 is slower than O2 */
                   9136:    /*
                   9137:      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
                   9138:      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
                   9139:      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
                   9140:      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
                   9141:    */
1.186     brouard  9142:    /* Link is */ /* /OUT:"visual studio
1.185     brouard  9143:       2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
                   9144:       /PDB:"visual studio
                   9145:       2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
                   9146:       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
                   9147:       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
                   9148:       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
                   9149:       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
                   9150:       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
                   9151:       uiAccess='false'"
                   9152:       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
                   9153:       /NOLOGO /TLBID:1
                   9154:    */
1.177     brouard  9155: #if defined __INTEL_COMPILER
1.178     brouard  9156: #if defined(__GNUC__)
                   9157:        struct utsname sysInfo;  /* For Intel on Linux and OS/X */
                   9158: #endif
1.177     brouard  9159: #elif defined(__GNUC__) 
1.179     brouard  9160: #ifndef  __APPLE__
1.174     brouard  9161: #include <gnu/libc-version.h>  /* Only on gnu */
1.179     brouard  9162: #endif
1.177     brouard  9163:    struct utsname sysInfo;
1.178     brouard  9164:    int cross = CROSS;
                   9165:    if (cross){
                   9166:           printf("Cross-");
1.191     brouard  9167:           if(logged) fprintf(ficlog, "Cross-");
1.178     brouard  9168:    }
1.174     brouard  9169: #endif
                   9170: 
1.171     brouard  9171: #include <stdint.h>
1.178     brouard  9172: 
1.191     brouard  9173:    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169     brouard  9174: #if defined(__clang__)
1.191     brouard  9175:    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");      /* Clang/LLVM. ---------------------------------------------- */
1.169     brouard  9176: #endif
                   9177: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191     brouard  9178:    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169     brouard  9179: #endif
                   9180: #if defined(__GNUC__) || defined(__GNUG__)
1.191     brouard  9181:    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169     brouard  9182: #endif
                   9183: #if defined(__HP_cc) || defined(__HP_aCC)
1.191     brouard  9184:    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169     brouard  9185: #endif
                   9186: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191     brouard  9187:    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169     brouard  9188: #endif
                   9189: #if defined(_MSC_VER)
1.191     brouard  9190:    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169     brouard  9191: #endif
                   9192: #if defined(__PGI)
1.191     brouard  9193:    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169     brouard  9194: #endif
                   9195: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191     brouard  9196:    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167     brouard  9197: #endif
1.191     brouard  9198:    printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169     brouard  9199:    
1.167     brouard  9200: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
                   9201: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
                   9202:     // Windows (x64 and x86)
1.191     brouard  9203:    printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167     brouard  9204: #elif __unix__ // all unices, not all compilers
                   9205:     // Unix
1.191     brouard  9206:    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167     brouard  9207: #elif __linux__
                   9208:     // linux
1.191     brouard  9209:    printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167     brouard  9210: #elif __APPLE__
1.174     brouard  9211:     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191     brouard  9212:    printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167     brouard  9213: #endif
                   9214: 
                   9215: /*  __MINGW32__          */
                   9216: /*  __CYGWIN__  */
                   9217: /* __MINGW64__  */
                   9218: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
                   9219: /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
                   9220: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
                   9221: /* _WIN64  // Defined for applications for Win64. */
                   9222: /* _M_X64 // Defined for compilations that target x64 processors. */
                   9223: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171     brouard  9224: 
1.167     brouard  9225: #if UINTPTR_MAX == 0xffffffff
1.191     brouard  9226:    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167     brouard  9227: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191     brouard  9228:    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167     brouard  9229: #else
1.191     brouard  9230:    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167     brouard  9231: #endif
                   9232: 
1.169     brouard  9233: #if defined(__GNUC__)
                   9234: # if defined(__GNUC_PATCHLEVEL__)
                   9235: #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                   9236:                             + __GNUC_MINOR__ * 100 \
                   9237:                             + __GNUC_PATCHLEVEL__)
                   9238: # else
                   9239: #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                   9240:                             + __GNUC_MINOR__ * 100)
                   9241: # endif
1.174     brouard  9242:    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191     brouard  9243:    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176     brouard  9244: 
                   9245:    if (uname(&sysInfo) != -1) {
                   9246:      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191     brouard  9247:         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  9248:    }
                   9249:    else
                   9250:       perror("uname() error");
1.179     brouard  9251:    //#ifndef __INTEL_COMPILER 
                   9252: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174     brouard  9253:    printf("GNU libc version: %s\n", gnu_get_libc_version()); 
1.191     brouard  9254:    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177     brouard  9255: #endif
1.169     brouard  9256: #endif
1.172     brouard  9257: 
                   9258:    //   void main()
                   9259:    //   {
1.169     brouard  9260: #if defined(_MSC_VER)
1.174     brouard  9261:    if (IsWow64()){
1.191     brouard  9262:           printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
                   9263:           if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174     brouard  9264:    }
                   9265:    else{
1.191     brouard  9266:           printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
                   9267:           if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174     brouard  9268:    }
1.172     brouard  9269:    //     printf("\nPress Enter to continue...");
                   9270:    //     getchar();
                   9271:    //   }
                   9272: 
1.169     brouard  9273: #endif
                   9274:    
1.167     brouard  9275: 
1.219     brouard  9276: }
1.136     brouard  9277: 
1.219     brouard  9278: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180     brouard  9279:   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
1.235     brouard  9280:   int i, j, k, i1, k4=0, nres=0 ;
1.202     brouard  9281:   /* double ftolpl = 1.e-10; */
1.180     brouard  9282:   double age, agebase, agelim;
1.203     brouard  9283:   double tot;
1.180     brouard  9284: 
1.202     brouard  9285:   strcpy(filerespl,"PL_");
                   9286:   strcat(filerespl,fileresu);
                   9287:   if((ficrespl=fopen(filerespl,"w"))==NULL) {
                   9288:     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
                   9289:     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
                   9290:   }
1.227     brouard  9291:   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
                   9292:   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202     brouard  9293:   pstamp(ficrespl);
1.203     brouard  9294:   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202     brouard  9295:   fprintf(ficrespl,"#Age ");
                   9296:   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
                   9297:   fprintf(ficrespl,"\n");
1.180     brouard  9298:   
1.219     brouard  9299:   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180     brouard  9300: 
1.219     brouard  9301:   agebase=ageminpar;
                   9302:   agelim=agemaxpar;
1.180     brouard  9303: 
1.227     brouard  9304:   /* i1=pow(2,ncoveff); */
1.234     brouard  9305:   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219     brouard  9306:   if (cptcovn < 1){i1=1;}
1.180     brouard  9307: 
1.238     brouard  9308:   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
                   9309:     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   9310:       if(TKresult[nres]!= k)
                   9311:        continue;
1.235     brouard  9312: 
1.238     brouard  9313:       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   9314:       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
                   9315:       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   9316:       /* k=k+1; */
                   9317:       /* to clean */
                   9318:       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
                   9319:       fprintf(ficrespl,"#******");
                   9320:       printf("#******");
                   9321:       fprintf(ficlog,"#******");
                   9322:       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
                   9323:        fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
                   9324:        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9325:        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9326:       }
                   9327:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   9328:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   9329:        fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   9330:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   9331:       }
                   9332:       fprintf(ficrespl,"******\n");
                   9333:       printf("******\n");
                   9334:       fprintf(ficlog,"******\n");
                   9335:       if(invalidvarcomb[k]){
                   9336:        printf("\nCombination (%d) ignored because no case \n",k); 
                   9337:        fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
                   9338:        fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
                   9339:        continue;
                   9340:       }
1.219     brouard  9341: 
1.238     brouard  9342:       fprintf(ficrespl,"#Age ");
                   9343:       for(j=1;j<=cptcoveff;j++) {
                   9344:        fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9345:       }
                   9346:       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
                   9347:       fprintf(ficrespl,"Total Years_to_converge\n");
1.227     brouard  9348:     
1.238     brouard  9349:       for (age=agebase; age<=agelim; age++){
                   9350:        /* for (age=agebase; age<=agebase; age++){ */
                   9351:        prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
                   9352:        fprintf(ficrespl,"%.0f ",age );
                   9353:        for(j=1;j<=cptcoveff;j++)
                   9354:          fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9355:        tot=0.;
                   9356:        for(i=1; i<=nlstate;i++){
                   9357:          tot +=  prlim[i][i];
                   9358:          fprintf(ficrespl," %.5f", prlim[i][i]);
                   9359:        }
                   9360:        fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
                   9361:       } /* Age */
                   9362:       /* was end of cptcod */
                   9363:     } /* cptcov */
                   9364:   } /* nres */
1.219     brouard  9365:   return 0;
1.180     brouard  9366: }
                   9367: 
1.218     brouard  9368: 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){
                   9369:        /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
                   9370:        
                   9371:        /* Computes the back prevalence limit  for any combination      of covariate values 
                   9372:    * at any age between ageminpar and agemaxpar
                   9373:         */
1.235     brouard  9374:   int i, j, k, i1, nres=0 ;
1.217     brouard  9375:   /* double ftolpl = 1.e-10; */
                   9376:   double age, agebase, agelim;
                   9377:   double tot;
1.218     brouard  9378:   /* double ***mobaverage; */
                   9379:   /* double     **dnewm, **doldm, **dsavm;  /\* for use *\/ */
1.217     brouard  9380: 
                   9381:   strcpy(fileresplb,"PLB_");
                   9382:   strcat(fileresplb,fileresu);
                   9383:   if((ficresplb=fopen(fileresplb,"w"))==NULL) {
                   9384:     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
                   9385:     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
                   9386:   }
                   9387:   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
                   9388:   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
                   9389:   pstamp(ficresplb);
                   9390:   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
                   9391:   fprintf(ficresplb,"#Age ");
                   9392:   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
                   9393:   fprintf(ficresplb,"\n");
                   9394:   
1.218     brouard  9395:   
                   9396:   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
                   9397:   
                   9398:   agebase=ageminpar;
                   9399:   agelim=agemaxpar;
                   9400:   
                   9401:   
1.227     brouard  9402:   i1=pow(2,cptcoveff);
1.218     brouard  9403:   if (cptcovn < 1){i1=1;}
1.227     brouard  9404:   
1.238     brouard  9405:   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   9406:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
                   9407:       if(TKresult[nres]!= k)
                   9408:        continue;
                   9409:       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
                   9410:       fprintf(ficresplb,"#******");
                   9411:       printf("#******");
                   9412:       fprintf(ficlog,"#******");
                   9413:       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
                   9414:        fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9415:        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9416:        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9417:       }
                   9418:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   9419:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9420:        fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9421:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9422:       }
                   9423:       fprintf(ficresplb,"******\n");
                   9424:       printf("******\n");
                   9425:       fprintf(ficlog,"******\n");
                   9426:       if(invalidvarcomb[k]){
                   9427:        printf("\nCombination (%d) ignored because no cases \n",k); 
                   9428:        fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
                   9429:        fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
                   9430:        continue;
                   9431:       }
1.218     brouard  9432:     
1.238     brouard  9433:       fprintf(ficresplb,"#Age ");
                   9434:       for(j=1;j<=cptcoveff;j++) {
                   9435:        fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9436:       }
                   9437:       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
                   9438:       fprintf(ficresplb,"Total Years_to_converge\n");
1.218     brouard  9439:     
                   9440:     
1.238     brouard  9441:       for (age=agebase; age<=agelim; age++){
                   9442:        /* for (age=agebase; age<=agebase; age++){ */
                   9443:        if(mobilavproj > 0){
                   9444:          /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
                   9445:          /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242     brouard  9446:          bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238     brouard  9447:        }else if (mobilavproj == 0){
                   9448:          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);
                   9449:          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);
                   9450:          exit(1);
                   9451:        }else{
                   9452:          /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242     brouard  9453:          bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.238     brouard  9454:        }
                   9455:        fprintf(ficresplb,"%.0f ",age );
                   9456:        for(j=1;j<=cptcoveff;j++)
                   9457:          fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9458:        tot=0.;
                   9459:        for(i=1; i<=nlstate;i++){
                   9460:          tot +=  bprlim[i][i];
                   9461:          fprintf(ficresplb," %.5f", bprlim[i][i]);
                   9462:        }
                   9463:        fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
                   9464:       } /* Age */
                   9465:       /* was end of cptcod */
                   9466:     } /* end of any combination */
                   9467:   } /* end of nres */  
1.218     brouard  9468:   /* hBijx(p, bage, fage); */
                   9469:   /* fclose(ficrespijb); */
                   9470:   
                   9471:   return 0;
1.217     brouard  9472: }
1.218     brouard  9473:  
1.180     brouard  9474: int hPijx(double *p, int bage, int fage){
                   9475:     /*------------- h Pij x at various ages ------------*/
                   9476: 
                   9477:   int stepsize;
                   9478:   int agelim;
                   9479:   int hstepm;
                   9480:   int nhstepm;
1.235     brouard  9481:   int h, i, i1, j, k, k4, nres=0;
1.180     brouard  9482: 
                   9483:   double agedeb;
                   9484:   double ***p3mat;
                   9485: 
1.201     brouard  9486:     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
1.180     brouard  9487:     if((ficrespij=fopen(filerespij,"w"))==NULL) {
                   9488:       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
                   9489:       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
                   9490:     }
                   9491:     printf("Computing pij: result on file '%s' \n", filerespij);
                   9492:     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
                   9493:   
                   9494:     stepsize=(int) (stepm+YEARM-1)/YEARM;
                   9495:     /*if (stepm<=24) stepsize=2;*/
                   9496: 
                   9497:     agelim=AGESUP;
                   9498:     hstepm=stepsize*YEARM; /* Every year of age */
                   9499:     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
1.218     brouard  9500:                
1.180     brouard  9501:     /* hstepm=1;   aff par mois*/
                   9502:     pstamp(ficrespij);
                   9503:     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227     brouard  9504:     i1= pow(2,cptcoveff);
1.218     brouard  9505:                /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   9506:                /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                   9507:                /*      k=k+1;  */
1.235     brouard  9508:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   9509:     for(k=1; k<=i1;k++){
                   9510:       if(TKresult[nres]!= k)
                   9511:        continue;
1.183     brouard  9512:       fprintf(ficrespij,"\n#****** ");
1.227     brouard  9513:       for(j=1;j<=cptcoveff;j++) 
1.198     brouard  9514:        fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235     brouard  9515:       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                   9516:        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   9517:        fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                   9518:       }
1.183     brouard  9519:       fprintf(ficrespij,"******\n");
                   9520:       
                   9521:       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
                   9522:        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   9523:        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   9524:        
                   9525:        /*        nhstepm=nhstepm*YEARM; aff par mois*/
1.180     brouard  9526:        
1.183     brouard  9527:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   9528:        oldm=oldms;savm=savms;
1.235     brouard  9529:        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);  
1.183     brouard  9530:        fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
                   9531:        for(i=1; i<=nlstate;i++)
                   9532:          for(j=1; j<=nlstate+ndeath;j++)
                   9533:            fprintf(ficrespij," %1d-%1d",i,j);
                   9534:        fprintf(ficrespij,"\n");
                   9535:        for (h=0; h<=nhstepm; h++){
                   9536:          /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
                   9537:          fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180     brouard  9538:          for(i=1; i<=nlstate;i++)
                   9539:            for(j=1; j<=nlstate+ndeath;j++)
1.183     brouard  9540:              fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180     brouard  9541:          fprintf(ficrespij,"\n");
                   9542:        }
1.183     brouard  9543:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   9544:        fprintf(ficrespij,"\n");
                   9545:       }
1.180     brouard  9546:       /*}*/
                   9547:     }
1.218     brouard  9548:     return 0;
1.180     brouard  9549: }
1.218     brouard  9550:  
                   9551:  int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217     brouard  9552:     /*------------- h Bij x at various ages ------------*/
                   9553: 
                   9554:   int stepsize;
1.218     brouard  9555:   /* int agelim; */
                   9556:        int ageminl;
1.217     brouard  9557:   int hstepm;
                   9558:   int nhstepm;
1.238     brouard  9559:   int h, i, i1, j, k, nres;
1.218     brouard  9560:        
1.217     brouard  9561:   double agedeb;
                   9562:   double ***p3mat;
1.218     brouard  9563:        
                   9564:   strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
                   9565:   if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
                   9566:     printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
                   9567:     fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
                   9568:   }
                   9569:   printf("Computing pij back: result on file '%s' \n", filerespijb);
                   9570:   fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
                   9571:   
                   9572:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   9573:   /*if (stepm<=24) stepsize=2;*/
1.217     brouard  9574:   
1.218     brouard  9575:   /* agelim=AGESUP; */
                   9576:   ageminl=30;
                   9577:   hstepm=stepsize*YEARM; /* Every year of age */
                   9578:   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
                   9579:   
                   9580:   /* hstepm=1;   aff par mois*/
                   9581:   pstamp(ficrespijb);
                   9582:   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227     brouard  9583:   i1= pow(2,cptcoveff);
1.218     brouard  9584:   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   9585:   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                   9586:   /*   k=k+1;  */
1.238     brouard  9587:   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                   9588:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
                   9589:       if(TKresult[nres]!= k)
                   9590:        continue;
                   9591:       fprintf(ficrespijb,"\n#****** ");
                   9592:       for(j=1;j<=cptcoveff;j++)
                   9593:        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   9594:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   9595:        fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   9596:       }
                   9597:       fprintf(ficrespijb,"******\n");
                   9598:       if(invalidvarcomb[k]){
                   9599:        fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
                   9600:        continue;
                   9601:       }
                   9602:       
                   9603:       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
                   9604:       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
                   9605:        /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
                   9606:        nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
                   9607:        nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
                   9608:        
                   9609:        /*        nhstepm=nhstepm*YEARM; aff par mois*/
                   9610:        
                   9611:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   9612:        /* oldm=oldms;savm=savms; */
                   9613:        /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
                   9614:        hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
                   9615:        /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
                   9616:        fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
1.217     brouard  9617:        for(i=1; i<=nlstate;i++)
                   9618:          for(j=1; j<=nlstate+ndeath;j++)
1.238     brouard  9619:            fprintf(ficrespijb," %1d-%1d",i,j);
1.217     brouard  9620:        fprintf(ficrespijb,"\n");
1.238     brouard  9621:        for (h=0; h<=nhstepm; h++){
                   9622:          /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
                   9623:          fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
                   9624:          /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
                   9625:          for(i=1; i<=nlstate;i++)
                   9626:            for(j=1; j<=nlstate+ndeath;j++)
                   9627:              fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
                   9628:          fprintf(ficrespijb,"\n");
                   9629:        }
                   9630:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   9631:        fprintf(ficrespijb,"\n");
                   9632:       } /* end age deb */
                   9633:     } /* end combination */
                   9634:   } /* end nres */
1.218     brouard  9635:   return 0;
                   9636:  } /*  hBijx */
1.217     brouard  9637: 
1.180     brouard  9638: 
1.136     brouard  9639: /***********************************************/
                   9640: /**************** Main Program *****************/
                   9641: /***********************************************/
                   9642: 
                   9643: int main(int argc, char *argv[])
                   9644: {
                   9645: #ifdef GSL
                   9646:   const gsl_multimin_fminimizer_type *T;
                   9647:   size_t iteri = 0, it;
                   9648:   int rval = GSL_CONTINUE;
                   9649:   int status = GSL_SUCCESS;
                   9650:   double ssval;
                   9651: #endif
                   9652:   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164     brouard  9653:   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209     brouard  9654:   int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164     brouard  9655:   int jj, ll, li, lj, lk;
1.136     brouard  9656:   int numlinepar=0; /* Current linenumber of parameter file */
1.197     brouard  9657:   int num_filled;
1.136     brouard  9658:   int itimes;
                   9659:   int NDIM=2;
                   9660:   int vpopbased=0;
1.235     brouard  9661:   int nres=0;
1.136     brouard  9662: 
1.164     brouard  9663:   char ca[32], cb[32];
1.136     brouard  9664:   /*  FILE *fichtm; *//* Html File */
                   9665:   /* FILE *ficgp;*/ /*Gnuplot File */
                   9666:   struct stat info;
1.191     brouard  9667:   double agedeb=0.;
1.194     brouard  9668: 
                   9669:   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219     brouard  9670:   double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136     brouard  9671: 
1.165     brouard  9672:   double fret;
1.191     brouard  9673:   double dum=0.; /* Dummy variable */
1.136     brouard  9674:   double ***p3mat;
1.218     brouard  9675:   /* double ***mobaverage; */
1.164     brouard  9676: 
                   9677:   char line[MAXLINE];
1.197     brouard  9678:   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
                   9679: 
1.234     brouard  9680:   char  modeltemp[MAXLINE];
1.230     brouard  9681:   char resultline[MAXLINE];
                   9682:   
1.136     brouard  9683:   char pathr[MAXLINE], pathimach[MAXLINE]; 
1.164     brouard  9684:   char *tok, *val; /* pathtot */
1.136     brouard  9685:   int firstobs=1, lastobs=10;
1.195     brouard  9686:   int c,  h , cpt, c2;
1.191     brouard  9687:   int jl=0;
                   9688:   int i1, j1, jk, stepsize=0;
1.194     brouard  9689:   int count=0;
                   9690: 
1.164     brouard  9691:   int *tab; 
1.136     brouard  9692:   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217     brouard  9693:   int backcast=0;
1.136     brouard  9694:   int mobilav=0,popforecast=0;
1.191     brouard  9695:   int hstepm=0, nhstepm=0;
1.136     brouard  9696:   int agemortsup;
                   9697:   float  sumlpop=0.;
                   9698:   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
                   9699:   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
                   9700: 
1.191     brouard  9701:   double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136     brouard  9702:   double ftolpl=FTOL;
                   9703:   double **prlim;
1.217     brouard  9704:   double **bprlim;
1.136     brouard  9705:   double ***param; /* Matrix of parameters */
1.251     brouard  9706:   double ***paramstart; /* Matrix of starting parameter values */
                   9707:   double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136     brouard  9708:   double **matcov; /* Matrix of covariance */
1.203     brouard  9709:   double **hess; /* Hessian matrix */
1.136     brouard  9710:   double ***delti3; /* Scale */
                   9711:   double *delti; /* Scale */
                   9712:   double ***eij, ***vareij;
                   9713:   double **varpl; /* Variances of prevalence limits by age */
                   9714:   double *epj, vepp;
1.164     brouard  9715: 
1.136     brouard  9716:   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217     brouard  9717:   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
                   9718: 
1.136     brouard  9719:   double **ximort;
1.145     brouard  9720:   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136     brouard  9721:   int *dcwave;
                   9722: 
1.164     brouard  9723:   char z[1]="c";
1.136     brouard  9724: 
                   9725:   /*char  *strt;*/
                   9726:   char strtend[80];
1.126     brouard  9727: 
1.164     brouard  9728: 
1.126     brouard  9729: /*   setlocale (LC_ALL, ""); */
                   9730: /*   bindtextdomain (PACKAGE, LOCALEDIR); */
                   9731: /*   textdomain (PACKAGE); */
                   9732: /*   setlocale (LC_CTYPE, ""); */
                   9733: /*   setlocale (LC_MESSAGES, ""); */
                   9734: 
                   9735:   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157     brouard  9736:   rstart_time = time(NULL);  
                   9737:   /*  (void) gettimeofday(&start_time,&tzp);*/
                   9738:   start_time = *localtime(&rstart_time);
1.126     brouard  9739:   curr_time=start_time;
1.157     brouard  9740:   /*tml = *localtime(&start_time.tm_sec);*/
                   9741:   /* strcpy(strstart,asctime(&tml)); */
                   9742:   strcpy(strstart,asctime(&start_time));
1.126     brouard  9743: 
                   9744: /*  printf("Localtime (at start)=%s",strstart); */
1.157     brouard  9745: /*  tp.tm_sec = tp.tm_sec +86400; */
                   9746: /*  tm = *localtime(&start_time.tm_sec); */
1.126     brouard  9747: /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
                   9748: /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
                   9749: /*   tmg.tm_hour=tmg.tm_hour + 1; */
1.157     brouard  9750: /*   tp.tm_sec = mktime(&tmg); */
1.126     brouard  9751: /*   strt=asctime(&tmg); */
                   9752: /*   printf("Time(after) =%s",strstart);  */
                   9753: /*  (void) time (&time_value);
                   9754: *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
                   9755: *  tm = *localtime(&time_value);
                   9756: *  strstart=asctime(&tm);
                   9757: *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
                   9758: */
                   9759: 
                   9760:   nberr=0; /* Number of errors and warnings */
                   9761:   nbwarn=0;
1.184     brouard  9762: #ifdef WIN32
                   9763:   _getcwd(pathcd, size);
                   9764: #else
1.126     brouard  9765:   getcwd(pathcd, size);
1.184     brouard  9766: #endif
1.191     brouard  9767:   syscompilerinfo(0);
1.196     brouard  9768:   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126     brouard  9769:   if(argc <=1){
                   9770:     printf("\nEnter the parameter file name: ");
1.205     brouard  9771:     if(!fgets(pathr,FILENAMELENGTH,stdin)){
                   9772:       printf("ERROR Empty parameter file name\n");
                   9773:       goto end;
                   9774:     }
1.126     brouard  9775:     i=strlen(pathr);
                   9776:     if(pathr[i-1]=='\n')
                   9777:       pathr[i-1]='\0';
1.156     brouard  9778:     i=strlen(pathr);
1.205     brouard  9779:     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156     brouard  9780:       pathr[i-1]='\0';
1.205     brouard  9781:     }
                   9782:     i=strlen(pathr);
                   9783:     if( i==0 ){
                   9784:       printf("ERROR Empty parameter file name\n");
                   9785:       goto end;
                   9786:     }
                   9787:     for (tok = pathr; tok != NULL; ){
1.126     brouard  9788:       printf("Pathr |%s|\n",pathr);
                   9789:       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
                   9790:       printf("val= |%s| pathr=%s\n",val,pathr);
                   9791:       strcpy (pathtot, val);
                   9792:       if(pathr[0] == '\0') break; /* Dirty */
                   9793:     }
                   9794:   }
                   9795:   else{
                   9796:     strcpy(pathtot,argv[1]);
                   9797:   }
                   9798:   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
                   9799:   /*cygwin_split_path(pathtot,path,optionfile);
                   9800:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
                   9801:   /* cutv(path,optionfile,pathtot,'\\');*/
                   9802: 
                   9803:   /* Split argv[0], imach program to get pathimach */
                   9804:   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
                   9805:   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   9806:   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   9807:  /*   strcpy(pathimach,argv[0]); */
                   9808:   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
                   9809:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
                   9810:   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184     brouard  9811: #ifdef WIN32
                   9812:   _chdir(path); /* Can be a relative path */
                   9813:   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
                   9814: #else
1.126     brouard  9815:   chdir(path); /* Can be a relative path */
1.184     brouard  9816:   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
                   9817: #endif
                   9818:   printf("Current directory %s!\n",pathcd);
1.126     brouard  9819:   strcpy(command,"mkdir ");
                   9820:   strcat(command,optionfilefiname);
                   9821:   if((outcmd=system(command)) != 0){
1.169     brouard  9822:     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126     brouard  9823:     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
                   9824:     /* fclose(ficlog); */
                   9825: /*     exit(1); */
                   9826:   }
                   9827: /*   if((imk=mkdir(optionfilefiname))<0){ */
                   9828: /*     perror("mkdir"); */
                   9829: /*   } */
                   9830: 
                   9831:   /*-------- arguments in the command line --------*/
                   9832: 
1.186     brouard  9833:   /* Main Log file */
1.126     brouard  9834:   strcat(filelog, optionfilefiname);
                   9835:   strcat(filelog,".log");    /* */
                   9836:   if((ficlog=fopen(filelog,"w"))==NULL)    {
                   9837:     printf("Problem with logfile %s\n",filelog);
                   9838:     goto end;
                   9839:   }
                   9840:   fprintf(ficlog,"Log filename:%s\n",filelog);
1.197     brouard  9841:   fprintf(ficlog,"Version %s %s",version,fullversion);
1.126     brouard  9842:   fprintf(ficlog,"\nEnter the parameter file name: \n");
                   9843:   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
                   9844:  path=%s \n\
                   9845:  optionfile=%s\n\
                   9846:  optionfilext=%s\n\
1.156     brouard  9847:  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126     brouard  9848: 
1.197     brouard  9849:   syscompilerinfo(1);
1.167     brouard  9850: 
1.126     brouard  9851:   printf("Local time (at start):%s",strstart);
                   9852:   fprintf(ficlog,"Local time (at start): %s",strstart);
                   9853:   fflush(ficlog);
                   9854: /*   (void) gettimeofday(&curr_time,&tzp); */
1.157     brouard  9855: /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126     brouard  9856: 
                   9857:   /* */
                   9858:   strcpy(fileres,"r");
                   9859:   strcat(fileres, optionfilefiname);
1.201     brouard  9860:   strcat(fileresu, optionfilefiname); /* Without r in front */
1.126     brouard  9861:   strcat(fileres,".txt");    /* Other files have txt extension */
1.201     brouard  9862:   strcat(fileresu,".txt");    /* Other files have txt extension */
1.126     brouard  9863: 
1.186     brouard  9864:   /* Main ---------arguments file --------*/
1.126     brouard  9865: 
                   9866:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
1.155     brouard  9867:     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
                   9868:     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126     brouard  9869:     fflush(ficlog);
1.149     brouard  9870:     /* goto end; */
                   9871:     exit(70); 
1.126     brouard  9872:   }
                   9873: 
                   9874: 
                   9875: 
                   9876:   strcpy(filereso,"o");
1.201     brouard  9877:   strcat(filereso,fileresu);
1.126     brouard  9878:   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
                   9879:     printf("Problem with Output resultfile: %s\n", filereso);
                   9880:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
                   9881:     fflush(ficlog);
                   9882:     goto end;
                   9883:   }
                   9884: 
                   9885:   /* Reads comments: lines beginning with '#' */
                   9886:   numlinepar=0;
1.197     brouard  9887: 
                   9888:     /* First parameter line */
                   9889:   while(fgets(line, MAXLINE, ficpar)) {
                   9890:     /* If line starts with a # it is a comment */
                   9891:     if (line[0] == '#') {
                   9892:       numlinepar++;
                   9893:       fputs(line,stdout);
                   9894:       fputs(line,ficparo);
                   9895:       fputs(line,ficlog);
                   9896:       continue;
                   9897:     }else
                   9898:       break;
                   9899:   }
                   9900:   if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                   9901:                        title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
                   9902:     if (num_filled != 5) {
                   9903:       printf("Should be 5 parameters\n");
                   9904:     }
1.126     brouard  9905:     numlinepar++;
1.197     brouard  9906:     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
                   9907:   }
                   9908:   /* Second parameter line */
                   9909:   while(fgets(line, MAXLINE, ficpar)) {
                   9910:     /* If line starts with a # it is a comment */
                   9911:     if (line[0] == '#') {
                   9912:       numlinepar++;
                   9913:       fputs(line,stdout);
                   9914:       fputs(line,ficparo);
                   9915:       fputs(line,ficlog);
                   9916:       continue;
                   9917:     }else
                   9918:       break;
                   9919:   }
1.223     brouard  9920:   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", \
                   9921:                        &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
                   9922:     if (num_filled != 11) {
                   9923:       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  9924:       printf("but line=%s\n",line);
1.197     brouard  9925:     }
1.223     brouard  9926:     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);
1.126     brouard  9927:   }
1.203     brouard  9928:   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209     brouard  9929:   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197     brouard  9930:   /* Third parameter line */
                   9931:   while(fgets(line, MAXLINE, ficpar)) {
                   9932:     /* If line starts with a # it is a comment */
                   9933:     if (line[0] == '#') {
                   9934:       numlinepar++;
                   9935:       fputs(line,stdout);
                   9936:       fputs(line,ficparo);
                   9937:       fputs(line,ficlog);
                   9938:       continue;
                   9939:     }else
                   9940:       break;
                   9941:   }
1.201     brouard  9942:   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
                   9943:     if (num_filled == 0)
                   9944:             model[0]='\0';
                   9945:     else if (num_filled != 1){
1.197     brouard  9946:       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
                   9947:       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
                   9948:       model[0]='\0';
                   9949:       goto end;
                   9950:     }
                   9951:     else{
                   9952:       if (model[0]=='+'){
                   9953:        for(i=1; i<=strlen(model);i++)
                   9954:          modeltemp[i-1]=model[i];
1.201     brouard  9955:        strcpy(model,modeltemp); 
1.197     brouard  9956:       }
                   9957:     }
1.199     brouard  9958:     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203     brouard  9959:     printf("model=1+age+%s\n",model);fflush(stdout);
1.197     brouard  9960:   }
                   9961:   /* 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); */
                   9962:   /* numlinepar=numlinepar+3; /\* In general *\/ */
                   9963:   /* 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); */
1.223     brouard  9964:   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);
                   9965:   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  9966:   fflush(ficlog);
1.190     brouard  9967:   /* if(model[0]=='#'|| model[0]== '\0'){ */
                   9968:   if(model[0]=='#'){
1.187     brouard  9969:     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
                   9970:  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
                   9971:  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");         \
                   9972:     if(mle != -1){
                   9973:       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
                   9974:       exit(1);
                   9975:     }
                   9976:   }
1.126     brouard  9977:   while((c=getc(ficpar))=='#' && c!= EOF){
                   9978:     ungetc(c,ficpar);
                   9979:     fgets(line, MAXLINE, ficpar);
                   9980:     numlinepar++;
1.195     brouard  9981:     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
                   9982:       z[0]=line[1];
                   9983:     }
                   9984:     /* printf("****line [1] = %c \n",line[1]); */
1.141     brouard  9985:     fputs(line, stdout);
                   9986:     //puts(line);
1.126     brouard  9987:     fputs(line,ficparo);
                   9988:     fputs(line,ficlog);
                   9989:   }
                   9990:   ungetc(c,ficpar);
                   9991: 
                   9992:    
1.145     brouard  9993:   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
1.225     brouard  9994:   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
1.233     brouard  9995:   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
1.225     brouard  9996:   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
1.136     brouard  9997:   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
                   9998:   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
                   9999:      v1+v2*age+v2*v3 makes cptcovn = 3
                   10000:   */
                   10001:   if (strlen(model)>1) 
1.187     brouard  10002:     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  10003:   else
1.187     brouard  10004:     ncovmodel=2; /* Constant and age */
1.133     brouard  10005:   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
                   10006:   npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131     brouard  10007:   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
                   10008:     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);
                   10009:     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);
                   10010:     fflush(stdout);
                   10011:     fclose (ficlog);
                   10012:     goto end;
                   10013:   }
1.126     brouard  10014:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   10015:   delti=delti3[1][1];
                   10016:   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
                   10017:   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247     brouard  10018: /* We could also provide initial parameters values giving by simple logistic regression 
                   10019:  * only one way, that is without matrix product. We will have nlstate maximizations */
                   10020:       /* for(i=1;i<nlstate;i++){ */
                   10021:       /*       /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
                   10022:       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
                   10023:       /* } */
1.126     brouard  10024:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191     brouard  10025:     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   10026:     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126     brouard  10027:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   10028:     fclose (ficparo);
                   10029:     fclose (ficlog);
                   10030:     goto end;
                   10031:     exit(0);
1.220     brouard  10032:   }  else if(mle==-5) { /* Main Wizard */
1.126     brouard  10033:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192     brouard  10034:     printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
                   10035:     fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126     brouard  10036:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   10037:     matcov=matrix(1,npar,1,npar);
1.203     brouard  10038:     hess=matrix(1,npar,1,npar);
1.220     brouard  10039:   }  else{ /* Begin of mle != -1 or -5 */
1.145     brouard  10040:     /* Read guessed parameters */
1.126     brouard  10041:     /* Reads comments: lines beginning with '#' */
                   10042:     while((c=getc(ficpar))=='#' && c!= EOF){
                   10043:       ungetc(c,ficpar);
                   10044:       fgets(line, MAXLINE, ficpar);
                   10045:       numlinepar++;
1.141     brouard  10046:       fputs(line,stdout);
1.126     brouard  10047:       fputs(line,ficparo);
                   10048:       fputs(line,ficlog);
                   10049:     }
                   10050:     ungetc(c,ficpar);
                   10051:     
                   10052:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251     brouard  10053:     paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126     brouard  10054:     for(i=1; i <=nlstate; i++){
1.234     brouard  10055:       j=0;
1.126     brouard  10056:       for(jj=1; jj <=nlstate+ndeath; jj++){
1.234     brouard  10057:        if(jj==i) continue;
                   10058:        j++;
                   10059:        fscanf(ficpar,"%1d%1d",&i1,&j1);
                   10060:        if ((i1 != i) || (j1 != jj)){
                   10061:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126     brouard  10062: It might be a problem of design; if ncovcol and the model are correct\n \
                   10063: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234     brouard  10064:          exit(1);
                   10065:        }
                   10066:        fprintf(ficparo,"%1d%1d",i1,j1);
                   10067:        if(mle==1)
                   10068:          printf("%1d%1d",i,jj);
                   10069:        fprintf(ficlog,"%1d%1d",i,jj);
                   10070:        for(k=1; k<=ncovmodel;k++){
                   10071:          fscanf(ficpar," %lf",&param[i][j][k]);
                   10072:          if(mle==1){
                   10073:            printf(" %lf",param[i][j][k]);
                   10074:            fprintf(ficlog," %lf",param[i][j][k]);
                   10075:          }
                   10076:          else
                   10077:            fprintf(ficlog," %lf",param[i][j][k]);
                   10078:          fprintf(ficparo," %lf",param[i][j][k]);
                   10079:        }
                   10080:        fscanf(ficpar,"\n");
                   10081:        numlinepar++;
                   10082:        if(mle==1)
                   10083:          printf("\n");
                   10084:        fprintf(ficlog,"\n");
                   10085:        fprintf(ficparo,"\n");
1.126     brouard  10086:       }
                   10087:     }  
                   10088:     fflush(ficlog);
1.234     brouard  10089:     
1.251     brouard  10090:     /* Reads parameters values */
1.126     brouard  10091:     p=param[1][1];
1.251     brouard  10092:     pstart=paramstart[1][1];
1.126     brouard  10093:     
                   10094:     /* Reads comments: lines beginning with '#' */
                   10095:     while((c=getc(ficpar))=='#' && c!= EOF){
                   10096:       ungetc(c,ficpar);
                   10097:       fgets(line, MAXLINE, ficpar);
                   10098:       numlinepar++;
1.141     brouard  10099:       fputs(line,stdout);
1.126     brouard  10100:       fputs(line,ficparo);
                   10101:       fputs(line,ficlog);
                   10102:     }
                   10103:     ungetc(c,ficpar);
                   10104: 
                   10105:     for(i=1; i <=nlstate; i++){
                   10106:       for(j=1; j <=nlstate+ndeath-1; j++){
1.234     brouard  10107:        fscanf(ficpar,"%1d%1d",&i1,&j1);
                   10108:        if ( (i1-i) * (j1-j) != 0){
                   10109:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   10110:          exit(1);
                   10111:        }
                   10112:        printf("%1d%1d",i,j);
                   10113:        fprintf(ficparo,"%1d%1d",i1,j1);
                   10114:        fprintf(ficlog,"%1d%1d",i1,j1);
                   10115:        for(k=1; k<=ncovmodel;k++){
                   10116:          fscanf(ficpar,"%le",&delti3[i][j][k]);
                   10117:          printf(" %le",delti3[i][j][k]);
                   10118:          fprintf(ficparo," %le",delti3[i][j][k]);
                   10119:          fprintf(ficlog," %le",delti3[i][j][k]);
                   10120:        }
                   10121:        fscanf(ficpar,"\n");
                   10122:        numlinepar++;
                   10123:        printf("\n");
                   10124:        fprintf(ficparo,"\n");
                   10125:        fprintf(ficlog,"\n");
1.126     brouard  10126:       }
                   10127:     }
                   10128:     fflush(ficlog);
1.234     brouard  10129:     
1.145     brouard  10130:     /* Reads covariance matrix */
1.126     brouard  10131:     delti=delti3[1][1];
1.220     brouard  10132:                
                   10133:                
1.126     brouard  10134:     /* 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  10135:                
1.126     brouard  10136:     /* Reads comments: lines beginning with '#' */
                   10137:     while((c=getc(ficpar))=='#' && c!= EOF){
                   10138:       ungetc(c,ficpar);
                   10139:       fgets(line, MAXLINE, ficpar);
                   10140:       numlinepar++;
1.141     brouard  10141:       fputs(line,stdout);
1.126     brouard  10142:       fputs(line,ficparo);
                   10143:       fputs(line,ficlog);
                   10144:     }
                   10145:     ungetc(c,ficpar);
1.220     brouard  10146:                
1.126     brouard  10147:     matcov=matrix(1,npar,1,npar);
1.203     brouard  10148:     hess=matrix(1,npar,1,npar);
1.131     brouard  10149:     for(i=1; i <=npar; i++)
                   10150:       for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220     brouard  10151:                
1.194     brouard  10152:     /* Scans npar lines */
1.126     brouard  10153:     for(i=1; i <=npar; i++){
1.226     brouard  10154:       count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194     brouard  10155:       if(count != 3){
1.226     brouard  10156:        printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194     brouard  10157: This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
                   10158: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226     brouard  10159:        fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194     brouard  10160: This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
                   10161: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226     brouard  10162:        exit(1);
1.220     brouard  10163:       }else{
1.226     brouard  10164:        if(mle==1)
                   10165:          printf("%1d%1d%d",i1,j1,jk);
                   10166:       }
                   10167:       fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
                   10168:       fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126     brouard  10169:       for(j=1; j <=i; j++){
1.226     brouard  10170:        fscanf(ficpar," %le",&matcov[i][j]);
                   10171:        if(mle==1){
                   10172:          printf(" %.5le",matcov[i][j]);
                   10173:        }
                   10174:        fprintf(ficlog," %.5le",matcov[i][j]);
                   10175:        fprintf(ficparo," %.5le",matcov[i][j]);
1.126     brouard  10176:       }
                   10177:       fscanf(ficpar,"\n");
                   10178:       numlinepar++;
                   10179:       if(mle==1)
1.220     brouard  10180:                                printf("\n");
1.126     brouard  10181:       fprintf(ficlog,"\n");
                   10182:       fprintf(ficparo,"\n");
                   10183:     }
1.194     brouard  10184:     /* End of read covariance matrix npar lines */
1.126     brouard  10185:     for(i=1; i <=npar; i++)
                   10186:       for(j=i+1;j<=npar;j++)
1.226     brouard  10187:        matcov[i][j]=matcov[j][i];
1.126     brouard  10188:     
                   10189:     if(mle==1)
                   10190:       printf("\n");
                   10191:     fprintf(ficlog,"\n");
                   10192:     
                   10193:     fflush(ficlog);
                   10194:     
                   10195:     /*-------- Rewriting parameter file ----------*/
                   10196:     strcpy(rfileres,"r");    /* "Rparameterfile */
                   10197:     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
                   10198:     strcat(rfileres,".");    /* */
                   10199:     strcat(rfileres,optionfilext);    /* Other files have txt extension */
                   10200:     if((ficres =fopen(rfileres,"w"))==NULL) {
1.201     brouard  10201:       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
                   10202:       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126     brouard  10203:     }
                   10204:     fprintf(ficres,"#%s\n",version);
                   10205:   }    /* End of mle != -3 */
1.218     brouard  10206:   
1.186     brouard  10207:   /*  Main data
                   10208:    */
1.126     brouard  10209:   n= lastobs;
                   10210:   num=lvector(1,n);
                   10211:   moisnais=vector(1,n);
                   10212:   annais=vector(1,n);
                   10213:   moisdc=vector(1,n);
                   10214:   andc=vector(1,n);
1.220     brouard  10215:   weight=vector(1,n);
1.126     brouard  10216:   agedc=vector(1,n);
                   10217:   cod=ivector(1,n);
1.220     brouard  10218:   for(i=1;i<=n;i++){
1.234     brouard  10219:     num[i]=0;
                   10220:     moisnais[i]=0;
                   10221:     annais[i]=0;
                   10222:     moisdc[i]=0;
                   10223:     andc[i]=0;
                   10224:     agedc[i]=0;
                   10225:     cod[i]=0;
                   10226:     weight[i]=1.0; /* Equal weights, 1 by default */
                   10227:   }
1.126     brouard  10228:   mint=matrix(1,maxwav,1,n);
                   10229:   anint=matrix(1,maxwav,1,n);
1.131     brouard  10230:   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
1.126     brouard  10231:   tab=ivector(1,NCOVMAX);
1.144     brouard  10232:   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192     brouard  10233:   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  10234: 
1.136     brouard  10235:   /* Reads data from file datafile */
                   10236:   if (readdata(datafile, firstobs, lastobs, &imx)==1)
                   10237:     goto end;
                   10238: 
                   10239:   /* Calculation of the number of parameters from char model */
1.234     brouard  10240:   /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
1.137     brouard  10241:        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
                   10242:        k=3 V4 Tvar[k=3]= 4 (from V4)
                   10243:        k=2 V1 Tvar[k=2]= 1 (from V1)
                   10244:        k=1 Tvar[1]=2 (from V2)
1.234     brouard  10245:   */
                   10246:   
                   10247:   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
                   10248:   TvarsDind=ivector(1,NCOVMAX); /*  */
                   10249:   TvarsD=ivector(1,NCOVMAX); /*  */
                   10250:   TvarsQind=ivector(1,NCOVMAX); /*  */
                   10251:   TvarsQ=ivector(1,NCOVMAX); /*  */
1.232     brouard  10252:   TvarF=ivector(1,NCOVMAX); /*  */
                   10253:   TvarFind=ivector(1,NCOVMAX); /*  */
                   10254:   TvarV=ivector(1,NCOVMAX); /*  */
                   10255:   TvarVind=ivector(1,NCOVMAX); /*  */
                   10256:   TvarA=ivector(1,NCOVMAX); /*  */
                   10257:   TvarAind=ivector(1,NCOVMAX); /*  */
1.231     brouard  10258:   TvarFD=ivector(1,NCOVMAX); /*  */
                   10259:   TvarFDind=ivector(1,NCOVMAX); /*  */
                   10260:   TvarFQ=ivector(1,NCOVMAX); /*  */
                   10261:   TvarFQind=ivector(1,NCOVMAX); /*  */
                   10262:   TvarVD=ivector(1,NCOVMAX); /*  */
                   10263:   TvarVDind=ivector(1,NCOVMAX); /*  */
                   10264:   TvarVQ=ivector(1,NCOVMAX); /*  */
                   10265:   TvarVQind=ivector(1,NCOVMAX); /*  */
                   10266: 
1.230     brouard  10267:   Tvalsel=vector(1,NCOVMAX); /*  */
1.233     brouard  10268:   Tvarsel=ivector(1,NCOVMAX); /*  */
1.226     brouard  10269:   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
                   10270:   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
                   10271:   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137     brouard  10272:   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
                   10273:       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
                   10274:       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
                   10275:   */
                   10276:   /* For model-covariate k tells which data-covariate to use but
                   10277:     because this model-covariate is a construction we invent a new column
                   10278:     ncovcol + k1
                   10279:     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
                   10280:     Tvar[3=V1*V4]=4+1 etc */
1.227     brouard  10281:   Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
                   10282:   Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137     brouard  10283:   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
                   10284:      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
1.227     brouard  10285:      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
1.137     brouard  10286:   */
1.145     brouard  10287:   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
                   10288:   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  10289:                            * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                   10290:                            * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145     brouard  10291:   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137     brouard  10292:                         4 covariates (3 plus signs)
                   10293:                         Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                   10294:                      */  
1.230     brouard  10295:   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227     brouard  10296:                                * individual dummy, fixed or varying:
                   10297:                                * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                   10298:                                * 3, 1, 0, 0, 0, 0, 0, 0},
1.230     brouard  10299:                                * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , 
                   10300:                                * V1 df, V2 qf, V3 & V4 dv, V5 qv
                   10301:                                * Tmodelind[1]@9={9,0,3,2,}*/
                   10302:   TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
                   10303:   TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228     brouard  10304:                                * individual quantitative, fixed or varying:
                   10305:                                * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                   10306:                                * 3, 1, 0, 0, 0, 0, 0, 0},
                   10307:                                * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186     brouard  10308: /* Main decodemodel */
                   10309: 
1.187     brouard  10310: 
1.223     brouard  10311:   if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
1.136     brouard  10312:     goto end;
                   10313: 
1.137     brouard  10314:   if((double)(lastobs-imx)/(double)imx > 1.10){
                   10315:     nbwarn++;
                   10316:     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); 
                   10317:     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); 
                   10318:   }
1.136     brouard  10319:     /*  if(mle==1){*/
1.137     brouard  10320:   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
                   10321:     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136     brouard  10322:   }
                   10323: 
                   10324:     /*-calculation of age at interview from date of interview and age at death -*/
                   10325:   agev=matrix(1,maxwav,1,imx);
                   10326: 
                   10327:   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
                   10328:     goto end;
                   10329: 
1.126     brouard  10330: 
1.136     brouard  10331:   agegomp=(int)agemin;
                   10332:   free_vector(moisnais,1,n);
                   10333:   free_vector(annais,1,n);
1.126     brouard  10334:   /* free_matrix(mint,1,maxwav,1,n);
                   10335:      free_matrix(anint,1,maxwav,1,n);*/
1.215     brouard  10336:   /* free_vector(moisdc,1,n); */
                   10337:   /* free_vector(andc,1,n); */
1.145     brouard  10338:   /* */
                   10339:   
1.126     brouard  10340:   wav=ivector(1,imx);
1.214     brouard  10341:   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
                   10342:   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
                   10343:   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
                   10344:   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.*/
                   10345:   bh=imatrix(1,lastpass-firstpass+2,1,imx);
                   10346:   mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126     brouard  10347:    
                   10348:   /* Concatenates waves */
1.214     brouard  10349:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   10350:      Death is a valid wave (if date is known).
                   10351:      mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
                   10352:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   10353:      and mw[mi+1][i]. dh depends on stepm.
                   10354:   */
                   10355: 
1.126     brouard  10356:   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
1.248     brouard  10357:   /* Concatenates waves */
1.145     brouard  10358:  
1.215     brouard  10359:   free_vector(moisdc,1,n);
                   10360:   free_vector(andc,1,n);
                   10361: 
1.126     brouard  10362:   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
                   10363:   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
                   10364:   ncodemax[1]=1;
1.145     brouard  10365:   Ndum =ivector(-1,NCOVMAX);  
1.225     brouard  10366:   cptcoveff=0;
1.220     brouard  10367:   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
                   10368:     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227     brouard  10369:   }
                   10370:   
                   10371:   ncovcombmax=pow(2,cptcoveff);
                   10372:   invalidvarcomb=ivector(1, ncovcombmax); 
                   10373:   for(i=1;i<ncovcombmax;i++)
                   10374:     invalidvarcomb[i]=0;
                   10375:   
1.211     brouard  10376:   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186     brouard  10377:      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211     brouard  10378:   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227     brouard  10379:   
1.200     brouard  10380:   /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198     brouard  10381:   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186     brouard  10382:   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211     brouard  10383:   /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, 
                   10384:    * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded 
                   10385:    * (currently 0 or 1) in the data.
                   10386:    * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of 
                   10387:    * corresponding modality (h,j).
                   10388:    */
                   10389: 
1.145     brouard  10390:   h=0;
                   10391:   /*if (cptcovn > 0) */
1.126     brouard  10392:   m=pow(2,cptcoveff);
                   10393:  
1.144     brouard  10394:          /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211     brouard  10395:           * For k=4 covariates, h goes from 1 to m=2**k
                   10396:           * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
                   10397:            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
1.186     brouard  10398:           *     h\k   1     2     3     4
1.143     brouard  10399:           *______________________________  
                   10400:           *     1 i=1 1 i=1 1 i=1 1 i=1 1
                   10401:           *     2     2     1     1     1
                   10402:           *     3 i=2 1     2     1     1
                   10403:           *     4     2     2     1     1
                   10404:           *     5 i=3 1 i=2 1     2     1
                   10405:           *     6     2     1     2     1
                   10406:           *     7 i=4 1     2     2     1
                   10407:           *     8     2     2     2     1
1.197     brouard  10408:           *     9 i=5 1 i=3 1 i=2 1     2
                   10409:           *    10     2     1     1     2
                   10410:           *    11 i=6 1     2     1     2
                   10411:           *    12     2     2     1     2
                   10412:           *    13 i=7 1 i=4 1     2     2    
                   10413:           *    14     2     1     2     2
                   10414:           *    15 i=8 1     2     2     2
                   10415:           *    16     2     2     2     2
1.143     brouard  10416:           */
1.212     brouard  10417:   /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211     brouard  10418:      /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
                   10419:      * and the value of each covariate?
                   10420:      * V1=1, V2=1, V3=2, V4=1 ?
                   10421:      * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
                   10422:      * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
                   10423:      * In order to get the real value in the data, we use nbcode
                   10424:      * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
                   10425:      * We are keeping this crazy system in order to be able (in the future?) 
                   10426:      * to have more than 2 values (0 or 1) for a covariate.
                   10427:      * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
                   10428:      * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
                   10429:      *              bbbbbbbb
                   10430:      *              76543210     
                   10431:      *   h-1        00000101 (6-1=5)
1.219     brouard  10432:      *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211     brouard  10433:      *           &
                   10434:      *     1        00000001 (1)
1.219     brouard  10435:      *              00000000        = 1 & ((h-1) >> (k-1))
                   10436:      *          +1= 00000001 =1 
1.211     brouard  10437:      *
                   10438:      * h=14, k=3 => h'=h-1=13, k'=k-1=2
                   10439:      *          h'      1101 =2^3+2^2+0x2^1+2^0
                   10440:      *    >>k'            11
                   10441:      *          &   00000001
                   10442:      *            = 00000001
                   10443:      *      +1    = 00000010=2    =  codtabm(14,3)   
                   10444:      * Reverse h=6 and m=16?
                   10445:      * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
                   10446:      * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
                   10447:      * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 
                   10448:      * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
                   10449:      * V3=decodtabm(14,3,2**4)=2
                   10450:      *          h'=13   1101 =2^3+2^2+0x2^1+2^0
                   10451:      *(h-1) >> (j-1)    0011 =13 >> 2
                   10452:      *          &1 000000001
                   10453:      *           = 000000001
                   10454:      *         +1= 000000010 =2
                   10455:      *                  2211
                   10456:      *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
                   10457:      *                  V3=2
1.220     brouard  10458:                 * codtabm and decodtabm are identical
1.211     brouard  10459:      */
                   10460: 
1.145     brouard  10461: 
                   10462:  free_ivector(Ndum,-1,NCOVMAX);
                   10463: 
                   10464: 
1.126     brouard  10465:     
1.186     brouard  10466:   /* Initialisation of ----------- gnuplot -------------*/
1.126     brouard  10467:   strcpy(optionfilegnuplot,optionfilefiname);
                   10468:   if(mle==-3)
1.201     brouard  10469:     strcat(optionfilegnuplot,"-MORT_");
1.126     brouard  10470:   strcat(optionfilegnuplot,".gp");
                   10471: 
                   10472:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
                   10473:     printf("Problem with file %s",optionfilegnuplot);
                   10474:   }
                   10475:   else{
1.204     brouard  10476:     fprintf(ficgp,"\n# IMaCh-%s\n", version); 
1.126     brouard  10477:     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
1.141     brouard  10478:     //fprintf(ficgp,"set missing 'NaNq'\n");
                   10479:     fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126     brouard  10480:   }
                   10481:   /*  fclose(ficgp);*/
1.186     brouard  10482: 
                   10483: 
                   10484:   /* Initialisation of --------- index.htm --------*/
1.126     brouard  10485: 
                   10486:   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
                   10487:   if(mle==-3)
1.201     brouard  10488:     strcat(optionfilehtm,"-MORT_");
1.126     brouard  10489:   strcat(optionfilehtm,".htm");
                   10490:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
1.131     brouard  10491:     printf("Problem with %s \n",optionfilehtm);
                   10492:     exit(0);
1.126     brouard  10493:   }
                   10494: 
                   10495:   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
                   10496:   strcat(optionfilehtmcov,"-cov.htm");
                   10497:   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
                   10498:     printf("Problem with %s \n",optionfilehtmcov), exit(0);
                   10499:   }
                   10500:   else{
                   10501:   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                   10502: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204     brouard  10503: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126     brouard  10504:          optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   10505:   }
                   10506: 
1.213     brouard  10507:   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  10508: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   10509: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126     brouard  10510: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204     brouard  10511: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126     brouard  10512: \n\
                   10513: <hr  size=\"2\" color=\"#EC5E5E\">\
                   10514:  <ul><li><h4>Parameter files</h4>\n\
                   10515:  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
                   10516:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
                   10517:  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
                   10518:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
                   10519:  - Date and time at start: %s</ul>\n",\
                   10520:          optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
                   10521:          optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
                   10522:          fileres,fileres,\
                   10523:          filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
                   10524:   fflush(fichtm);
                   10525: 
                   10526:   strcpy(pathr,path);
                   10527:   strcat(pathr,optionfilefiname);
1.184     brouard  10528: #ifdef WIN32
                   10529:   _chdir(optionfilefiname); /* Move to directory named optionfile */
                   10530: #else
1.126     brouard  10531:   chdir(optionfilefiname); /* Move to directory named optionfile */
1.184     brouard  10532: #endif
                   10533:          
1.126     brouard  10534:   
1.220     brouard  10535:   /* Calculates basic frequencies. Computes observed prevalence at single age 
                   10536:                 and for any valid combination of covariates
1.126     brouard  10537:      and prints on file fileres'p'. */
1.251     brouard  10538:   freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227     brouard  10539:              firstpass, lastpass,  stepm,  weightopt, model);
1.126     brouard  10540: 
                   10541:   fprintf(fichtm,"\n");
                   10542:   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
                   10543: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
                   10544: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
                   10545:          imx,agemin,agemax,jmin,jmax,jmean);
                   10546:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220     brouard  10547:        oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   10548:        newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   10549:        savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   10550:        oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218     brouard  10551: 
1.126     brouard  10552:   /* For Powell, parameters are in a vector p[] starting at p[1]
                   10553:      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
                   10554:   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
                   10555: 
                   10556:   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186     brouard  10557:   /* For mortality only */
1.126     brouard  10558:   if (mle==-3){
1.136     brouard  10559:     ximort=matrix(1,NDIM,1,NDIM); 
1.248     brouard  10560:     for(i=1;i<=NDIM;i++)
                   10561:       for(j=1;j<=NDIM;j++)
                   10562:        ximort[i][j]=0.;
1.186     brouard  10563:     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126     brouard  10564:     cens=ivector(1,n);
                   10565:     ageexmed=vector(1,n);
                   10566:     agecens=vector(1,n);
                   10567:     dcwave=ivector(1,n);
1.223     brouard  10568:                
1.126     brouard  10569:     for (i=1; i<=imx; i++){
                   10570:       dcwave[i]=-1;
                   10571:       for (m=firstpass; m<=lastpass; m++)
1.226     brouard  10572:        if (s[m][i]>nlstate) {
                   10573:          dcwave[i]=m;
                   10574:          /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                   10575:          break;
                   10576:        }
1.126     brouard  10577:     }
1.226     brouard  10578:     
1.126     brouard  10579:     for (i=1; i<=imx; i++) {
                   10580:       if (wav[i]>0){
1.226     brouard  10581:        ageexmed[i]=agev[mw[1][i]][i];
                   10582:        j=wav[i];
                   10583:        agecens[i]=1.; 
                   10584:        
                   10585:        if (ageexmed[i]> 1 && wav[i] > 0){
                   10586:          agecens[i]=agev[mw[j][i]][i];
                   10587:          cens[i]= 1;
                   10588:        }else if (ageexmed[i]< 1) 
                   10589:          cens[i]= -1;
                   10590:        if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                   10591:          cens[i]=0 ;
1.126     brouard  10592:       }
                   10593:       else cens[i]=-1;
                   10594:     }
                   10595:     
                   10596:     for (i=1;i<=NDIM;i++) {
                   10597:       for (j=1;j<=NDIM;j++)
1.226     brouard  10598:        ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126     brouard  10599:     }
                   10600:     
1.145     brouard  10601:     /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126     brouard  10602:     /*printf("%lf %lf", p[1], p[2]);*/
                   10603:     
                   10604:     
1.136     brouard  10605: #ifdef GSL
                   10606:     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
1.162     brouard  10607: #else
1.126     brouard  10608:     printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.136     brouard  10609: #endif
1.201     brouard  10610:     strcpy(filerespow,"POW-MORT_"); 
                   10611:     strcat(filerespow,fileresu);
1.126     brouard  10612:     if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   10613:       printf("Problem with resultfile: %s\n", filerespow);
                   10614:       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   10615:     }
1.136     brouard  10616: #ifdef GSL
                   10617:     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162     brouard  10618: #else
1.126     brouard  10619:     fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136     brouard  10620: #endif
1.126     brouard  10621:     /*  for (i=1;i<=nlstate;i++)
                   10622:        for(j=1;j<=nlstate+ndeath;j++)
                   10623:        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   10624:     */
                   10625:     fprintf(ficrespow,"\n");
1.136     brouard  10626: #ifdef GSL
                   10627:     /* gsl starts here */ 
                   10628:     T = gsl_multimin_fminimizer_nmsimplex;
                   10629:     gsl_multimin_fminimizer *sfm = NULL;
                   10630:     gsl_vector *ss, *x;
                   10631:     gsl_multimin_function minex_func;
                   10632: 
                   10633:     /* Initial vertex size vector */
                   10634:     ss = gsl_vector_alloc (NDIM);
                   10635:     
                   10636:     if (ss == NULL){
                   10637:       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
                   10638:     }
                   10639:     /* Set all step sizes to 1 */
                   10640:     gsl_vector_set_all (ss, 0.001);
                   10641: 
                   10642:     /* Starting point */
1.126     brouard  10643:     
1.136     brouard  10644:     x = gsl_vector_alloc (NDIM);
                   10645:     
                   10646:     if (x == NULL){
                   10647:       gsl_vector_free(ss);
                   10648:       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
                   10649:     }
                   10650:   
                   10651:     /* Initialize method and iterate */
                   10652:     /*     p[1]=0.0268; p[NDIM]=0.083; */
1.186     brouard  10653:     /*     gsl_vector_set(x, 0, 0.0268); */
                   10654:     /*     gsl_vector_set(x, 1, 0.083); */
1.136     brouard  10655:     gsl_vector_set(x, 0, p[1]);
                   10656:     gsl_vector_set(x, 1, p[2]);
                   10657: 
                   10658:     minex_func.f = &gompertz_f;
                   10659:     minex_func.n = NDIM;
                   10660:     minex_func.params = (void *)&p; /* ??? */
                   10661:     
                   10662:     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
                   10663:     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
                   10664:     
                   10665:     printf("Iterations beginning .....\n\n");
                   10666:     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
                   10667: 
                   10668:     iteri=0;
                   10669:     while (rval == GSL_CONTINUE){
                   10670:       iteri++;
                   10671:       status = gsl_multimin_fminimizer_iterate(sfm);
                   10672:       
                   10673:       if (status) printf("error: %s\n", gsl_strerror (status));
                   10674:       fflush(0);
                   10675:       
                   10676:       if (status) 
                   10677:         break;
                   10678:       
                   10679:       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
                   10680:       ssval = gsl_multimin_fminimizer_size (sfm);
                   10681:       
                   10682:       if (rval == GSL_SUCCESS)
                   10683:         printf ("converged to a local maximum at\n");
                   10684:       
                   10685:       printf("%5d ", iteri);
                   10686:       for (it = 0; it < NDIM; it++){
                   10687:        printf ("%10.5f ", gsl_vector_get (sfm->x, it));
                   10688:       }
                   10689:       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
                   10690:     }
                   10691:     
                   10692:     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
                   10693:     
                   10694:     gsl_vector_free(x); /* initial values */
                   10695:     gsl_vector_free(ss); /* inital step size */
                   10696:     for (it=0; it<NDIM; it++){
                   10697:       p[it+1]=gsl_vector_get(sfm->x,it);
                   10698:       fprintf(ficrespow," %.12lf", p[it]);
                   10699:     }
                   10700:     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
                   10701: #endif
                   10702: #ifdef POWELL
                   10703:      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
                   10704: #endif  
1.126     brouard  10705:     fclose(ficrespow);
                   10706:     
1.203     brouard  10707:     hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
1.126     brouard  10708: 
                   10709:     for(i=1; i <=NDIM; i++)
                   10710:       for(j=i+1;j<=NDIM;j++)
1.220     brouard  10711:                                matcov[i][j]=matcov[j][i];
1.126     brouard  10712:     
                   10713:     printf("\nCovariance matrix\n ");
1.203     brouard  10714:     fprintf(ficlog,"\nCovariance matrix\n ");
1.126     brouard  10715:     for(i=1; i <=NDIM; i++) {
                   10716:       for(j=1;j<=NDIM;j++){ 
1.220     brouard  10717:                                printf("%f ",matcov[i][j]);
                   10718:                                fprintf(ficlog,"%f ",matcov[i][j]);
1.126     brouard  10719:       }
1.203     brouard  10720:       printf("\n ");  fprintf(ficlog,"\n ");
1.126     brouard  10721:     }
                   10722:     
                   10723:     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193     brouard  10724:     for (i=1;i<=NDIM;i++) {
1.126     brouard  10725:       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193     brouard  10726:       fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
                   10727:     }
1.126     brouard  10728:     lsurv=vector(1,AGESUP);
                   10729:     lpop=vector(1,AGESUP);
                   10730:     tpop=vector(1,AGESUP);
                   10731:     lsurv[agegomp]=100000;
                   10732:     
                   10733:     for (k=agegomp;k<=AGESUP;k++) {
                   10734:       agemortsup=k;
                   10735:       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
                   10736:     }
                   10737:     
                   10738:     for (k=agegomp;k<agemortsup;k++)
                   10739:       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
                   10740:     
                   10741:     for (k=agegomp;k<agemortsup;k++){
                   10742:       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
                   10743:       sumlpop=sumlpop+lpop[k];
                   10744:     }
                   10745:     
                   10746:     tpop[agegomp]=sumlpop;
                   10747:     for (k=agegomp;k<(agemortsup-3);k++){
                   10748:       /*  tpop[k+1]=2;*/
                   10749:       tpop[k+1]=tpop[k]-lpop[k];
                   10750:     }
                   10751:     
                   10752:     
                   10753:     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
                   10754:     for (k=agegomp;k<(agemortsup-2);k++) 
                   10755:       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]);
                   10756:     
                   10757:     
                   10758:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220     brouard  10759:                ageminpar=50;
                   10760:                agemaxpar=100;
1.194     brouard  10761:     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
                   10762:        printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
                   10763: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   10764: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
                   10765:        fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
                   10766: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   10767: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220     brouard  10768:     }else{
                   10769:                        printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
                   10770:                        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  10771:       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220     brouard  10772:                }
1.201     brouard  10773:     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126     brouard  10774:                     stepm, weightopt,\
                   10775:                     model,imx,p,matcov,agemortsup);
                   10776:     
                   10777:     free_vector(lsurv,1,AGESUP);
                   10778:     free_vector(lpop,1,AGESUP);
                   10779:     free_vector(tpop,1,AGESUP);
1.220     brouard  10780:     free_matrix(ximort,1,NDIM,1,NDIM);
1.136     brouard  10781:     free_ivector(cens,1,n);
                   10782:     free_vector(agecens,1,n);
                   10783:     free_ivector(dcwave,1,n);
1.220     brouard  10784: #ifdef GSL
1.136     brouard  10785: #endif
1.186     brouard  10786:   } /* Endof if mle==-3 mortality only */
1.205     brouard  10787:   /* Standard  */
                   10788:   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
                   10789:     globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
                   10790:     /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132     brouard  10791:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126     brouard  10792:     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   10793:     for (k=1; k<=npar;k++)
                   10794:       printf(" %d %8.5f",k,p[k]);
                   10795:     printf("\n");
1.205     brouard  10796:     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
                   10797:       /* mlikeli uses func not funcone */
1.247     brouard  10798:       /* for(i=1;i<nlstate;i++){ */
                   10799:       /*       /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
                   10800:       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
                   10801:       /* } */
1.205     brouard  10802:       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
                   10803:     }
                   10804:     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
                   10805:       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
                   10806:       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
                   10807:       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   10808:     }
                   10809:     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126     brouard  10810:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   10811:     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   10812:     for (k=1; k<=npar;k++)
                   10813:       printf(" %d %8.5f",k,p[k]);
                   10814:     printf("\n");
                   10815:     
                   10816:     /*--------- results files --------------*/
1.224     brouard  10817:     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  10818:     
                   10819:     
                   10820:     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   10821:     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   10822:     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   10823:     for(i=1,jk=1; i <=nlstate; i++){
                   10824:       for(k=1; k <=(nlstate+ndeath); k++){
1.225     brouard  10825:        if (k != i) {
                   10826:          printf("%d%d ",i,k);
                   10827:          fprintf(ficlog,"%d%d ",i,k);
                   10828:          fprintf(ficres,"%1d%1d ",i,k);
                   10829:          for(j=1; j <=ncovmodel; j++){
                   10830:            printf("%12.7f ",p[jk]);
                   10831:            fprintf(ficlog,"%12.7f ",p[jk]);
                   10832:            fprintf(ficres,"%12.7f ",p[jk]);
                   10833:            jk++; 
                   10834:          }
                   10835:          printf("\n");
                   10836:          fprintf(ficlog,"\n");
                   10837:          fprintf(ficres,"\n");
                   10838:        }
1.126     brouard  10839:       }
                   10840:     }
1.203     brouard  10841:     if(mle != 0){
                   10842:       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126     brouard  10843:       ftolhess=ftol; /* Usually correct */
1.203     brouard  10844:       hesscov(matcov, hess, p, npar, delti, ftolhess, func);
                   10845:       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");
                   10846:       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");
                   10847:       for(i=1,jk=1; i <=nlstate; i++){
1.225     brouard  10848:        for(k=1; k <=(nlstate+ndeath); k++){
                   10849:          if (k != i) {
                   10850:            printf("%d%d ",i,k);
                   10851:            fprintf(ficlog,"%d%d ",i,k);
                   10852:            for(j=1; j <=ncovmodel; j++){
                   10853:              printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                   10854:              fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                   10855:              jk++; 
                   10856:            }
                   10857:            printf("\n");
                   10858:            fprintf(ficlog,"\n");
                   10859:          }
                   10860:        }
1.193     brouard  10861:       }
1.203     brouard  10862:     } /* end of hesscov and Wald tests */
1.225     brouard  10863:     
1.203     brouard  10864:     /*  */
1.126     brouard  10865:     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
                   10866:     printf("# Scales (for hessian or gradient estimation)\n");
                   10867:     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
                   10868:     for(i=1,jk=1; i <=nlstate; i++){
                   10869:       for(j=1; j <=nlstate+ndeath; j++){
1.225     brouard  10870:        if (j!=i) {
                   10871:          fprintf(ficres,"%1d%1d",i,j);
                   10872:          printf("%1d%1d",i,j);
                   10873:          fprintf(ficlog,"%1d%1d",i,j);
                   10874:          for(k=1; k<=ncovmodel;k++){
                   10875:            printf(" %.5e",delti[jk]);
                   10876:            fprintf(ficlog," %.5e",delti[jk]);
                   10877:            fprintf(ficres," %.5e",delti[jk]);
                   10878:            jk++;
                   10879:          }
                   10880:          printf("\n");
                   10881:          fprintf(ficlog,"\n");
                   10882:          fprintf(ficres,"\n");
                   10883:        }
1.126     brouard  10884:       }
                   10885:     }
                   10886:     
                   10887:     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  10888:     if(mle >= 1) /* To big for the screen */
1.126     brouard  10889:       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");
                   10890:     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");
                   10891:     /* # 121 Var(a12)\n\ */
                   10892:     /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   10893:     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   10894:     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   10895:     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   10896:     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   10897:     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   10898:     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   10899:     
                   10900:     
                   10901:     /* Just to have a covariance matrix which will be more understandable
                   10902:        even is we still don't want to manage dictionary of variables
                   10903:     */
                   10904:     for(itimes=1;itimes<=2;itimes++){
                   10905:       jj=0;
                   10906:       for(i=1; i <=nlstate; i++){
1.225     brouard  10907:        for(j=1; j <=nlstate+ndeath; j++){
                   10908:          if(j==i) continue;
                   10909:          for(k=1; k<=ncovmodel;k++){
                   10910:            jj++;
                   10911:            ca[0]= k+'a'-1;ca[1]='\0';
                   10912:            if(itimes==1){
                   10913:              if(mle>=1)
                   10914:                printf("#%1d%1d%d",i,j,k);
                   10915:              fprintf(ficlog,"#%1d%1d%d",i,j,k);
                   10916:              fprintf(ficres,"#%1d%1d%d",i,j,k);
                   10917:            }else{
                   10918:              if(mle>=1)
                   10919:                printf("%1d%1d%d",i,j,k);
                   10920:              fprintf(ficlog,"%1d%1d%d",i,j,k);
                   10921:              fprintf(ficres,"%1d%1d%d",i,j,k);
                   10922:            }
                   10923:            ll=0;
                   10924:            for(li=1;li <=nlstate; li++){
                   10925:              for(lj=1;lj <=nlstate+ndeath; lj++){
                   10926:                if(lj==li) continue;
                   10927:                for(lk=1;lk<=ncovmodel;lk++){
                   10928:                  ll++;
                   10929:                  if(ll<=jj){
                   10930:                    cb[0]= lk +'a'-1;cb[1]='\0';
                   10931:                    if(ll<jj){
                   10932:                      if(itimes==1){
                   10933:                        if(mle>=1)
                   10934:                          printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   10935:                        fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   10936:                        fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   10937:                      }else{
                   10938:                        if(mle>=1)
                   10939:                          printf(" %.5e",matcov[jj][ll]); 
                   10940:                        fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   10941:                        fprintf(ficres," %.5e",matcov[jj][ll]); 
                   10942:                      }
                   10943:                    }else{
                   10944:                      if(itimes==1){
                   10945:                        if(mle>=1)
                   10946:                          printf(" Var(%s%1d%1d)",ca,i,j);
                   10947:                        fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                   10948:                        fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                   10949:                      }else{
                   10950:                        if(mle>=1)
                   10951:                          printf(" %.7e",matcov[jj][ll]); 
                   10952:                        fprintf(ficlog," %.7e",matcov[jj][ll]); 
                   10953:                        fprintf(ficres," %.7e",matcov[jj][ll]); 
                   10954:                      }
                   10955:                    }
                   10956:                  }
                   10957:                } /* end lk */
                   10958:              } /* end lj */
                   10959:            } /* end li */
                   10960:            if(mle>=1)
                   10961:              printf("\n");
                   10962:            fprintf(ficlog,"\n");
                   10963:            fprintf(ficres,"\n");
                   10964:            numlinepar++;
                   10965:          } /* end k*/
                   10966:        } /*end j */
1.126     brouard  10967:       } /* end i */
                   10968:     } /* end itimes */
                   10969:     
                   10970:     fflush(ficlog);
                   10971:     fflush(ficres);
1.225     brouard  10972:     while(fgets(line, MAXLINE, ficpar)) {
                   10973:       /* If line starts with a # it is a comment */
                   10974:       if (line[0] == '#') {
                   10975:        numlinepar++;
                   10976:        fputs(line,stdout);
                   10977:        fputs(line,ficparo);
                   10978:        fputs(line,ficlog);
                   10979:        continue;
                   10980:       }else
                   10981:        break;
                   10982:     }
                   10983:     
1.209     brouard  10984:     /* while((c=getc(ficpar))=='#' && c!= EOF){ */
                   10985:     /*   ungetc(c,ficpar); */
                   10986:     /*   fgets(line, MAXLINE, ficpar); */
                   10987:     /*   fputs(line,stdout); */
                   10988:     /*   fputs(line,ficparo); */
                   10989:     /* } */
                   10990:     /* ungetc(c,ficpar); */
1.126     brouard  10991:     
                   10992:     estepm=0;
1.209     brouard  10993:     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  10994:       
                   10995:       if (num_filled != 6) {
                   10996:        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);
                   10997:        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);
                   10998:        goto end;
                   10999:       }
                   11000:       printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
                   11001:     }
                   11002:     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
                   11003:     /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
                   11004:     
1.209     brouard  11005:     /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126     brouard  11006:     if (estepm==0 || estepm < stepm) estepm=stepm;
                   11007:     if (fage <= 2) {
                   11008:       bage = ageminpar;
                   11009:       fage = agemaxpar;
                   11010:     }
                   11011:     
                   11012:     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211     brouard  11013:     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                   11014:     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220     brouard  11015:                
1.186     brouard  11016:     /* Other stuffs, more or less useful */    
1.126     brouard  11017:     while((c=getc(ficpar))=='#' && c!= EOF){
                   11018:       ungetc(c,ficpar);
                   11019:       fgets(line, MAXLINE, ficpar);
1.141     brouard  11020:       fputs(line,stdout);
1.126     brouard  11021:       fputs(line,ficparo);
                   11022:     }
                   11023:     ungetc(c,ficpar);
                   11024:     
                   11025:     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
                   11026:     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);
                   11027:     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);
                   11028:     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   11029:     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);
                   11030:     
                   11031:     while((c=getc(ficpar))=='#' && c!= EOF){
                   11032:       ungetc(c,ficpar);
                   11033:       fgets(line, MAXLINE, ficpar);
1.141     brouard  11034:       fputs(line,stdout);
1.126     brouard  11035:       fputs(line,ficparo);
                   11036:     }
                   11037:     ungetc(c,ficpar);
                   11038:     
                   11039:     
                   11040:     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
                   11041:     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
                   11042:     
                   11043:     fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193     brouard  11044:     fprintf(ficlog,"pop_based=%d\n",popbased);
1.126     brouard  11045:     fprintf(ficparo,"pop_based=%d\n",popbased);   
                   11046:     fprintf(ficres,"pop_based=%d\n",popbased);   
                   11047:     
                   11048:     while((c=getc(ficpar))=='#' && c!= EOF){
                   11049:       ungetc(c,ficpar);
                   11050:       fgets(line, MAXLINE, ficpar);
1.141     brouard  11051:       fputs(line,stdout);
1.238     brouard  11052:       fputs(line,ficres);
1.126     brouard  11053:       fputs(line,ficparo);
                   11054:     }
                   11055:     ungetc(c,ficpar);
                   11056:     
                   11057:     fscanf(ficpar,"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);
                   11058:     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);
                   11059:     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);
                   11060:     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);
                   11061:     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);
                   11062:     /* day and month of proj2 are not used but only year anproj2.*/
                   11063:     
1.217     brouard  11064:     while((c=getc(ficpar))=='#' && c!= EOF){
                   11065:       ungetc(c,ficpar);
                   11066:       fgets(line, MAXLINE, ficpar);
                   11067:       fputs(line,stdout);
                   11068:       fputs(line,ficparo);
1.238     brouard  11069:       fputs(line,ficres);
1.217     brouard  11070:     }
                   11071:     ungetc(c,ficpar);
                   11072:     
                   11073:     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
1.223     brouard  11074:     fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
                   11075:     fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
                   11076:     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
1.217     brouard  11077:     /* day and month of proj2 are not used but only year anproj2.*/
1.126     brouard  11078:     
1.230     brouard  11079:     /* Results */
1.235     brouard  11080:     nresult=0;
1.230     brouard  11081:     while(fgets(line, MAXLINE, ficpar)) {
                   11082:       /* If line starts with a # it is a comment */
                   11083:       if (line[0] == '#') {
                   11084:        numlinepar++;
                   11085:        fputs(line,stdout);
                   11086:        fputs(line,ficparo);
                   11087:        fputs(line,ficlog);
1.238     brouard  11088:        fputs(line,ficres);
1.230     brouard  11089:        continue;
                   11090:       }else
                   11091:        break;
                   11092:     }
1.240     brouard  11093:     if (!feof(ficpar))
1.230     brouard  11094:     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
1.240     brouard  11095:       if (num_filled == 0){
1.230     brouard  11096:        resultline[0]='\0';
1.240     brouard  11097:       break;
                   11098:       } else if (num_filled != 1){
1.230     brouard  11099:        printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
                   11100:       }
1.235     brouard  11101:       nresult++; /* Sum of resultlines */
                   11102:       printf("Result %d: result=%s\n",nresult, resultline);
                   11103:       if(nresult > MAXRESULTLINES){
                   11104:        printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
                   11105:        fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
                   11106:        goto end;
                   11107:       }
                   11108:       decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.238     brouard  11109:       fprintf(ficparo,"result: %s\n",resultline);
                   11110:       fprintf(ficres,"result: %s\n",resultline);
                   11111:       fprintf(ficlog,"result: %s\n",resultline);
1.230     brouard  11112:       while(fgets(line, MAXLINE, ficpar)) {
                   11113:        /* If line starts with a # it is a comment */
                   11114:        if (line[0] == '#') {
                   11115:          numlinepar++;
                   11116:          fputs(line,stdout);
                   11117:          fputs(line,ficparo);
1.238     brouard  11118:          fputs(line,ficres);
1.230     brouard  11119:          fputs(line,ficlog);
                   11120:          continue;
                   11121:        }else
                   11122:          break;
                   11123:       }
                   11124:       if (feof(ficpar))
                   11125:        break;
                   11126:       else{ /* Processess output results for this combination of covariate values */
                   11127:       }                                   
1.240     brouard  11128:     } /* end while */
1.230     brouard  11129: 
                   11130: 
1.126     brouard  11131:     
1.230     brouard  11132:     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145     brouard  11133:     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126     brouard  11134:     
                   11135:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194     brouard  11136:     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230     brouard  11137:       printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194     brouard  11138: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   11139: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230     brouard  11140:       fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194     brouard  11141: This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                   11142: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220     brouard  11143:     }else{
1.218     brouard  11144:       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220     brouard  11145:     }
                   11146:     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225     brouard  11147:                 model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
                   11148:                 jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220     brouard  11149:                
1.225     brouard  11150:     /*------------ free_vector  -------------*/
                   11151:     /*  chdir(path); */
1.220     brouard  11152:                
1.215     brouard  11153:     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
                   11154:     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
                   11155:     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
                   11156:     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
1.126     brouard  11157:     free_lvector(num,1,n);
                   11158:     free_vector(agedc,1,n);
                   11159:     /*free_matrix(covar,0,NCOVMAX,1,n);*/
                   11160:     /*free_matrix(covar,1,NCOVMAX,1,n);*/
                   11161:     fclose(ficparo);
                   11162:     fclose(ficres);
1.220     brouard  11163:                
                   11164:                
1.186     brouard  11165:     /* Other results (useful)*/
1.220     brouard  11166:                
                   11167:                
1.126     brouard  11168:     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
1.180     brouard  11169:     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
                   11170:     prlim=matrix(1,nlstate,1,nlstate);
1.209     brouard  11171:     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126     brouard  11172:     fclose(ficrespl);
                   11173: 
                   11174:     /*------------- h Pij x at various ages ------------*/
1.180     brouard  11175:     /*#include "hpijx.h"*/
                   11176:     hPijx(p, bage, fage);
1.145     brouard  11177:     fclose(ficrespij);
1.227     brouard  11178:     
1.220     brouard  11179:     /* ncovcombmax=  pow(2,cptcoveff); */
1.219     brouard  11180:     /*-------------- Variance of one-step probabilities---*/
1.145     brouard  11181:     k=1;
1.126     brouard  11182:     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227     brouard  11183:     
1.219     brouard  11184:     /* Prevalence for each covariates in probs[age][status][cov] */
1.218     brouard  11185:     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126     brouard  11186:     for(i=1;i<=AGESUP;i++)
1.219     brouard  11187:       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225     brouard  11188:        for(k=1;k<=ncovcombmax;k++)
                   11189:          probs[i][j][k]=0.;
1.219     brouard  11190:     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
                   11191:     if (mobilav!=0 ||mobilavproj !=0 ) {
                   11192:       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227     brouard  11193:       for(i=1;i<=AGESUP;i++)
                   11194:        for(j=1;j<=nlstate;j++)
                   11195:          for(k=1;k<=ncovcombmax;k++)
                   11196:            mobaverages[i][j][k]=0.;
1.219     brouard  11197:       mobaverage=mobaverages;
                   11198:       if (mobilav!=0) {
1.235     brouard  11199:        printf("Movingaveraging observed prevalence\n");
1.227     brouard  11200:        if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
                   11201:          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   11202:          printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   11203:        }
1.219     brouard  11204:       }
                   11205:       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
                   11206:       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
                   11207:       else if (mobilavproj !=0) {
1.235     brouard  11208:        printf("Movingaveraging projected observed prevalence\n");
1.227     brouard  11209:        if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
                   11210:          fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
                   11211:          printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
                   11212:        }
1.219     brouard  11213:       }
                   11214:     }/* end if moving average */
1.227     brouard  11215:     
1.126     brouard  11216:     /*---------- Forecasting ------------------*/
                   11217:     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
                   11218:     if(prevfcast==1){
                   11219:       /*    if(stepm ==1){*/
1.225     brouard  11220:       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126     brouard  11221:     }
1.217     brouard  11222:     if(backcast==1){
1.219     brouard  11223:       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);       
                   11224:       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);       
                   11225:       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
                   11226: 
                   11227:       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
                   11228: 
                   11229:       bprlim=matrix(1,nlstate,1,nlstate);
                   11230:       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
                   11231:       fclose(ficresplb);
                   11232: 
1.222     brouard  11233:       hBijx(p, bage, fage, mobaverage);
                   11234:       fclose(ficrespijb);
1.219     brouard  11235:       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
                   11236: 
                   11237:       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225     brouard  11238:         bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219     brouard  11239:       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
                   11240:       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
                   11241:       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
                   11242:     }
1.217     brouard  11243:     
1.186     brouard  11244:  
                   11245:     /* ------ Other prevalence ratios------------ */
1.126     brouard  11246: 
1.215     brouard  11247:     free_ivector(wav,1,imx);
                   11248:     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
                   11249:     free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
                   11250:     free_imatrix(mw,1,lastpass-firstpass+2,1,imx);   
1.218     brouard  11251:                
                   11252:                
1.127     brouard  11253:     /*---------- Health expectancies, no variances ------------*/
1.218     brouard  11254:                
1.201     brouard  11255:     strcpy(filerese,"E_");
                   11256:     strcat(filerese,fileresu);
1.126     brouard  11257:     if((ficreseij=fopen(filerese,"w"))==NULL) {
                   11258:       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   11259:       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   11260:     }
1.208     brouard  11261:     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
                   11262:     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238     brouard  11263: 
                   11264:     pstamp(ficreseij);
1.219     brouard  11265:                
1.235     brouard  11266:     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
                   11267:     if (cptcovn < 1){i1=1;}
                   11268:     
                   11269:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   11270:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
                   11271:       if(TKresult[nres]!= k)
                   11272:        continue;
1.219     brouard  11273:       fprintf(ficreseij,"\n#****** ");
1.235     brouard  11274:       printf("\n#****** ");
1.225     brouard  11275:       for(j=1;j<=cptcoveff;j++) {
1.227     brouard  11276:        fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235     brouard  11277:        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11278:       }
                   11279:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   11280:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11281:        fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219     brouard  11282:       }
                   11283:       fprintf(ficreseij,"******\n");
1.235     brouard  11284:       printf("******\n");
1.219     brouard  11285:       
                   11286:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   11287:       oldm=oldms;savm=savms;
1.235     brouard  11288:       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
1.127     brouard  11289:       
1.219     brouard  11290:       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127     brouard  11291:     }
                   11292:     fclose(ficreseij);
1.208     brouard  11293:     printf("done evsij\n");fflush(stdout);
                   11294:     fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218     brouard  11295:                
1.227     brouard  11296:     /*---------- State-specific expectancies and variances ------------*/
1.218     brouard  11297:                
                   11298:                
1.201     brouard  11299:     strcpy(filerest,"T_");
                   11300:     strcat(filerest,fileresu);
1.127     brouard  11301:     if((ficrest=fopen(filerest,"w"))==NULL) {
                   11302:       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
                   11303:       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
                   11304:     }
1.208     brouard  11305:     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
                   11306:     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218     brouard  11307:                
1.126     brouard  11308: 
1.201     brouard  11309:     strcpy(fileresstde,"STDE_");
                   11310:     strcat(fileresstde,fileresu);
1.126     brouard  11311:     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227     brouard  11312:       printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
                   11313:       fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126     brouard  11314:     }
1.227     brouard  11315:     printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
                   11316:     fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126     brouard  11317: 
1.201     brouard  11318:     strcpy(filerescve,"CVE_");
                   11319:     strcat(filerescve,fileresu);
1.126     brouard  11320:     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227     brouard  11321:       printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
                   11322:       fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126     brouard  11323:     }
1.227     brouard  11324:     printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
                   11325:     fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126     brouard  11326: 
1.201     brouard  11327:     strcpy(fileresv,"V_");
                   11328:     strcat(fileresv,fileresu);
1.126     brouard  11329:     if((ficresvij=fopen(fileresv,"w"))==NULL) {
                   11330:       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
                   11331:       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
                   11332:     }
1.227     brouard  11333:     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
                   11334:     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126     brouard  11335: 
1.145     brouard  11336:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   11337:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   11338:           
1.235     brouard  11339:     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
                   11340:     if (cptcovn < 1){i1=1;}
                   11341:     
                   11342:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   11343:     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
                   11344:       if(TKresult[nres]!= k)
                   11345:        continue;
1.242     brouard  11346:       printf("\n#****** Result for:");
                   11347:       fprintf(ficrest,"\n#****** Result for:");
                   11348:       fprintf(ficlog,"\n#****** Result for:");
1.227     brouard  11349:       for(j=1;j<=cptcoveff;j++){ 
                   11350:        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11351:        fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11352:        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11353:       }
1.235     brouard  11354:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   11355:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11356:        fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11357:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11358:       }        
1.208     brouard  11359:       fprintf(ficrest,"******\n");
1.227     brouard  11360:       fprintf(ficlog,"******\n");
                   11361:       printf("******\n");
1.208     brouard  11362:       
                   11363:       fprintf(ficresstdeij,"\n#****** ");
                   11364:       fprintf(ficrescveij,"\n#****** ");
1.225     brouard  11365:       for(j=1;j<=cptcoveff;j++) {
1.227     brouard  11366:        fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11367:        fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208     brouard  11368:       }
1.235     brouard  11369:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   11370:        fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11371:        fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11372:       }        
1.208     brouard  11373:       fprintf(ficresstdeij,"******\n");
                   11374:       fprintf(ficrescveij,"******\n");
                   11375:       
                   11376:       fprintf(ficresvij,"\n#****** ");
1.238     brouard  11377:       /* pstamp(ficresvij); */
1.225     brouard  11378:       for(j=1;j<=cptcoveff;j++) 
1.227     brouard  11379:        fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235     brouard  11380:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   11381:        fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11382:       }        
1.208     brouard  11383:       fprintf(ficresvij,"******\n");
                   11384:       
                   11385:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   11386:       oldm=oldms;savm=savms;
1.235     brouard  11387:       printf(" cvevsij ");
                   11388:       fprintf(ficlog, " cvevsij ");
                   11389:       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208     brouard  11390:       printf(" end cvevsij \n ");
                   11391:       fprintf(ficlog, " end cvevsij \n ");
                   11392:       
                   11393:       /*
                   11394:        */
                   11395:       /* goto endfree; */
                   11396:       
                   11397:       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   11398:       pstamp(ficrest);
                   11399:       
                   11400:       
                   11401:       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227     brouard  11402:        oldm=oldms;savm=savms; /* ZZ Segmentation fault */
                   11403:        cptcod= 0; /* To be deleted */
                   11404:        printf("varevsij vpopbased=%d \n",vpopbased);
                   11405:        fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235     brouard  11406:        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  11407:        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 ");
                   11408:        if(vpopbased==1)
                   11409:          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);
                   11410:        else
                   11411:          fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
                   11412:        fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
                   11413:        for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                   11414:        fprintf(ficrest,"\n");
                   11415:        /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
                   11416:        epj=vector(1,nlstate+1);
                   11417:        printf("Computing age specific period (stable) prevalences in each health state \n");
                   11418:        fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
                   11419:        for(age=bage; age <=fage ;age++){
1.235     brouard  11420:          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227     brouard  11421:          if (vpopbased==1) {
                   11422:            if(mobilav ==0){
                   11423:              for(i=1; i<=nlstate;i++)
                   11424:                prlim[i][i]=probs[(int)age][i][k];
                   11425:            }else{ /* mobilav */ 
                   11426:              for(i=1; i<=nlstate;i++)
                   11427:                prlim[i][i]=mobaverage[(int)age][i][k];
                   11428:            }
                   11429:          }
1.219     brouard  11430:          
1.227     brouard  11431:          fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
                   11432:          /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
                   11433:          /* printf(" age %4.0f ",age); */
                   11434:          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                   11435:            for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   11436:              epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   11437:              /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                   11438:              /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
                   11439:            }
                   11440:            epj[nlstate+1] +=epj[j];
                   11441:          }
                   11442:          /* printf(" age %4.0f \n",age); */
1.219     brouard  11443:          
1.227     brouard  11444:          for(i=1, vepp=0.;i <=nlstate;i++)
                   11445:            for(j=1;j <=nlstate;j++)
                   11446:              vepp += vareij[i][j][(int)age];
                   11447:          fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                   11448:          for(j=1;j <=nlstate;j++){
                   11449:            fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                   11450:          }
                   11451:          fprintf(ficrest,"\n");
                   11452:        }
1.208     brouard  11453:       } /* End vpopbased */
                   11454:       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   11455:       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   11456:       free_vector(epj,1,nlstate+1);
1.235     brouard  11457:       printf("done selection\n");fflush(stdout);
                   11458:       fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208     brouard  11459:       
1.145     brouard  11460:       /*}*/
1.235     brouard  11461:     } /* End k selection */
1.227     brouard  11462: 
                   11463:     printf("done State-specific expectancies\n");fflush(stdout);
                   11464:     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
                   11465: 
1.126     brouard  11466:     /*------- Variance of period (stable) prevalence------*/   
1.227     brouard  11467:     
1.201     brouard  11468:     strcpy(fileresvpl,"VPL_");
                   11469:     strcat(fileresvpl,fileresu);
1.126     brouard  11470:     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
                   11471:       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
                   11472:       exit(0);
                   11473:     }
1.208     brouard  11474:     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
                   11475:     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227     brouard  11476:     
1.145     brouard  11477:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   11478:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227     brouard  11479:     
1.235     brouard  11480:     i1=pow(2,cptcoveff);
                   11481:     if (cptcovn < 1){i1=1;}
                   11482: 
                   11483:     for(nres=1; nres <= nresult; nres++) /* For each resultline */
                   11484:     for(k=1; k<=i1;k++){
                   11485:       if(TKresult[nres]!= k)
                   11486:        continue;
1.227     brouard  11487:       fprintf(ficresvpl,"\n#****** ");
                   11488:       printf("\n#****** ");
                   11489:       fprintf(ficlog,"\n#****** ");
                   11490:       for(j=1;j<=cptcoveff;j++) {
                   11491:        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11492:        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11493:        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                   11494:       }
1.235     brouard  11495:       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
                   11496:        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11497:        fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11498:        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
                   11499:       }        
1.227     brouard  11500:       fprintf(ficresvpl,"******\n");
                   11501:       printf("******\n");
                   11502:       fprintf(ficlog,"******\n");
                   11503:       
                   11504:       varpl=matrix(1,nlstate,(int) bage, (int) fage);
                   11505:       oldm=oldms;savm=savms;
1.235     brouard  11506:       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
1.227     brouard  11507:       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145     brouard  11508:       /*}*/
1.126     brouard  11509:     }
1.227     brouard  11510:     
1.126     brouard  11511:     fclose(ficresvpl);
1.208     brouard  11512:     printf("done variance-covariance of period prevalence\n");fflush(stdout);
                   11513:     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227     brouard  11514:     
                   11515:     free_vector(weight,1,n);
                   11516:     free_imatrix(Tvard,1,NCOVMAX,1,2);
                   11517:     free_imatrix(s,1,maxwav+1,1,n);
                   11518:     free_matrix(anint,1,maxwav,1,n); 
                   11519:     free_matrix(mint,1,maxwav,1,n);
                   11520:     free_ivector(cod,1,n);
                   11521:     free_ivector(tab,1,NCOVMAX);
                   11522:     fclose(ficresstdeij);
                   11523:     fclose(ficrescveij);
                   11524:     fclose(ficresvij);
                   11525:     fclose(ficrest);
                   11526:     fclose(ficpar);
                   11527:     
                   11528:     
1.126     brouard  11529:     /*---------- End : free ----------------*/
1.219     brouard  11530:     if (mobilav!=0 ||mobilavproj !=0)
                   11531:       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
1.218     brouard  11532:     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220     brouard  11533:     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
                   11534:     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126     brouard  11535:   }  /* mle==-3 arrives here for freeing */
1.227     brouard  11536:   /* endfree:*/
                   11537:   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   11538:   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   11539:   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   11540:   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
1.233     brouard  11541:   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
1.227     brouard  11542:   free_matrix(coqvar,1,maxwav,1,n);
                   11543:   free_matrix(covar,0,NCOVMAX,1,n);
                   11544:   free_matrix(matcov,1,npar,1,npar);
                   11545:   free_matrix(hess,1,npar,1,npar);
                   11546:   /*free_vector(delti,1,npar);*/
                   11547:   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   11548:   free_matrix(agev,1,maxwav,1,imx);
                   11549:   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
                   11550:   
                   11551:   free_ivector(ncodemax,1,NCOVMAX);
                   11552:   free_ivector(ncodemaxwundef,1,NCOVMAX);
                   11553:   free_ivector(Dummy,-1,NCOVMAX);
                   11554:   free_ivector(Fixed,-1,NCOVMAX);
1.238     brouard  11555:   free_ivector(DummyV,1,NCOVMAX);
                   11556:   free_ivector(FixedV,1,NCOVMAX);
1.227     brouard  11557:   free_ivector(Typevar,-1,NCOVMAX);
                   11558:   free_ivector(Tvar,1,NCOVMAX);
1.234     brouard  11559:   free_ivector(TvarsQ,1,NCOVMAX);
                   11560:   free_ivector(TvarsQind,1,NCOVMAX);
                   11561:   free_ivector(TvarsD,1,NCOVMAX);
                   11562:   free_ivector(TvarsDind,1,NCOVMAX);
1.231     brouard  11563:   free_ivector(TvarFD,1,NCOVMAX);
                   11564:   free_ivector(TvarFDind,1,NCOVMAX);
1.232     brouard  11565:   free_ivector(TvarF,1,NCOVMAX);
                   11566:   free_ivector(TvarFind,1,NCOVMAX);
                   11567:   free_ivector(TvarV,1,NCOVMAX);
                   11568:   free_ivector(TvarVind,1,NCOVMAX);
                   11569:   free_ivector(TvarA,1,NCOVMAX);
                   11570:   free_ivector(TvarAind,1,NCOVMAX);
1.231     brouard  11571:   free_ivector(TvarFQ,1,NCOVMAX);
                   11572:   free_ivector(TvarFQind,1,NCOVMAX);
                   11573:   free_ivector(TvarVD,1,NCOVMAX);
                   11574:   free_ivector(TvarVDind,1,NCOVMAX);
                   11575:   free_ivector(TvarVQ,1,NCOVMAX);
                   11576:   free_ivector(TvarVQind,1,NCOVMAX);
1.230     brouard  11577:   free_ivector(Tvarsel,1,NCOVMAX);
                   11578:   free_vector(Tvalsel,1,NCOVMAX);
1.227     brouard  11579:   free_ivector(Tposprod,1,NCOVMAX);
                   11580:   free_ivector(Tprod,1,NCOVMAX);
                   11581:   free_ivector(Tvaraff,1,NCOVMAX);
                   11582:   free_ivector(invalidvarcomb,1,ncovcombmax);
                   11583:   free_ivector(Tage,1,NCOVMAX);
                   11584:   free_ivector(Tmodelind,1,NCOVMAX);
1.228     brouard  11585:   free_ivector(TmodelInvind,1,NCOVMAX);
                   11586:   free_ivector(TmodelInvQind,1,NCOVMAX);
1.227     brouard  11587:   
                   11588:   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
                   11589:   /* free_imatrix(codtab,1,100,1,10); */
1.126     brouard  11590:   fflush(fichtm);
                   11591:   fflush(ficgp);
                   11592:   
1.227     brouard  11593:   
1.126     brouard  11594:   if((nberr >0) || (nbwarn>0)){
1.216     brouard  11595:     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
                   11596:     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  11597:   }else{
                   11598:     printf("End of Imach\n");
                   11599:     fprintf(ficlog,"End of Imach\n");
                   11600:   }
                   11601:   printf("See log file on %s\n",filelog);
                   11602:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
1.157     brouard  11603:   /*(void) gettimeofday(&end_time,&tzp);*/
                   11604:   rend_time = time(NULL);  
                   11605:   end_time = *localtime(&rend_time);
                   11606:   /* tml = *localtime(&end_time.tm_sec); */
                   11607:   strcpy(strtend,asctime(&end_time));
1.126     brouard  11608:   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
                   11609:   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
1.157     brouard  11610:   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227     brouard  11611:   
1.157     brouard  11612:   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
                   11613:   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
                   11614:   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126     brouard  11615:   /*  printf("Total time was %d uSec.\n", total_usecs);*/
                   11616: /*   if(fileappend(fichtm,optionfilehtm)){ */
                   11617:   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   11618:   fclose(fichtm);
                   11619:   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   11620:   fclose(fichtmcov);
                   11621:   fclose(ficgp);
                   11622:   fclose(ficlog);
                   11623:   /*------ End -----------*/
1.227     brouard  11624:   
                   11625:   
                   11626:   printf("Before Current directory %s!\n",pathcd);
1.184     brouard  11627: #ifdef WIN32
1.227     brouard  11628:   if (_chdir(pathcd) != 0)
                   11629:     printf("Can't move to directory %s!\n",path);
                   11630:   if(_getcwd(pathcd,MAXLINE) > 0)
1.184     brouard  11631: #else
1.227     brouard  11632:     if(chdir(pathcd) != 0)
                   11633:       printf("Can't move to directory %s!\n", path);
                   11634:   if (getcwd(pathcd, MAXLINE) > 0)
1.184     brouard  11635: #endif 
1.126     brouard  11636:     printf("Current directory %s!\n",pathcd);
                   11637:   /*strcat(plotcmd,CHARSEPARATOR);*/
                   11638:   sprintf(plotcmd,"gnuplot");
1.157     brouard  11639: #ifdef _WIN32
1.126     brouard  11640:   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
                   11641: #endif
                   11642:   if(!stat(plotcmd,&info)){
1.158     brouard  11643:     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126     brouard  11644:     if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158     brouard  11645:       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126     brouard  11646:     }else
                   11647:       strcpy(pplotcmd,plotcmd);
1.157     brouard  11648: #ifdef __unix
1.126     brouard  11649:     strcpy(plotcmd,GNUPLOTPROGRAM);
                   11650:     if(!stat(plotcmd,&info)){
1.158     brouard  11651:       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126     brouard  11652:     }else
                   11653:       strcpy(pplotcmd,plotcmd);
                   11654: #endif
                   11655:   }else
                   11656:     strcpy(pplotcmd,plotcmd);
                   11657:   
                   11658:   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158     brouard  11659:   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227     brouard  11660:   
1.126     brouard  11661:   if((outcmd=system(plotcmd)) != 0){
1.158     brouard  11662:     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154     brouard  11663:     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152     brouard  11664:     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150     brouard  11665:     if((outcmd=system(plotcmd)) != 0)
1.153     brouard  11666:       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126     brouard  11667:   }
1.158     brouard  11668:   printf(" Successful, please wait...");
1.126     brouard  11669:   while (z[0] != 'q') {
                   11670:     /* chdir(path); */
1.154     brouard  11671:     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126     brouard  11672:     scanf("%s",z);
                   11673: /*     if (z[0] == 'c') system("./imach"); */
                   11674:     if (z[0] == 'e') {
1.158     brouard  11675: #ifdef __APPLE__
1.152     brouard  11676:       sprintf(pplotcmd, "open %s", optionfilehtm);
1.157     brouard  11677: #elif __linux
                   11678:       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153     brouard  11679: #else
1.152     brouard  11680:       sprintf(pplotcmd, "%s", optionfilehtm);
1.153     brouard  11681: #endif
                   11682:       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
                   11683:       system(pplotcmd);
1.126     brouard  11684:     }
                   11685:     else if (z[0] == 'g') system(plotcmd);
                   11686:     else if (z[0] == 'q') exit(0);
                   11687:   }
1.227     brouard  11688: end:
1.126     brouard  11689:   while (z[0] != 'q') {
1.195     brouard  11690:     printf("\nType  q for exiting: "); fflush(stdout);
1.126     brouard  11691:     scanf("%s",z);
                   11692:   }
                   11693: }

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