Annotation of imach/src/imach.c, revision 1.184

1.184   ! brouard     1: /* $Id: imach.c,v 1.183 2015/03/10 20:34:32 brouard Exp $
1.126     brouard     2:   $State: Exp $
1.163     brouard     3:   $Log: imach.c,v $
1.184   ! brouard     4:   Revision 1.183  2015/03/10 20:34:32  brouard
        !             5:   Summary: 0.98q0, trying with directest, mnbrak fixed
        !             6: 
        !             7:   We use directest instead of original Powell test; probably no
        !             8:   incidence on the results, but better justifications;
        !             9:   We fixed Numerical Recipes mnbrak routine which was wrong and gave
        !            10:   wrong results.
        !            11: 
1.183     brouard    12:   Revision 1.182  2015/02/12 08:19:57  brouard
                     13:   Summary: Trying to keep directest which seems simpler and more general
                     14:   Author: Nicolas Brouard
                     15: 
1.182     brouard    16:   Revision 1.181  2015/02/11 23:22:24  brouard
                     17:   Summary: Comments on Powell added
                     18: 
                     19:   Author:
                     20: 
1.181     brouard    21:   Revision 1.180  2015/02/11 17:33:45  brouard
                     22:   Summary: Finishing move from main to function (hpijx and prevalence_limit)
                     23: 
1.180     brouard    24:   Revision 1.179  2015/01/04 09:57:06  brouard
                     25:   Summary: back to OS/X
                     26: 
1.179     brouard    27:   Revision 1.178  2015/01/04 09:35:48  brouard
                     28:   *** empty log message ***
                     29: 
1.178     brouard    30:   Revision 1.177  2015/01/03 18:40:56  brouard
                     31:   Summary: Still testing ilc32 on OSX
                     32: 
1.177     brouard    33:   Revision 1.176  2015/01/03 16:45:04  brouard
                     34:   *** empty log message ***
                     35: 
1.176     brouard    36:   Revision 1.175  2015/01/03 16:33:42  brouard
                     37:   *** empty log message ***
                     38: 
1.175     brouard    39:   Revision 1.174  2015/01/03 16:15:49  brouard
                     40:   Summary: Still in cross-compilation
                     41: 
1.174     brouard    42:   Revision 1.173  2015/01/03 12:06:26  brouard
                     43:   Summary: trying to detect cross-compilation
                     44: 
1.173     brouard    45:   Revision 1.172  2014/12/27 12:07:47  brouard
                     46:   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
                     47: 
1.172     brouard    48:   Revision 1.171  2014/12/23 13:26:59  brouard
                     49:   Summary: Back from Visual C
                     50: 
                     51:   Still problem with utsname.h on Windows
                     52: 
1.171     brouard    53:   Revision 1.170  2014/12/23 11:17:12  brouard
                     54:   Summary: Cleaning some \%% back to %%
                     55: 
                     56:   The escape was mandatory for a specific compiler (which one?), but too many warnings.
                     57: 
1.170     brouard    58:   Revision 1.169  2014/12/22 23:08:31  brouard
                     59:   Summary: 0.98p
                     60: 
                     61:   Outputs some informations on compiler used, OS etc. Testing on different platforms.
                     62: 
1.169     brouard    63:   Revision 1.168  2014/12/22 15:17:42  brouard
1.170     brouard    64:   Summary: update
1.169     brouard    65: 
1.168     brouard    66:   Revision 1.167  2014/12/22 13:50:56  brouard
                     67:   Summary: Testing uname and compiler version and if compiled 32 or 64
                     68: 
                     69:   Testing on Linux 64
                     70: 
1.167     brouard    71:   Revision 1.166  2014/12/22 11:40:47  brouard
                     72:   *** empty log message ***
                     73: 
1.166     brouard    74:   Revision 1.165  2014/12/16 11:20:36  brouard
                     75:   Summary: After compiling on Visual C
                     76: 
                     77:   * imach.c (Module): Merging 1.61 to 1.162
                     78: 
1.165     brouard    79:   Revision 1.164  2014/12/16 10:52:11  brouard
                     80:   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
                     81: 
                     82:   * imach.c (Module): Merging 1.61 to 1.162
                     83: 
1.164     brouard    84:   Revision 1.163  2014/12/16 10:30:11  brouard
                     85:   * imach.c (Module): Merging 1.61 to 1.162
                     86: 
1.163     brouard    87:   Revision 1.162  2014/09/25 11:43:39  brouard
                     88:   Summary: temporary backup 0.99!
                     89: 
1.162     brouard    90:   Revision 1.1  2014/09/16 11:06:58  brouard
                     91:   Summary: With some code (wrong) for nlopt
                     92: 
                     93:   Author:
                     94: 
                     95:   Revision 1.161  2014/09/15 20:41:41  brouard
                     96:   Summary: Problem with macro SQR on Intel compiler
                     97: 
1.161     brouard    98:   Revision 1.160  2014/09/02 09:24:05  brouard
                     99:   *** empty log message ***
                    100: 
1.160     brouard   101:   Revision 1.159  2014/09/01 10:34:10  brouard
                    102:   Summary: WIN32
                    103:   Author: Brouard
                    104: 
1.159     brouard   105:   Revision 1.158  2014/08/27 17:11:51  brouard
                    106:   *** empty log message ***
                    107: 
1.158     brouard   108:   Revision 1.157  2014/08/27 16:26:55  brouard
                    109:   Summary: Preparing windows Visual studio version
                    110:   Author: Brouard
                    111: 
                    112:   In order to compile on Visual studio, time.h is now correct and time_t
                    113:   and tm struct should be used. difftime should be used but sometimes I
                    114:   just make the differences in raw time format (time(&now).
                    115:   Trying to suppress #ifdef LINUX
                    116:   Add xdg-open for __linux in order to open default browser.
                    117: 
1.157     brouard   118:   Revision 1.156  2014/08/25 20:10:10  brouard
                    119:   *** empty log message ***
                    120: 
1.156     brouard   121:   Revision 1.155  2014/08/25 18:32:34  brouard
                    122:   Summary: New compile, minor changes
                    123:   Author: Brouard
                    124: 
1.155     brouard   125:   Revision 1.154  2014/06/20 17:32:08  brouard
                    126:   Summary: Outputs now all graphs of convergence to period prevalence
                    127: 
1.154     brouard   128:   Revision 1.153  2014/06/20 16:45:46  brouard
                    129:   Summary: If 3 live state, convergence to period prevalence on same graph
                    130:   Author: Brouard
                    131: 
1.153     brouard   132:   Revision 1.152  2014/06/18 17:54:09  brouard
                    133:   Summary: open browser, use gnuplot on same dir than imach if not found in the path
                    134: 
1.152     brouard   135:   Revision 1.151  2014/06/18 16:43:30  brouard
                    136:   *** empty log message ***
                    137: 
1.151     brouard   138:   Revision 1.150  2014/06/18 16:42:35  brouard
                    139:   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
                    140:   Author: brouard
                    141: 
1.150     brouard   142:   Revision 1.149  2014/06/18 15:51:14  brouard
                    143:   Summary: Some fixes in parameter files errors
                    144:   Author: Nicolas Brouard
                    145: 
1.149     brouard   146:   Revision 1.148  2014/06/17 17:38:48  brouard
                    147:   Summary: Nothing new
                    148:   Author: Brouard
                    149: 
                    150:   Just a new packaging for OS/X version 0.98nS
                    151: 
1.148     brouard   152:   Revision 1.147  2014/06/16 10:33:11  brouard
                    153:   *** empty log message ***
                    154: 
1.147     brouard   155:   Revision 1.146  2014/06/16 10:20:28  brouard
                    156:   Summary: Merge
                    157:   Author: Brouard
                    158: 
                    159:   Merge, before building revised version.
                    160: 
1.146     brouard   161:   Revision 1.145  2014/06/10 21:23:15  brouard
                    162:   Summary: Debugging with valgrind
                    163:   Author: Nicolas Brouard
                    164: 
                    165:   Lot of changes in order to output the results with some covariates
                    166:   After the Edimburgh REVES conference 2014, it seems mandatory to
                    167:   improve the code.
                    168:   No more memory valgrind error but a lot has to be done in order to
                    169:   continue the work of splitting the code into subroutines.
                    170:   Also, decodemodel has been improved. Tricode is still not
                    171:   optimal. nbcode should be improved. Documentation has been added in
                    172:   the source code.
                    173: 
1.144     brouard   174:   Revision 1.143  2014/01/26 09:45:38  brouard
                    175:   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
                    176: 
                    177:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    178:   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
                    179: 
1.143     brouard   180:   Revision 1.142  2014/01/26 03:57:36  brouard
                    181:   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
                    182: 
                    183:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    184: 
1.142     brouard   185:   Revision 1.141  2014/01/26 02:42:01  brouard
                    186:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
                    187: 
1.141     brouard   188:   Revision 1.140  2011/09/02 10:37:54  brouard
                    189:   Summary: times.h is ok with mingw32 now.
                    190: 
1.140     brouard   191:   Revision 1.139  2010/06/14 07:50:17  brouard
                    192:   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
                    193:   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
                    194: 
1.139     brouard   195:   Revision 1.138  2010/04/30 18:19:40  brouard
                    196:   *** empty log message ***
                    197: 
1.138     brouard   198:   Revision 1.137  2010/04/29 18:11:38  brouard
                    199:   (Module): Checking covariates for more complex models
                    200:   than V1+V2. A lot of change to be done. Unstable.
                    201: 
1.137     brouard   202:   Revision 1.136  2010/04/26 20:30:53  brouard
                    203:   (Module): merging some libgsl code. Fixing computation
                    204:   of likelione (using inter/intrapolation if mle = 0) in order to
                    205:   get same likelihood as if mle=1.
                    206:   Some cleaning of code and comments added.
                    207: 
1.136     brouard   208:   Revision 1.135  2009/10/29 15:33:14  brouard
                    209:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                    210: 
1.135     brouard   211:   Revision 1.134  2009/10/29 13:18:53  brouard
                    212:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
                    213: 
1.134     brouard   214:   Revision 1.133  2009/07/06 10:21:25  brouard
                    215:   just nforces
                    216: 
1.133     brouard   217:   Revision 1.132  2009/07/06 08:22:05  brouard
                    218:   Many tings
                    219: 
1.132     brouard   220:   Revision 1.131  2009/06/20 16:22:47  brouard
                    221:   Some dimensions resccaled
                    222: 
1.131     brouard   223:   Revision 1.130  2009/05/26 06:44:34  brouard
                    224:   (Module): Max Covariate is now set to 20 instead of 8. A
                    225:   lot of cleaning with variables initialized to 0. Trying to make
                    226:   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
                    227: 
1.130     brouard   228:   Revision 1.129  2007/08/31 13:49:27  lievre
                    229:   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
                    230: 
1.129     lievre    231:   Revision 1.128  2006/06/30 13:02:05  brouard
                    232:   (Module): Clarifications on computing e.j
                    233: 
1.128     brouard   234:   Revision 1.127  2006/04/28 18:11:50  brouard
                    235:   (Module): Yes the sum of survivors was wrong since
                    236:   imach-114 because nhstepm was no more computed in the age
                    237:   loop. Now we define nhstepma in the age loop.
                    238:   (Module): In order to speed up (in case of numerous covariates) we
                    239:   compute health expectancies (without variances) in a first step
                    240:   and then all the health expectancies with variances or standard
                    241:   deviation (needs data from the Hessian matrices) which slows the
                    242:   computation.
                    243:   In the future we should be able to stop the program is only health
                    244:   expectancies and graph are needed without standard deviations.
                    245: 
1.127     brouard   246:   Revision 1.126  2006/04/28 17:23:28  brouard
                    247:   (Module): Yes the sum of survivors was wrong since
                    248:   imach-114 because nhstepm was no more computed in the age
                    249:   loop. Now we define nhstepma in the age loop.
                    250:   Version 0.98h
                    251: 
1.126     brouard   252:   Revision 1.125  2006/04/04 15:20:31  lievre
                    253:   Errors in calculation of health expectancies. Age was not initialized.
                    254:   Forecasting file added.
                    255: 
                    256:   Revision 1.124  2006/03/22 17:13:53  lievre
                    257:   Parameters are printed with %lf instead of %f (more numbers after the comma).
                    258:   The log-likelihood is printed in the log file
                    259: 
                    260:   Revision 1.123  2006/03/20 10:52:43  brouard
                    261:   * imach.c (Module): <title> changed, corresponds to .htm file
                    262:   name. <head> headers where missing.
                    263: 
                    264:   * imach.c (Module): Weights can have a decimal point as for
                    265:   English (a comma might work with a correct LC_NUMERIC environment,
                    266:   otherwise the weight is truncated).
                    267:   Modification of warning when the covariates values are not 0 or
                    268:   1.
                    269:   Version 0.98g
                    270: 
                    271:   Revision 1.122  2006/03/20 09:45:41  brouard
                    272:   (Module): Weights can have a decimal point as for
                    273:   English (a comma might work with a correct LC_NUMERIC environment,
                    274:   otherwise the weight is truncated).
                    275:   Modification of warning when the covariates values are not 0 or
                    276:   1.
                    277:   Version 0.98g
                    278: 
                    279:   Revision 1.121  2006/03/16 17:45:01  lievre
                    280:   * imach.c (Module): Comments concerning covariates added
                    281: 
                    282:   * imach.c (Module): refinements in the computation of lli if
                    283:   status=-2 in order to have more reliable computation if stepm is
                    284:   not 1 month. Version 0.98f
                    285: 
                    286:   Revision 1.120  2006/03/16 15:10:38  lievre
                    287:   (Module): refinements in the computation of lli if
                    288:   status=-2 in order to have more reliable computation if stepm is
                    289:   not 1 month. Version 0.98f
                    290: 
                    291:   Revision 1.119  2006/03/15 17:42:26  brouard
                    292:   (Module): Bug if status = -2, the loglikelihood was
                    293:   computed as likelihood omitting the logarithm. Version O.98e
                    294: 
                    295:   Revision 1.118  2006/03/14 18:20:07  brouard
                    296:   (Module): varevsij Comments added explaining the second
                    297:   table of variances if popbased=1 .
                    298:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    299:   (Module): Function pstamp added
                    300:   (Module): Version 0.98d
                    301: 
                    302:   Revision 1.117  2006/03/14 17:16:22  brouard
                    303:   (Module): varevsij Comments added explaining the second
                    304:   table of variances if popbased=1 .
                    305:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
                    306:   (Module): Function pstamp added
                    307:   (Module): Version 0.98d
                    308: 
                    309:   Revision 1.116  2006/03/06 10:29:27  brouard
                    310:   (Module): Variance-covariance wrong links and
                    311:   varian-covariance of ej. is needed (Saito).
                    312: 
                    313:   Revision 1.115  2006/02/27 12:17:45  brouard
                    314:   (Module): One freematrix added in mlikeli! 0.98c
                    315: 
                    316:   Revision 1.114  2006/02/26 12:57:58  brouard
                    317:   (Module): Some improvements in processing parameter
                    318:   filename with strsep.
                    319: 
                    320:   Revision 1.113  2006/02/24 14:20:24  brouard
                    321:   (Module): Memory leaks checks with valgrind and:
                    322:   datafile was not closed, some imatrix were not freed and on matrix
                    323:   allocation too.
                    324: 
                    325:   Revision 1.112  2006/01/30 09:55:26  brouard
                    326:   (Module): Back to gnuplot.exe instead of wgnuplot.exe
                    327: 
                    328:   Revision 1.111  2006/01/25 20:38:18  brouard
                    329:   (Module): Lots of cleaning and bugs added (Gompertz)
                    330:   (Module): Comments can be added in data file. Missing date values
                    331:   can be a simple dot '.'.
                    332: 
                    333:   Revision 1.110  2006/01/25 00:51:50  brouard
                    334:   (Module): Lots of cleaning and bugs added (Gompertz)
                    335: 
                    336:   Revision 1.109  2006/01/24 19:37:15  brouard
                    337:   (Module): Comments (lines starting with a #) are allowed in data.
                    338: 
                    339:   Revision 1.108  2006/01/19 18:05:42  lievre
                    340:   Gnuplot problem appeared...
                    341:   To be fixed
                    342: 
                    343:   Revision 1.107  2006/01/19 16:20:37  brouard
                    344:   Test existence of gnuplot in imach path
                    345: 
                    346:   Revision 1.106  2006/01/19 13:24:36  brouard
                    347:   Some cleaning and links added in html output
                    348: 
                    349:   Revision 1.105  2006/01/05 20:23:19  lievre
                    350:   *** empty log message ***
                    351: 
                    352:   Revision 1.104  2005/09/30 16:11:43  lievre
                    353:   (Module): sump fixed, loop imx fixed, and simplifications.
                    354:   (Module): If the status is missing at the last wave but we know
                    355:   that the person is alive, then we can code his/her status as -2
                    356:   (instead of missing=-1 in earlier versions) and his/her
                    357:   contributions to the likelihood is 1 - Prob of dying from last
                    358:   health status (= 1-p13= p11+p12 in the easiest case of somebody in
                    359:   the healthy state at last known wave). Version is 0.98
                    360: 
                    361:   Revision 1.103  2005/09/30 15:54:49  lievre
                    362:   (Module): sump fixed, loop imx fixed, and simplifications.
                    363: 
                    364:   Revision 1.102  2004/09/15 17:31:30  brouard
                    365:   Add the possibility to read data file including tab characters.
                    366: 
                    367:   Revision 1.101  2004/09/15 10:38:38  brouard
                    368:   Fix on curr_time
                    369: 
                    370:   Revision 1.100  2004/07/12 18:29:06  brouard
                    371:   Add version for Mac OS X. Just define UNIX in Makefile
                    372: 
                    373:   Revision 1.99  2004/06/05 08:57:40  brouard
                    374:   *** empty log message ***
                    375: 
                    376:   Revision 1.98  2004/05/16 15:05:56  brouard
                    377:   New version 0.97 . First attempt to estimate force of mortality
                    378:   directly from the data i.e. without the need of knowing the health
                    379:   state at each age, but using a Gompertz model: log u =a + b*age .
                    380:   This is the basic analysis of mortality and should be done before any
                    381:   other analysis, in order to test if the mortality estimated from the
                    382:   cross-longitudinal survey is different from the mortality estimated
                    383:   from other sources like vital statistic data.
                    384: 
                    385:   The same imach parameter file can be used but the option for mle should be -3.
                    386: 
1.133     brouard   387:   Agnès, who wrote this part of the code, tried to keep most of the
1.126     brouard   388:   former routines in order to include the new code within the former code.
                    389: 
                    390:   The output is very simple: only an estimate of the intercept and of
                    391:   the slope with 95% confident intervals.
                    392: 
                    393:   Current limitations:
                    394:   A) Even if you enter covariates, i.e. with the
                    395:   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
                    396:   B) There is no computation of Life Expectancy nor Life Table.
                    397: 
                    398:   Revision 1.97  2004/02/20 13:25:42  lievre
                    399:   Version 0.96d. Population forecasting command line is (temporarily)
                    400:   suppressed.
                    401: 
                    402:   Revision 1.96  2003/07/15 15:38:55  brouard
                    403:   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
                    404:   rewritten within the same printf. Workaround: many printfs.
                    405: 
                    406:   Revision 1.95  2003/07/08 07:54:34  brouard
                    407:   * imach.c (Repository):
                    408:   (Repository): Using imachwizard code to output a more meaningful covariance
                    409:   matrix (cov(a12,c31) instead of numbers.
                    410: 
                    411:   Revision 1.94  2003/06/27 13:00:02  brouard
                    412:   Just cleaning
                    413: 
                    414:   Revision 1.93  2003/06/25 16:33:55  brouard
                    415:   (Module): On windows (cygwin) function asctime_r doesn't
                    416:   exist so I changed back to asctime which exists.
                    417:   (Module): Version 0.96b
                    418: 
                    419:   Revision 1.92  2003/06/25 16:30:45  brouard
                    420:   (Module): On windows (cygwin) function asctime_r doesn't
                    421:   exist so I changed back to asctime which exists.
                    422: 
                    423:   Revision 1.91  2003/06/25 15:30:29  brouard
                    424:   * imach.c (Repository): Duplicated warning errors corrected.
                    425:   (Repository): Elapsed time after each iteration is now output. It
                    426:   helps to forecast when convergence will be reached. Elapsed time
                    427:   is stamped in powell.  We created a new html file for the graphs
                    428:   concerning matrix of covariance. It has extension -cov.htm.
                    429: 
                    430:   Revision 1.90  2003/06/24 12:34:15  brouard
                    431:   (Module): Some bugs corrected for windows. Also, when
                    432:   mle=-1 a template is output in file "or"mypar.txt with the design
                    433:   of the covariance matrix to be input.
                    434: 
                    435:   Revision 1.89  2003/06/24 12:30:52  brouard
                    436:   (Module): Some bugs corrected for windows. Also, when
                    437:   mle=-1 a template is output in file "or"mypar.txt with the design
                    438:   of the covariance matrix to be input.
                    439: 
                    440:   Revision 1.88  2003/06/23 17:54:56  brouard
                    441:   * 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.
                    442: 
                    443:   Revision 1.87  2003/06/18 12:26:01  brouard
                    444:   Version 0.96
                    445: 
                    446:   Revision 1.86  2003/06/17 20:04:08  brouard
                    447:   (Module): Change position of html and gnuplot routines and added
                    448:   routine fileappend.
                    449: 
                    450:   Revision 1.85  2003/06/17 13:12:43  brouard
                    451:   * imach.c (Repository): Check when date of death was earlier that
                    452:   current date of interview. It may happen when the death was just
                    453:   prior to the death. In this case, dh was negative and likelihood
                    454:   was wrong (infinity). We still send an "Error" but patch by
                    455:   assuming that the date of death was just one stepm after the
                    456:   interview.
                    457:   (Repository): Because some people have very long ID (first column)
                    458:   we changed int to long in num[] and we added a new lvector for
                    459:   memory allocation. But we also truncated to 8 characters (left
                    460:   truncation)
                    461:   (Repository): No more line truncation errors.
                    462: 
                    463:   Revision 1.84  2003/06/13 21:44:43  brouard
                    464:   * imach.c (Repository): Replace "freqsummary" at a correct
                    465:   place. It differs from routine "prevalence" which may be called
                    466:   many times. Probs is memory consuming and must be used with
                    467:   parcimony.
                    468:   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
                    469: 
                    470:   Revision 1.83  2003/06/10 13:39:11  lievre
                    471:   *** empty log message ***
                    472: 
                    473:   Revision 1.82  2003/06/05 15:57:20  brouard
                    474:   Add log in  imach.c and  fullversion number is now printed.
                    475: 
                    476: */
                    477: /*
                    478:    Interpolated Markov Chain
                    479: 
                    480:   Short summary of the programme:
                    481:   
                    482:   This program computes Healthy Life Expectancies from
                    483:   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
                    484:   first survey ("cross") where individuals from different ages are
                    485:   interviewed on their health status or degree of disability (in the
                    486:   case of a health survey which is our main interest) -2- at least a
                    487:   second wave of interviews ("longitudinal") which measure each change
                    488:   (if any) in individual health status.  Health expectancies are
                    489:   computed from the time spent in each health state according to a
                    490:   model. More health states you consider, more time is necessary to reach the
                    491:   Maximum Likelihood of the parameters involved in the model.  The
                    492:   simplest model is the multinomial logistic model where pij is the
                    493:   probability to be observed in state j at the second wave
                    494:   conditional to be observed in state i at the first wave. Therefore
                    495:   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
                    496:   'age' is age and 'sex' is a covariate. If you want to have a more
                    497:   complex model than "constant and age", you should modify the program
                    498:   where the markup *Covariates have to be included here again* invites
                    499:   you to do it.  More covariates you add, slower the
                    500:   convergence.
                    501: 
                    502:   The advantage of this computer programme, compared to a simple
                    503:   multinomial logistic model, is clear when the delay between waves is not
                    504:   identical for each individual. Also, if a individual missed an
                    505:   intermediate interview, the information is lost, but taken into
                    506:   account using an interpolation or extrapolation.  
                    507: 
                    508:   hPijx is the probability to be observed in state i at age x+h
                    509:   conditional to the observed state i at age x. The delay 'h' can be
                    510:   split into an exact number (nh*stepm) of unobserved intermediate
                    511:   states. This elementary transition (by month, quarter,
                    512:   semester or year) is modelled as a multinomial logistic.  The hPx
                    513:   matrix is simply the matrix product of nh*stepm elementary matrices
                    514:   and the contribution of each individual to the likelihood is simply
                    515:   hPijx.
                    516: 
                    517:   Also this programme outputs the covariance matrix of the parameters but also
                    518:   of the life expectancies. It also computes the period (stable) prevalence. 
                    519:   
1.133     brouard   520:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                    521:            Institut national d'études démographiques, Paris.
1.126     brouard   522:   This software have been partly granted by Euro-REVES, a concerted action
                    523:   from the European Union.
                    524:   It is copyrighted identically to a GNU software product, ie programme and
                    525:   software can be distributed freely for non commercial use. Latest version
                    526:   can be accessed at http://euroreves.ined.fr/imach .
                    527: 
                    528:   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
                    529:   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
                    530:   
                    531:   **********************************************************************/
                    532: /*
                    533:   main
                    534:   read parameterfile
                    535:   read datafile
                    536:   concatwav
                    537:   freqsummary
                    538:   if (mle >= 1)
                    539:     mlikeli
                    540:   print results files
                    541:   if mle==1 
                    542:      computes hessian
                    543:   read end of parameter file: agemin, agemax, bage, fage, estepm
                    544:       begin-prev-date,...
                    545:   open gnuplot file
                    546:   open html file
1.145     brouard   547:   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
                    548:    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
                    549:                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
                    550:     freexexit2 possible for memory heap.
                    551: 
                    552:   h Pij x                         | pij_nom  ficrestpij
                    553:    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
                    554:        1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
                    555:        1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
                    556: 
                    557:        1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
                    558:        1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
                    559:   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
                    560:    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
                    561:    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
                    562: 
1.126     brouard   563:   forecasting if prevfcast==1 prevforecast call prevalence()
                    564:   health expectancies
                    565:   Variance-covariance of DFLE
                    566:   prevalence()
                    567:    movingaverage()
                    568:   varevsij() 
                    569:   if popbased==1 varevsij(,popbased)
                    570:   total life expectancies
                    571:   Variance of period (stable) prevalence
                    572:  end
                    573: */
                    574: 
1.165     brouard   575: #define POWELL /* Instead of NLOPT */
1.183     brouard   576: /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
1.184   ! brouard   577: /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
1.126     brouard   578: 
                    579: #include <math.h>
                    580: #include <stdio.h>
                    581: #include <stdlib.h>
                    582: #include <string.h>
1.159     brouard   583: 
                    584: #ifdef _WIN32
                    585: #include <io.h>
1.172     brouard   586: #include <windows.h>
                    587: #include <tchar.h>
1.159     brouard   588: #else
1.126     brouard   589: #include <unistd.h>
1.159     brouard   590: #endif
1.126     brouard   591: 
                    592: #include <limits.h>
                    593: #include <sys/types.h>
1.171     brouard   594: 
                    595: #if defined(__GNUC__)
                    596: #include <sys/utsname.h> /* Doesn't work on Windows */
                    597: #endif
                    598: 
1.126     brouard   599: #include <sys/stat.h>
                    600: #include <errno.h>
1.159     brouard   601: /* extern int errno; */
1.126     brouard   602: 
1.157     brouard   603: /* #ifdef LINUX */
                    604: /* #include <time.h> */
                    605: /* #include "timeval.h" */
                    606: /* #else */
                    607: /* #include <sys/time.h> */
                    608: /* #endif */
                    609: 
1.126     brouard   610: #include <time.h>
                    611: 
1.136     brouard   612: #ifdef GSL
                    613: #include <gsl/gsl_errno.h>
                    614: #include <gsl/gsl_multimin.h>
                    615: #endif
                    616: 
1.167     brouard   617: 
1.162     brouard   618: #ifdef NLOPT
                    619: #include <nlopt.h>
                    620: typedef struct {
                    621:   double (* function)(double [] );
                    622: } myfunc_data ;
                    623: #endif
                    624: 
1.126     brouard   625: /* #include <libintl.h> */
                    626: /* #define _(String) gettext (String) */
                    627: 
1.141     brouard   628: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126     brouard   629: 
                    630: #define GNUPLOTPROGRAM "gnuplot"
                    631: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
                    632: #define FILENAMELENGTH 132
                    633: 
                    634: #define        GLOCK_ERROR_NOPATH              -1      /* empty path */
                    635: #define        GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
                    636: 
1.144     brouard   637: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
                    638: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126     brouard   639: 
                    640: #define NINTERVMAX 8
1.144     brouard   641: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
                    642: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
                    643: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145     brouard   644: #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
1.126     brouard   645: #define MAXN 20000
1.144     brouard   646: #define YEARM 12. /**< Number of months per year */
1.126     brouard   647: #define AGESUP 130
                    648: #define AGEBASE 40
1.164     brouard   649: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157     brouard   650: #ifdef _WIN32
                    651: #define DIRSEPARATOR '\\'
                    652: #define CHARSEPARATOR "\\"
                    653: #define ODIRSEPARATOR '/'
                    654: #else
1.126     brouard   655: #define DIRSEPARATOR '/'
                    656: #define CHARSEPARATOR "/"
                    657: #define ODIRSEPARATOR '\\'
                    658: #endif
                    659: 
1.184   ! brouard   660: /* $Id: imach.c,v 1.183 2015/03/10 20:34:32 brouard Exp $ */
1.126     brouard   661: /* $State: Exp $ */
                    662: 
1.183     brouard   663: char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.184   ! brouard   664: char fullversion[]="$Revision: 1.183 $ $Date: 2015/03/10 20:34:32 $"; 
1.126     brouard   665: char strstart[80];
                    666: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130     brouard   667: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
1.133     brouard   668: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145     brouard   669: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
                    670: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
                    671: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
                    672: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
                    673: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
                    674: int cptcovprodnoage=0; /**< Number of covariate products without age */   
                    675: int cptcoveff=0; /* Total number of covariates to vary for printing results */
                    676: int cptcov=0; /* Working variable */
1.126     brouard   677: int npar=NPARMAX;
                    678: int nlstate=2; /* Number of live states */
                    679: int ndeath=1; /* Number of dead states */
1.130     brouard   680: int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126     brouard   681: int popbased=0;
                    682: 
                    683: int *wav; /* Number of waves for this individuual 0 is possible */
1.130     brouard   684: int maxwav=0; /* Maxim number of waves */
                    685: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
                    686: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
                    687: int gipmx=0, gsw=0; /* Global variables on the number of contributions 
1.126     brouard   688:                   to the likelihood and the sum of weights (done by funcone)*/
1.130     brouard   689: int mle=1, weightopt=0;
1.126     brouard   690: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
                    691: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
                    692: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
                    693:           * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162     brouard   694: int countcallfunc=0;  /* Count the number of calls to func */
1.130     brouard   695: double jmean=1; /* Mean space between 2 waves */
1.145     brouard   696: double **matprod2(); /* test */
1.126     brouard   697: double **oldm, **newm, **savm; /* Working pointers to matrices */
                    698: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136     brouard   699: /*FILE *fic ; */ /* Used in readdata only */
                    700: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126     brouard   701: FILE *ficlog, *ficrespow;
1.130     brouard   702: int globpr=0; /* Global variable for printing or not */
1.126     brouard   703: double fretone; /* Only one call to likelihood */
1.130     brouard   704: long ipmx=0; /* Number of contributions */
1.126     brouard   705: double sw; /* Sum of weights */
                    706: char filerespow[FILENAMELENGTH];
                    707: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
                    708: FILE *ficresilk;
                    709: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
                    710: FILE *ficresprobmorprev;
                    711: FILE *fichtm, *fichtmcov; /* Html File */
                    712: FILE *ficreseij;
                    713: char filerese[FILENAMELENGTH];
                    714: FILE *ficresstdeij;
                    715: char fileresstde[FILENAMELENGTH];
                    716: FILE *ficrescveij;
                    717: char filerescve[FILENAMELENGTH];
                    718: FILE  *ficresvij;
                    719: char fileresv[FILENAMELENGTH];
                    720: FILE  *ficresvpl;
                    721: char fileresvpl[FILENAMELENGTH];
                    722: char title[MAXLINE];
                    723: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
                    724: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
                    725: char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
                    726: char command[FILENAMELENGTH];
                    727: int  outcmd=0;
                    728: 
                    729: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
                    730: 
                    731: char filelog[FILENAMELENGTH]; /* Log file */
                    732: char filerest[FILENAMELENGTH];
                    733: char fileregp[FILENAMELENGTH];
                    734: char popfile[FILENAMELENGTH];
                    735: 
                    736: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
                    737: 
1.157     brouard   738: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
                    739: /* struct timezone tzp; */
                    740: /* extern int gettimeofday(); */
                    741: struct tm tml, *gmtime(), *localtime();
                    742: 
                    743: extern time_t time();
                    744: 
                    745: struct tm start_time, end_time, curr_time, last_time, forecast_time;
                    746: time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
                    747: struct tm tm;
                    748: 
1.126     brouard   749: char strcurr[80], strfor[80];
                    750: 
                    751: char *endptr;
                    752: long lval;
                    753: double dval;
                    754: 
                    755: #define NR_END 1
                    756: #define FREE_ARG char*
                    757: #define FTOL 1.0e-10
                    758: 
                    759: #define NRANSI 
                    760: #define ITMAX 200 
                    761: 
                    762: #define TOL 2.0e-4 
                    763: 
                    764: #define CGOLD 0.3819660 
                    765: #define ZEPS 1.0e-10 
                    766: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
                    767: 
                    768: #define GOLD 1.618034 
                    769: #define GLIMIT 100.0 
                    770: #define TINY 1.0e-20 
                    771: 
                    772: static double maxarg1,maxarg2;
                    773: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
                    774: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                    775:   
                    776: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
                    777: #define rint(a) floor(a+0.5)
1.166     brouard   778: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183     brouard   779: #define mytinydouble 1.0e-16
1.166     brouard   780: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
                    781: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
                    782: /* static double dsqrarg; */
                    783: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126     brouard   784: static double sqrarg;
                    785: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
                    786: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                    787: int agegomp= AGEGOMP;
                    788: 
                    789: int imx; 
                    790: int stepm=1;
                    791: /* Stepm, step in month: minimum step interpolation*/
                    792: 
                    793: int estepm;
                    794: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
                    795: 
                    796: int m,nb;
                    797: long *num;
                    798: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
                    799: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
                    800: double **pmmij, ***probs;
                    801: double *ageexmed,*agecens;
                    802: double dateintmean=0;
                    803: 
                    804: double *weight;
                    805: int **s; /* Status */
1.141     brouard   806: double *agedc;
1.145     brouard   807: double  **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141     brouard   808:                  * covar=matrix(0,NCOVMAX,1,n); 
                    809:                  * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
                    810: double  idx; 
                    811: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145     brouard   812: int *Ndum; /** Freq of modality (tricode */
1.141     brouard   813: int **codtab; /**< codtab=imatrix(1,100,1,10); */
                    814: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126     brouard   815: double *lsurv, *lpop, *tpop;
                    816: 
1.143     brouard   817: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
                    818: double ftolhess; /**< Tolerance for computing hessian */
1.126     brouard   819: 
                    820: /**************** split *************************/
                    821: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
                    822: {
                    823:   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
                    824:      the name of the file (name), its extension only (ext) and its first part of the name (finame)
                    825:   */ 
                    826:   char *ss;                            /* pointer */
                    827:   int  l1, l2;                         /* length counters */
                    828: 
                    829:   l1 = strlen(path );                  /* length of path */
                    830:   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
                    831:   ss= strrchr( path, DIRSEPARATOR );           /* find last / */
                    832:   if ( ss == NULL ) {                  /* no directory, so determine current directory */
                    833:     strcpy( name, path );              /* we got the fullname name because no directory */
                    834:     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
                    835:       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
                    836:     /* get current working directory */
                    837:     /*    extern  char* getcwd ( char *buf , int len);*/
1.184   ! brouard   838: #ifdef WIN32
        !           839:     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
        !           840: #else
        !           841:        if (getcwd(dirc, FILENAME_MAX) == NULL) {
        !           842: #endif
1.126     brouard   843:       return( GLOCK_ERROR_GETCWD );
                    844:     }
                    845:     /* got dirc from getcwd*/
                    846:     printf(" DIRC = %s \n",dirc);
                    847:   } else {                             /* strip direcotry from path */
                    848:     ss++;                              /* after this, the filename */
                    849:     l2 = strlen( ss );                 /* length of filename */
                    850:     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
                    851:     strcpy( name, ss );                /* save file name */
                    852:     strncpy( dirc, path, l1 - l2 );    /* now the directory */
                    853:     dirc[l1-l2] = 0;                   /* add zero */
                    854:     printf(" DIRC2 = %s \n",dirc);
                    855:   }
                    856:   /* We add a separator at the end of dirc if not exists */
                    857:   l1 = strlen( dirc );                 /* length of directory */
                    858:   if( dirc[l1-1] != DIRSEPARATOR ){
                    859:     dirc[l1] =  DIRSEPARATOR;
                    860:     dirc[l1+1] = 0; 
                    861:     printf(" DIRC3 = %s \n",dirc);
                    862:   }
                    863:   ss = strrchr( name, '.' );           /* find last / */
                    864:   if (ss >0){
                    865:     ss++;
                    866:     strcpy(ext,ss);                    /* save extension */
                    867:     l1= strlen( name);
                    868:     l2= strlen(ss)+1;
                    869:     strncpy( finame, name, l1-l2);
                    870:     finame[l1-l2]= 0;
                    871:   }
                    872: 
                    873:   return( 0 );                         /* we're done */
                    874: }
                    875: 
                    876: 
                    877: /******************************************/
                    878: 
                    879: void replace_back_to_slash(char *s, char*t)
                    880: {
                    881:   int i;
                    882:   int lg=0;
                    883:   i=0;
                    884:   lg=strlen(t);
                    885:   for(i=0; i<= lg; i++) {
                    886:     (s[i] = t[i]);
                    887:     if (t[i]== '\\') s[i]='/';
                    888:   }
                    889: }
                    890: 
1.132     brouard   891: char *trimbb(char *out, char *in)
1.137     brouard   892: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132     brouard   893:   char *s;
                    894:   s=out;
                    895:   while (*in != '\0'){
1.137     brouard   896:     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132     brouard   897:       in++;
                    898:     }
                    899:     *out++ = *in++;
                    900:   }
                    901:   *out='\0';
                    902:   return s;
                    903: }
                    904: 
1.145     brouard   905: char *cutl(char *blocc, char *alocc, char *in, char occ)
                    906: {
                    907:   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
                    908:      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                    909:      gives blocc="abcdef2ghi" and alocc="j".
                    910:      If occ is not found blocc is null and alocc is equal to in. Returns blocc
                    911:   */
1.160     brouard   912:   char *s, *t;
1.145     brouard   913:   t=in;s=in;
                    914:   while ((*in != occ) && (*in != '\0')){
                    915:     *alocc++ = *in++;
                    916:   }
                    917:   if( *in == occ){
                    918:     *(alocc)='\0';
                    919:     s=++in;
                    920:   }
                    921:  
                    922:   if (s == t) {/* occ not found */
                    923:     *(alocc-(in-s))='\0';
                    924:     in=s;
                    925:   }
                    926:   while ( *in != '\0'){
                    927:     *blocc++ = *in++;
                    928:   }
                    929: 
                    930:   *blocc='\0';
                    931:   return t;
                    932: }
1.137     brouard   933: char *cutv(char *blocc, char *alocc, char *in, char occ)
                    934: {
                    935:   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
                    936:      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
                    937:      gives blocc="abcdef2ghi" and alocc="j".
                    938:      If occ is not found blocc is null and alocc is equal to in. Returns alocc
                    939:   */
                    940:   char *s, *t;
                    941:   t=in;s=in;
                    942:   while (*in != '\0'){
                    943:     while( *in == occ){
                    944:       *blocc++ = *in++;
                    945:       s=in;
                    946:     }
                    947:     *blocc++ = *in++;
                    948:   }
                    949:   if (s == t) /* occ not found */
                    950:     *(blocc-(in-s))='\0';
                    951:   else
                    952:     *(blocc-(in-s)-1)='\0';
                    953:   in=s;
                    954:   while ( *in != '\0'){
                    955:     *alocc++ = *in++;
                    956:   }
                    957: 
                    958:   *alocc='\0';
                    959:   return s;
                    960: }
                    961: 
1.126     brouard   962: int nbocc(char *s, char occ)
                    963: {
                    964:   int i,j=0;
                    965:   int lg=20;
                    966:   i=0;
                    967:   lg=strlen(s);
                    968:   for(i=0; i<= lg; i++) {
                    969:   if  (s[i] == occ ) j++;
                    970:   }
                    971:   return j;
                    972: }
                    973: 
1.137     brouard   974: /* void cutv(char *u,char *v, char*t, char occ) */
                    975: /* { */
                    976: /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
                    977: /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
                    978: /*      gives u="abcdef2ghi" and v="j" *\/ */
                    979: /*   int i,lg,j,p=0; */
                    980: /*   i=0; */
                    981: /*   lg=strlen(t); */
                    982: /*   for(j=0; j<=lg-1; j++) { */
                    983: /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
                    984: /*   } */
1.126     brouard   985: 
1.137     brouard   986: /*   for(j=0; j<p; j++) { */
                    987: /*     (u[j] = t[j]); */
                    988: /*   } */
                    989: /*      u[p]='\0'; */
1.126     brouard   990: 
1.137     brouard   991: /*    for(j=0; j<= lg; j++) { */
                    992: /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
                    993: /*   } */
                    994: /* } */
1.126     brouard   995: 
1.160     brouard   996: #ifdef _WIN32
                    997: char * strsep(char **pp, const char *delim)
                    998: {
                    999:   char *p, *q;
                   1000:          
                   1001:   if ((p = *pp) == NULL)
                   1002:     return 0;
                   1003:   if ((q = strpbrk (p, delim)) != NULL)
                   1004:   {
                   1005:     *pp = q + 1;
                   1006:     *q = '\0';
                   1007:   }
                   1008:   else
                   1009:     *pp = 0;
                   1010:   return p;
                   1011: }
                   1012: #endif
                   1013: 
1.126     brouard  1014: /********************** nrerror ********************/
                   1015: 
                   1016: void nrerror(char error_text[])
                   1017: {
                   1018:   fprintf(stderr,"ERREUR ...\n");
                   1019:   fprintf(stderr,"%s\n",error_text);
                   1020:   exit(EXIT_FAILURE);
                   1021: }
                   1022: /*********************** vector *******************/
                   1023: double *vector(int nl, int nh)
                   1024: {
                   1025:   double *v;
                   1026:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
                   1027:   if (!v) nrerror("allocation failure in vector");
                   1028:   return v-nl+NR_END;
                   1029: }
                   1030: 
                   1031: /************************ free vector ******************/
                   1032: void free_vector(double*v, int nl, int nh)
                   1033: {
                   1034:   free((FREE_ARG)(v+nl-NR_END));
                   1035: }
                   1036: 
                   1037: /************************ivector *******************************/
                   1038: int *ivector(long nl,long nh)
                   1039: {
                   1040:   int *v;
                   1041:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                   1042:   if (!v) nrerror("allocation failure in ivector");
                   1043:   return v-nl+NR_END;
                   1044: }
                   1045: 
                   1046: /******************free ivector **************************/
                   1047: void free_ivector(int *v, long nl, long nh)
                   1048: {
                   1049:   free((FREE_ARG)(v+nl-NR_END));
                   1050: }
                   1051: 
                   1052: /************************lvector *******************************/
                   1053: long *lvector(long nl,long nh)
                   1054: {
                   1055:   long *v;
                   1056:   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
                   1057:   if (!v) nrerror("allocation failure in ivector");
                   1058:   return v-nl+NR_END;
                   1059: }
                   1060: 
                   1061: /******************free lvector **************************/
                   1062: void free_lvector(long *v, long nl, long nh)
                   1063: {
                   1064:   free((FREE_ARG)(v+nl-NR_END));
                   1065: }
                   1066: 
                   1067: /******************* imatrix *******************************/
                   1068: int **imatrix(long nrl, long nrh, long ncl, long nch) 
                   1069:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
                   1070: { 
                   1071:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
                   1072:   int **m; 
                   1073:   
                   1074:   /* allocate pointers to rows */ 
                   1075:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
                   1076:   if (!m) nrerror("allocation failure 1 in matrix()"); 
                   1077:   m += NR_END; 
                   1078:   m -= nrl; 
                   1079:   
                   1080:   
                   1081:   /* allocate rows and set pointers to them */ 
                   1082:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
                   1083:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
                   1084:   m[nrl] += NR_END; 
                   1085:   m[nrl] -= ncl; 
                   1086:   
                   1087:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
                   1088:   
                   1089:   /* return pointer to array of pointers to rows */ 
                   1090:   return m; 
                   1091: } 
                   1092: 
                   1093: /****************** free_imatrix *************************/
                   1094: void free_imatrix(m,nrl,nrh,ncl,nch)
                   1095:       int **m;
                   1096:       long nch,ncl,nrh,nrl; 
                   1097:      /* free an int matrix allocated by imatrix() */ 
                   1098: { 
                   1099:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
                   1100:   free((FREE_ARG) (m+nrl-NR_END)); 
                   1101: } 
                   1102: 
                   1103: /******************* matrix *******************************/
                   1104: double **matrix(long nrl, long nrh, long ncl, long nch)
                   1105: {
                   1106:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
                   1107:   double **m;
                   1108: 
                   1109:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                   1110:   if (!m) nrerror("allocation failure 1 in matrix()");
                   1111:   m += NR_END;
                   1112:   m -= nrl;
                   1113: 
                   1114:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                   1115:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                   1116:   m[nrl] += NR_END;
                   1117:   m[nrl] -= ncl;
                   1118: 
                   1119:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                   1120:   return m;
1.145     brouard  1121:   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
                   1122: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
                   1123: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126     brouard  1124:    */
                   1125: }
                   1126: 
                   1127: /*************************free matrix ************************/
                   1128: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
                   1129: {
                   1130:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                   1131:   free((FREE_ARG)(m+nrl-NR_END));
                   1132: }
                   1133: 
                   1134: /******************* ma3x *******************************/
                   1135: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
                   1136: {
                   1137:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
                   1138:   double ***m;
                   1139: 
                   1140:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                   1141:   if (!m) nrerror("allocation failure 1 in matrix()");
                   1142:   m += NR_END;
                   1143:   m -= nrl;
                   1144: 
                   1145:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                   1146:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                   1147:   m[nrl] += NR_END;
                   1148:   m[nrl] -= ncl;
                   1149: 
                   1150:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                   1151: 
                   1152:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                   1153:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
                   1154:   m[nrl][ncl] += NR_END;
                   1155:   m[nrl][ncl] -= nll;
                   1156:   for (j=ncl+1; j<=nch; j++) 
                   1157:     m[nrl][j]=m[nrl][j-1]+nlay;
                   1158:   
                   1159:   for (i=nrl+1; i<=nrh; i++) {
                   1160:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
                   1161:     for (j=ncl+1; j<=nch; j++) 
                   1162:       m[i][j]=m[i][j-1]+nlay;
                   1163:   }
                   1164:   return m; 
                   1165:   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                   1166:            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
                   1167:   */
                   1168: }
                   1169: 
                   1170: /*************************free ma3x ************************/
                   1171: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                   1172: {
                   1173:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                   1174:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                   1175:   free((FREE_ARG)(m+nrl-NR_END));
                   1176: }
                   1177: 
                   1178: /*************** function subdirf ***********/
                   1179: char *subdirf(char fileres[])
                   1180: {
                   1181:   /* Caution optionfilefiname is hidden */
                   1182:   strcpy(tmpout,optionfilefiname);
                   1183:   strcat(tmpout,"/"); /* Add to the right */
                   1184:   strcat(tmpout,fileres);
                   1185:   return tmpout;
                   1186: }
                   1187: 
                   1188: /*************** function subdirf2 ***********/
                   1189: char *subdirf2(char fileres[], char *preop)
                   1190: {
                   1191:   
                   1192:   /* Caution optionfilefiname is hidden */
                   1193:   strcpy(tmpout,optionfilefiname);
                   1194:   strcat(tmpout,"/");
                   1195:   strcat(tmpout,preop);
                   1196:   strcat(tmpout,fileres);
                   1197:   return tmpout;
                   1198: }
                   1199: 
                   1200: /*************** function subdirf3 ***********/
                   1201: char *subdirf3(char fileres[], char *preop, char *preop2)
                   1202: {
                   1203:   
                   1204:   /* Caution optionfilefiname is hidden */
                   1205:   strcpy(tmpout,optionfilefiname);
                   1206:   strcat(tmpout,"/");
                   1207:   strcat(tmpout,preop);
                   1208:   strcat(tmpout,preop2);
                   1209:   strcat(tmpout,fileres);
                   1210:   return tmpout;
                   1211: }
                   1212: 
1.162     brouard  1213: char *asc_diff_time(long time_sec, char ascdiff[])
                   1214: {
                   1215:   long sec_left, days, hours, minutes;
                   1216:   days = (time_sec) / (60*60*24);
                   1217:   sec_left = (time_sec) % (60*60*24);
                   1218:   hours = (sec_left) / (60*60) ;
                   1219:   sec_left = (sec_left) %(60*60);
                   1220:   minutes = (sec_left) /60;
                   1221:   sec_left = (sec_left) % (60);
                   1222:   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
                   1223:   return ascdiff;
                   1224: }
                   1225: 
1.126     brouard  1226: /***************** f1dim *************************/
                   1227: extern int ncom; 
                   1228: extern double *pcom,*xicom;
                   1229: extern double (*nrfunc)(double []); 
                   1230:  
                   1231: double f1dim(double x) 
                   1232: { 
                   1233:   int j; 
                   1234:   double f;
                   1235:   double *xt; 
                   1236:  
                   1237:   xt=vector(1,ncom); 
                   1238:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
                   1239:   f=(*nrfunc)(xt); 
                   1240:   free_vector(xt,1,ncom); 
                   1241:   return f; 
                   1242: } 
                   1243: 
                   1244: /*****************brent *************************/
                   1245: double brent(double ax, double bx, double cx, double (*f)(double), double tol,         double *xmin) 
                   1246: { 
                   1247:   int iter; 
                   1248:   double a,b,d,etemp;
1.159     brouard  1249:   double fu=0,fv,fw,fx;
1.164     brouard  1250:   double ftemp=0.;
1.126     brouard  1251:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
                   1252:   double e=0.0; 
                   1253:  
                   1254:   a=(ax < cx ? ax : cx); 
                   1255:   b=(ax > cx ? ax : cx); 
                   1256:   x=w=v=bx; 
                   1257:   fw=fv=fx=(*f)(x); 
                   1258:   for (iter=1;iter<=ITMAX;iter++) { 
                   1259:     xm=0.5*(a+b); 
                   1260:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                   1261:     /*         if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                   1262:     printf(".");fflush(stdout);
                   1263:     fprintf(ficlog,".");fflush(ficlog);
1.162     brouard  1264: #ifdef DEBUGBRENT
1.126     brouard  1265:     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);
                   1266:     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);
                   1267:     /*         if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                   1268: #endif
                   1269:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                   1270:       *xmin=x; 
                   1271:       return fx; 
                   1272:     } 
                   1273:     ftemp=fu;
                   1274:     if (fabs(e) > tol1) { 
                   1275:       r=(x-w)*(fx-fv); 
                   1276:       q=(x-v)*(fx-fw); 
                   1277:       p=(x-v)*q-(x-w)*r; 
                   1278:       q=2.0*(q-r); 
                   1279:       if (q > 0.0) p = -p; 
                   1280:       q=fabs(q); 
                   1281:       etemp=e; 
                   1282:       e=d; 
                   1283:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
                   1284:        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                   1285:       else { 
                   1286:        d=p/q; 
                   1287:        u=x+d; 
                   1288:        if (u-a < tol2 || b-u < tol2) 
                   1289:          d=SIGN(tol1,xm-x); 
                   1290:       } 
                   1291:     } else { 
                   1292:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                   1293:     } 
                   1294:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                   1295:     fu=(*f)(u); 
                   1296:     if (fu <= fx) { 
                   1297:       if (u >= x) a=x; else b=x; 
                   1298:       SHFT(v,w,x,u) 
1.183     brouard  1299:       SHFT(fv,fw,fx,fu) 
                   1300:     } else { 
                   1301:       if (u < x) a=u; else b=u; 
                   1302:       if (fu <= fw || w == x) { 
                   1303:        v=w; 
                   1304:        w=u; 
                   1305:        fv=fw; 
                   1306:        fw=fu; 
                   1307:       } else if (fu <= fv || v == x || v == w) { 
                   1308:        v=u; 
                   1309:        fv=fu; 
                   1310:       } 
                   1311:     } 
1.126     brouard  1312:   } 
                   1313:   nrerror("Too many iterations in brent"); 
                   1314:   *xmin=x; 
                   1315:   return fx; 
                   1316: } 
                   1317: 
                   1318: /****************** mnbrak ***********************/
                   1319: 
                   1320: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                   1321:            double (*func)(double)) 
1.183     brouard  1322: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
                   1323: the downhill direction (defined by the function as evaluated at the initial points) and returns
                   1324: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
                   1325: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
                   1326:    */
1.126     brouard  1327:   double ulim,u,r,q, dum;
                   1328:   double fu; 
                   1329:  
                   1330:   *fa=(*func)(*ax); 
                   1331:   *fb=(*func)(*bx); 
                   1332:   if (*fb > *fa) { 
                   1333:     SHFT(dum,*ax,*bx,dum) 
1.183     brouard  1334:     SHFT(dum,*fb,*fa,dum) 
                   1335:   } 
1.126     brouard  1336:   *cx=(*bx)+GOLD*(*bx-*ax); 
                   1337:   *fc=(*func)(*cx); 
1.183     brouard  1338: #ifdef DEBUG
                   1339:   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
                   1340:   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
                   1341: #endif
                   1342:   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126     brouard  1343:     r=(*bx-*ax)*(*fb-*fc); 
                   1344:     q=(*bx-*cx)*(*fb-*fa); 
                   1345:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
1.183     brouard  1346:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
                   1347:     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
                   1348:     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126     brouard  1349:       fu=(*func)(u); 
1.163     brouard  1350: #ifdef DEBUG
                   1351:       /* f(x)=A(x-u)**2+f(u) */
                   1352:       double A, fparabu; 
                   1353:       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
                   1354:       fparabu= *fa - A*(*ax-u)*(*ax-u);
                   1355:       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
                   1356:       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1.183     brouard  1357:       /* And thus,it can be that fu > *fc even if fparabu < *fc */
                   1358:       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
                   1359:         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
                   1360:       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163     brouard  1361: #endif 
1.184   ! brouard  1362: #ifdef MNBRAKORIGINAL
1.183     brouard  1363: #else
                   1364:       if (fu > *fc) {
                   1365: #ifdef DEBUG
                   1366:       printf("mnbrak4  fu > fc \n");
                   1367:       fprintf(ficlog, "mnbrak4 fu > fc\n");
                   1368: #endif
                   1369:        /* 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 *\/  */
                   1370:        /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
                   1371:        dum=u; /* Shifting c and u */
                   1372:        u = *cx;
                   1373:        *cx = dum;
                   1374:        dum = fu;
                   1375:        fu = *fc;
                   1376:        *fc =dum;
                   1377:       } else { /* end */
                   1378: #ifdef DEBUG
                   1379:       printf("mnbrak3  fu < fc \n");
                   1380:       fprintf(ficlog, "mnbrak3 fu < fc\n");
                   1381: #endif
                   1382:        dum=u; /* Shifting c and u */
                   1383:        u = *cx;
                   1384:        *cx = dum;
                   1385:        dum = fu;
                   1386:        fu = *fc;
                   1387:        *fc =dum;
                   1388:       }
                   1389: #endif
1.162     brouard  1390:     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183     brouard  1391: #ifdef DEBUG
                   1392:       printf("mnbrak2  u after c but before ulim\n");
                   1393:       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
                   1394: #endif
1.126     brouard  1395:       fu=(*func)(u); 
                   1396:       if (fu < *fc) { 
1.183     brouard  1397: #ifdef DEBUG
                   1398:       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
                   1399:       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
                   1400: #endif
1.126     brouard  1401:        SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
1.183     brouard  1402:        SHFT(*fb,*fc,fu,(*func)(u)) 
                   1403:       } 
1.162     brouard  1404:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183     brouard  1405: #ifdef DEBUG
                   1406:       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
                   1407:       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
                   1408: #endif
1.126     brouard  1409:       u=ulim; 
                   1410:       fu=(*func)(u); 
1.183     brouard  1411:     } else { /* u could be left to b (if r > q parabola has a maximum) */
                   1412: #ifdef DEBUG
                   1413:       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
                   1414:       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
                   1415: #endif
1.126     brouard  1416:       u=(*cx)+GOLD*(*cx-*bx); 
                   1417:       fu=(*func)(u); 
1.183     brouard  1418:     } /* end tests */
1.126     brouard  1419:     SHFT(*ax,*bx,*cx,u) 
1.183     brouard  1420:     SHFT(*fa,*fb,*fc,fu) 
                   1421: #ifdef DEBUG
                   1422:       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
                   1423:       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
                   1424: #endif
                   1425:   } /* 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  1426: } 
                   1427: 
                   1428: /*************** linmin ************************/
1.162     brouard  1429: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
                   1430: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
                   1431: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
                   1432: the value of func at the returned location p . This is actually all accomplished by calling the
                   1433: routines mnbrak and brent .*/
1.126     brouard  1434: int ncom; 
                   1435: double *pcom,*xicom;
                   1436: double (*nrfunc)(double []); 
                   1437:  
                   1438: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
                   1439: { 
                   1440:   double brent(double ax, double bx, double cx, 
                   1441:               double (*f)(double), double tol, double *xmin); 
                   1442:   double f1dim(double x); 
                   1443:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                   1444:              double *fc, double (*func)(double)); 
                   1445:   int j; 
                   1446:   double xx,xmin,bx,ax; 
                   1447:   double fx,fb,fa;
                   1448:  
                   1449:   ncom=n; 
                   1450:   pcom=vector(1,n); 
                   1451:   xicom=vector(1,n); 
                   1452:   nrfunc=func; 
                   1453:   for (j=1;j<=n;j++) { 
                   1454:     pcom[j]=p[j]; 
                   1455:     xicom[j]=xi[j]; 
                   1456:   } 
                   1457:   ax=0.0; 
                   1458:   xx=1.0; 
1.162     brouard  1459:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
                   1460:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1.126     brouard  1461: #ifdef DEBUG
                   1462:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                   1463:   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                   1464: #endif
                   1465:   for (j=1;j<=n;j++) { 
                   1466:     xi[j] *= xmin; 
                   1467:     p[j] += xi[j]; 
                   1468:   } 
                   1469:   free_vector(xicom,1,n); 
                   1470:   free_vector(pcom,1,n); 
                   1471: } 
                   1472: 
                   1473: 
                   1474: /*************** powell ************************/
1.162     brouard  1475: /*
                   1476: Minimization of a function func of n variables. Input consists of an initial starting point
                   1477: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
                   1478: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
                   1479: such that failure to decrease by more than this amount on one iteration signals doneness. On
                   1480: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
                   1481: function value at p , and iter is the number of iterations taken. The routine linmin is used.
                   1482:  */
1.126     brouard  1483: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                   1484:            double (*func)(double [])) 
                   1485: { 
                   1486:   void linmin(double p[], double xi[], int n, double *fret, 
                   1487:              double (*func)(double [])); 
                   1488:   int i,ibig,j; 
                   1489:   double del,t,*pt,*ptt,*xit;
1.181     brouard  1490:   double directest;
1.126     brouard  1491:   double fp,fptt;
                   1492:   double *xits;
                   1493:   int niterf, itmp;
                   1494: 
                   1495:   pt=vector(1,n); 
                   1496:   ptt=vector(1,n); 
                   1497:   xit=vector(1,n); 
                   1498:   xits=vector(1,n); 
                   1499:   *fret=(*func)(p); 
                   1500:   for (j=1;j<=n;j++) pt[j]=p[j]; 
1.157     brouard  1501:     rcurr_time = time(NULL);  
1.126     brouard  1502:   for (*iter=1;;++(*iter)) { 
                   1503:     fp=(*fret); 
                   1504:     ibig=0; 
                   1505:     del=0.0; 
1.157     brouard  1506:     rlast_time=rcurr_time;
                   1507:     /* (void) gettimeofday(&curr_time,&tzp); */
                   1508:     rcurr_time = time(NULL);  
                   1509:     curr_time = *localtime(&rcurr_time);
                   1510:     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
                   1511:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
                   1512: /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126     brouard  1513:    for (i=1;i<=n;i++) {
                   1514:       printf(" %d %.12f",i, p[i]);
                   1515:       fprintf(ficlog," %d %.12lf",i, p[i]);
                   1516:       fprintf(ficrespow," %.12lf", p[i]);
                   1517:     }
                   1518:     printf("\n");
                   1519:     fprintf(ficlog,"\n");
                   1520:     fprintf(ficrespow,"\n");fflush(ficrespow);
                   1521:     if(*iter <=3){
1.157     brouard  1522:       tml = *localtime(&rcurr_time);
                   1523:       strcpy(strcurr,asctime(&tml));
                   1524:       rforecast_time=rcurr_time; 
1.126     brouard  1525:       itmp = strlen(strcurr);
                   1526:       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                   1527:        strcurr[itmp-1]='\0';
1.162     brouard  1528:       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157     brouard  1529:       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126     brouard  1530:       for(niterf=10;niterf<=30;niterf+=10){
1.157     brouard  1531:        rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                   1532:        forecast_time = *localtime(&rforecast_time);
                   1533:        strcpy(strfor,asctime(&forecast_time));
1.126     brouard  1534:        itmp = strlen(strfor);
                   1535:        if(strfor[itmp-1]=='\n')
                   1536:        strfor[itmp-1]='\0';
1.157     brouard  1537:        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);
                   1538:        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  1539:       }
                   1540:     }
                   1541:     for (i=1;i<=n;i++) { 
                   1542:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
                   1543:       fptt=(*fret); 
                   1544: #ifdef DEBUG
1.164     brouard  1545:          printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
                   1546:          fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126     brouard  1547: #endif
                   1548:       printf("%d",i);fflush(stdout);
                   1549:       fprintf(ficlog,"%d",i);fflush(ficlog);
1.183     brouard  1550:       linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
1.181     brouard  1551:       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
                   1552:                                       because that direction will be replaced unless the gain del is small
                   1553:                                      in comparison with the 'probable' gain, mu^2, with the last average direction.
                   1554:                                      Unless the n directions are conjugate some gain in the determinant may be obtained
                   1555:                                      with the new direction.
                   1556:                                      */
1.126     brouard  1557:        del=fabs(fptt-(*fret)); 
                   1558:        ibig=i; 
                   1559:       } 
                   1560: #ifdef DEBUG
                   1561:       printf("%d %.12e",i,(*fret));
                   1562:       fprintf(ficlog,"%d %.12e",i,(*fret));
                   1563:       for (j=1;j<=n;j++) {
                   1564:        xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                   1565:        printf(" x(%d)=%.12e",j,xit[j]);
                   1566:        fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
                   1567:       }
                   1568:       for(j=1;j<=n;j++) {
1.162     brouard  1569:        printf(" p(%d)=%.12e",j,p[j]);
                   1570:        fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126     brouard  1571:       }
                   1572:       printf("\n");
                   1573:       fprintf(ficlog,"\n");
                   1574: #endif
1.162     brouard  1575:     } /* end i */
1.182     brouard  1576:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.126     brouard  1577: #ifdef DEBUG
                   1578:       int k[2],l;
                   1579:       k[0]=1;
                   1580:       k[1]=-1;
                   1581:       printf("Max: %.12e",(*func)(p));
                   1582:       fprintf(ficlog,"Max: %.12e",(*func)(p));
                   1583:       for (j=1;j<=n;j++) {
                   1584:        printf(" %.12e",p[j]);
                   1585:        fprintf(ficlog," %.12e",p[j]);
                   1586:       }
                   1587:       printf("\n");
                   1588:       fprintf(ficlog,"\n");
                   1589:       for(l=0;l<=1;l++) {
                   1590:        for (j=1;j<=n;j++) {
                   1591:          ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                   1592:          printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   1593:          fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                   1594:        }
                   1595:        printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   1596:        fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                   1597:       }
                   1598: #endif
                   1599: 
                   1600: 
                   1601:       free_vector(xit,1,n); 
                   1602:       free_vector(xits,1,n); 
                   1603:       free_vector(ptt,1,n); 
                   1604:       free_vector(pt,1,n); 
                   1605:       return; 
                   1606:     } 
                   1607:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
1.181     brouard  1608:     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126     brouard  1609:       ptt[j]=2.0*p[j]-pt[j]; 
                   1610:       xit[j]=p[j]-pt[j]; 
                   1611:       pt[j]=p[j]; 
                   1612:     } 
1.181     brouard  1613:     fptt=(*func)(ptt); /* f_3 */
1.161     brouard  1614:     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162     brouard  1615:       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161     brouard  1616:       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162     brouard  1617:       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
                   1618:       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
                   1619:       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181     brouard  1620:       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161     brouard  1621:       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183     brouard  1622: #ifdef NRCORIGINAL
                   1623:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
                   1624: #else
                   1625:       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  1626:       t= t- del*SQR(fp-fptt);
1.183     brouard  1627: #endif
1.182     brouard  1628:       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161     brouard  1629: #ifdef DEBUG
1.181     brouard  1630:       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);
                   1631:       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  1632:       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                   1633:             (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
                   1634:       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                   1635:             (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
                   1636:       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);
                   1637:       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);
                   1638: #endif
1.183     brouard  1639: #ifdef POWELLORIGINAL
                   1640:       if (t < 0.0) { /* Then we use it for new direction */
                   1641: #else
1.182     brouard  1642:       if (directest*t < 0.0) { /* Contradiction between both tests */
1.184   ! brouard  1643:       printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.182     brouard  1644:       printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.184   ! brouard  1645:       fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.182     brouard  1646:       fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
                   1647:     } 
1.181     brouard  1648:       if (directest < 0.0) { /* Then we use it for new direction */
                   1649: #endif
                   1650:        linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
1.126     brouard  1651:        for (j=1;j<=n;j++) { 
1.181     brouard  1652:          xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                   1653:          xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
1.126     brouard  1654:        }
1.181     brouard  1655:        printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                   1656:        fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161     brouard  1657: 
1.126     brouard  1658: #ifdef DEBUG
1.164     brouard  1659:        printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                   1660:        fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126     brouard  1661:        for(j=1;j<=n;j++){
                   1662:          printf(" %.12e",xit[j]);
                   1663:          fprintf(ficlog," %.12e",xit[j]);
                   1664:        }
                   1665:        printf("\n");
                   1666:        fprintf(ficlog,"\n");
                   1667: #endif
1.162     brouard  1668:       } /* end of t negative */
                   1669:     } /* end if (fptt < fp)  */
1.126     brouard  1670:   } 
                   1671: } 
                   1672: 
                   1673: /**** Prevalence limit (stable or period prevalence)  ****************/
                   1674: 
                   1675: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
                   1676: {
                   1677:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
                   1678:      matrix by transitions matrix until convergence is reached */
1.169     brouard  1679:   
1.126     brouard  1680:   int i, ii,j,k;
                   1681:   double min, max, maxmin, maxmax,sumnew=0.;
1.145     brouard  1682:   /* double **matprod2(); */ /* test */
1.131     brouard  1683:   double **out, cov[NCOVMAX+1], **pmij();
1.126     brouard  1684:   double **newm;
                   1685:   double agefin, delaymax=50 ; /* Max number of years to converge */
1.169     brouard  1686:   
1.126     brouard  1687:   for (ii=1;ii<=nlstate+ndeath;ii++)
                   1688:     for (j=1;j<=nlstate+ndeath;j++){
                   1689:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1690:     }
1.169     brouard  1691:   
                   1692:   cov[1]=1.;
                   1693:   
                   1694:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126     brouard  1695:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
                   1696:     newm=savm;
                   1697:     /* Covariates have to be included here again */
1.138     brouard  1698:     cov[2]=agefin;
                   1699:     
                   1700:     for (k=1; k<=cptcovn;k++) {
                   1701:       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145     brouard  1702:       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138     brouard  1703:     }
1.145     brouard  1704:     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                   1705:     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
                   1706:     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1.138     brouard  1707:     
                   1708:     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                   1709:     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                   1710:     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145     brouard  1711:     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                   1712:     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142     brouard  1713:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138     brouard  1714:     
1.126     brouard  1715:     savm=oldm;
                   1716:     oldm=newm;
                   1717:     maxmax=0.;
                   1718:     for(j=1;j<=nlstate;j++){
                   1719:       min=1.;
                   1720:       max=0.;
                   1721:       for(i=1; i<=nlstate; i++) {
                   1722:        sumnew=0;
                   1723:        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                   1724:        prlim[i][j]= newm[i][j]/(1-sumnew);
1.145     brouard  1725:         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126     brouard  1726:        max=FMAX(max,prlim[i][j]);
                   1727:        min=FMIN(min,prlim[i][j]);
                   1728:       }
                   1729:       maxmin=max-min;
                   1730:       maxmax=FMAX(maxmax,maxmin);
1.169     brouard  1731:     } /* j loop */
1.126     brouard  1732:     if(maxmax < ftolpl){
                   1733:       return prlim;
                   1734:     }
1.169     brouard  1735:   } /* age loop */
                   1736:   return prlim; /* should not reach here */
1.126     brouard  1737: }
                   1738: 
                   1739: /*************** transition probabilities ***************/ 
                   1740: 
                   1741: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                   1742: {
1.138     brouard  1743:   /* According to parameters values stored in x and the covariate's values stored in cov,
                   1744:      computes the probability to be observed in state j being in state i by appying the
                   1745:      model to the ncovmodel covariates (including constant and age).
                   1746:      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
                   1747:      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
                   1748:      ncth covariate in the global vector x is given by the formula:
                   1749:      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
                   1750:      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
                   1751:      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
                   1752:      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
                   1753:      Outputs ps[i][j] the probability to be observed in j being in j according to
                   1754:      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
                   1755:   */
                   1756:   double s1, lnpijopii;
1.126     brouard  1757:   /*double t34;*/
1.164     brouard  1758:   int i,j, nc, ii, jj;
1.126     brouard  1759: 
                   1760:     for(i=1; i<= nlstate; i++){
                   1761:       for(j=1; j<i;j++){
1.138     brouard  1762:        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   1763:          /*lnpijopii += param[i][j][nc]*cov[nc];*/
                   1764:          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                   1765: /*      printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126     brouard  1766:        }
1.138     brouard  1767:        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   1768: /*     printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126     brouard  1769:       }
                   1770:       for(j=i+1; j<=nlstate+ndeath;j++){
1.138     brouard  1771:        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                   1772:          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                   1773:          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                   1774: /*       printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126     brouard  1775:        }
1.138     brouard  1776:        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126     brouard  1777:       }
                   1778:     }
                   1779:     
                   1780:     for(i=1; i<= nlstate; i++){
                   1781:       s1=0;
1.131     brouard  1782:       for(j=1; j<i; j++){
1.138     brouard  1783:        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131     brouard  1784:        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   1785:       }
                   1786:       for(j=i+1; j<=nlstate+ndeath; j++){
1.138     brouard  1787:        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131     brouard  1788:        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   1789:       }
1.138     brouard  1790:       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126     brouard  1791:       ps[i][i]=1./(s1+1.);
1.138     brouard  1792:       /* Computing other pijs */
1.126     brouard  1793:       for(j=1; j<i; j++)
                   1794:        ps[i][j]= exp(ps[i][j])*ps[i][i];
                   1795:       for(j=i+1; j<=nlstate+ndeath; j++)
                   1796:        ps[i][j]= exp(ps[i][j])*ps[i][i];
                   1797:       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                   1798:     } /* end i */
                   1799:     
                   1800:     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   1801:       for(jj=1; jj<= nlstate+ndeath; jj++){
                   1802:        ps[ii][jj]=0;
                   1803:        ps[ii][ii]=1;
                   1804:       }
                   1805:     }
                   1806:     
1.145     brouard  1807:     
                   1808:     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
                   1809:     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
                   1810:     /*         printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
                   1811:     /*   } */
                   1812:     /*   printf("\n "); */
                   1813:     /* } */
                   1814:     /* printf("\n ");printf("%lf ",cov[2]);*/
                   1815:     /*
1.126     brouard  1816:       for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   1817:       goto end;*/
                   1818:     return ps;
                   1819: }
                   1820: 
                   1821: /**************** Product of 2 matrices ******************/
                   1822: 
1.145     brouard  1823: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126     brouard  1824: {
                   1825:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                   1826:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                   1827:   /* in, b, out are matrice of pointers which should have been initialized 
                   1828:      before: only the contents of out is modified. The function returns
                   1829:      a pointer to pointers identical to out */
1.145     brouard  1830:   int i, j, k;
1.126     brouard  1831:   for(i=nrl; i<= nrh; i++)
1.145     brouard  1832:     for(k=ncolol; k<=ncoloh; k++){
                   1833:       out[i][k]=0.;
                   1834:       for(j=ncl; j<=nch; j++)
                   1835:        out[i][k] +=in[i][j]*b[j][k];
                   1836:     }
1.126     brouard  1837:   return out;
                   1838: }
                   1839: 
                   1840: 
                   1841: /************* Higher Matrix Product ***************/
                   1842: 
                   1843: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
                   1844: {
                   1845:   /* Computes the transition matrix starting at age 'age' over 
                   1846:      'nhstepm*hstepm*stepm' months (i.e. until
                   1847:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                   1848:      nhstepm*hstepm matrices. 
                   1849:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
                   1850:      (typically every 2 years instead of every month which is too big 
                   1851:      for the memory).
                   1852:      Model is determined by parameters x and covariates have to be 
                   1853:      included manually here. 
                   1854: 
                   1855:      */
                   1856: 
                   1857:   int i, j, d, h, k;
1.131     brouard  1858:   double **out, cov[NCOVMAX+1];
1.126     brouard  1859:   double **newm;
                   1860: 
                   1861:   /* Hstepm could be zero and should return the unit matrix */
                   1862:   for (i=1;i<=nlstate+ndeath;i++)
                   1863:     for (j=1;j<=nlstate+ndeath;j++){
                   1864:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   1865:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   1866:     }
                   1867:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   1868:   for(h=1; h <=nhstepm; h++){
                   1869:     for(d=1; d <=hstepm; d++){
                   1870:       newm=savm;
                   1871:       /* Covariates have to be included here again */
                   1872:       cov[1]=1.;
                   1873:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131     brouard  1874:       for (k=1; k<=cptcovn;k++) 
                   1875:        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126     brouard  1876:       for (k=1; k<=cptcovage;k++)
                   1877:        cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145     brouard  1878:       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126     brouard  1879:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   1880: 
                   1881: 
                   1882:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   1883:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                   1884:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                   1885:                   pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1886:       savm=oldm;
                   1887:       oldm=newm;
                   1888:     }
                   1889:     for(i=1; i<=nlstate+ndeath; i++)
                   1890:       for(j=1;j<=nlstate+ndeath;j++) {
                   1891:        po[i][j][h]=newm[i][j];
1.128     brouard  1892:        /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126     brouard  1893:       }
1.128     brouard  1894:     /*printf("h=%d ",h);*/
1.126     brouard  1895:   } /* end h */
1.128     brouard  1896: /*     printf("\n H=%d \n",h); */
1.126     brouard  1897:   return po;
                   1898: }
                   1899: 
1.162     brouard  1900: #ifdef NLOPT
                   1901:   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
                   1902:   double fret;
                   1903:   double *xt;
                   1904:   int j;
                   1905:   myfunc_data *d2 = (myfunc_data *) pd;
                   1906: /* xt = (p1-1); */
                   1907:   xt=vector(1,n); 
                   1908:   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
                   1909: 
                   1910:   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
                   1911:   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
                   1912:   printf("Function = %.12lf ",fret);
                   1913:   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
                   1914:   printf("\n");
                   1915:  free_vector(xt,1,n);
                   1916:   return fret;
                   1917: }
                   1918: #endif
1.126     brouard  1919: 
                   1920: /*************** log-likelihood *************/
                   1921: double func( double *x)
                   1922: {
                   1923:   int i, ii, j, k, mi, d, kk;
1.131     brouard  1924:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126     brouard  1925:   double **out;
                   1926:   double sw; /* Sum of weights */
                   1927:   double lli; /* Individual log likelihood */
                   1928:   int s1, s2;
                   1929:   double bbh, survp;
                   1930:   long ipmx;
                   1931:   /*extern weight */
                   1932:   /* We are differentiating ll according to initial status */
                   1933:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   1934:   /*for(i=1;i<imx;i++) 
                   1935:     printf(" %d\n",s[4][i]);
                   1936:   */
1.162     brouard  1937: 
                   1938:   ++countcallfunc;
                   1939: 
1.126     brouard  1940:   cov[1]=1.;
                   1941: 
                   1942:   for(k=1; k<=nlstate; k++) ll[k]=0.;
                   1943: 
                   1944:   if(mle==1){
                   1945:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138     brouard  1946:       /* Computes the values of the ncovmodel covariates of the model
                   1947:         depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
                   1948:         Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
                   1949:         to be observed in j being in i according to the model.
                   1950:        */
1.145     brouard  1951:       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
                   1952:        cov[2+k]=covar[Tvar[k]][i];
                   1953:       }
1.137     brouard  1954:       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
1.138     brouard  1955:         is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
1.137     brouard  1956:         has been calculated etc */
1.126     brouard  1957:       for(mi=1; mi<= wav[i]-1; mi++){
                   1958:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1959:          for (j=1;j<=nlstate+ndeath;j++){
                   1960:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1961:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1962:          }
                   1963:        for(d=0; d<dh[mi][i]; d++){
                   1964:          newm=savm;
                   1965:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1966:          for (kk=1; kk<=cptcovage;kk++) {
1.137     brouard  1967:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126     brouard  1968:          }
                   1969:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1970:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1971:          savm=oldm;
                   1972:          oldm=newm;
                   1973:        } /* end mult */
                   1974:       
                   1975:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   1976:        /* But now since version 0.9 we anticipate for bias at large stepm.
                   1977:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   1978:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   1979:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   1980:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   1981:         * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                   1982:         * probability in order to take into account the bias as a fraction of the way
                   1983:         * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                   1984:         * -stepm/2 to stepm/2 .
                   1985:         * For stepm=1 the results are the same as for previous versions of Imach.
                   1986:         * For stepm > 1 the results are less biased than in previous versions. 
                   1987:         */
                   1988:        s1=s[mw[mi][i]][i];
                   1989:        s2=s[mw[mi+1][i]][i];
                   1990:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1991:        /* bias bh is positive if real duration
                   1992:         * is higher than the multiple of stepm and negative otherwise.
                   1993:         */
                   1994:        /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                   1995:        if( s2 > nlstate){ 
                   1996:          /* i.e. if s2 is a death state and if the date of death is known 
                   1997:             then the contribution to the likelihood is the probability to 
                   1998:             die between last step unit time and current  step unit time, 
                   1999:             which is also equal to probability to die before dh 
                   2000:             minus probability to die before dh-stepm . 
                   2001:             In version up to 0.92 likelihood was computed
                   2002:        as if date of death was unknown. Death was treated as any other
                   2003:        health state: the date of the interview describes the actual state
                   2004:        and not the date of a change in health state. The former idea was
                   2005:        to consider that at each interview the state was recorded
                   2006:        (healthy, disable or death) and IMaCh was corrected; but when we
                   2007:        introduced the exact date of death then we should have modified
                   2008:        the contribution of an exact death to the likelihood. This new
                   2009:        contribution is smaller and very dependent of the step unit
                   2010:        stepm. It is no more the probability to die between last interview
                   2011:        and month of death but the probability to survive from last
                   2012:        interview up to one month before death multiplied by the
                   2013:        probability to die within a month. Thanks to Chris
                   2014:        Jackson for correcting this bug.  Former versions increased
                   2015:        mortality artificially. The bad side is that we add another loop
                   2016:        which slows down the processing. The difference can be up to 10%
                   2017:        lower mortality.
                   2018:          */
1.183     brouard  2019:        /* If, at the beginning of the maximization mostly, the
                   2020:           cumulative probability or probability to be dead is
                   2021:           constant (ie = 1) over time d, the difference is equal to
                   2022:           0.  out[s1][3] = savm[s1][3]: probability, being at state
                   2023:           s1 at precedent wave, to be dead a month before current
                   2024:           wave is equal to probability, being at state s1 at
                   2025:           precedent wave, to be dead at mont of the current
                   2026:           wave. Then the observed probability (that this person died)
                   2027:           is null according to current estimated parameter. In fact,
                   2028:           it should be very low but not zero otherwise the log go to
                   2029:           infinity.
                   2030:        */
                   2031: /* #ifdef INFINITYORIGINAL */
                   2032: /*         lli=log(out[s1][s2] - savm[s1][s2]); */
                   2033: /* #else */
                   2034: /*       if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
                   2035: /*         lli=log(mytinydouble); */
                   2036: /*       else */
                   2037: /*         lli=log(out[s1][s2] - savm[s1][s2]); */
                   2038: /* #endif */
                   2039:            lli=log(out[s1][s2] - savm[s1][s2]);
1.126     brouard  2040: 
                   2041:        } else if  (s2==-2) {
                   2042:          for (j=1,survp=0. ; j<=nlstate; j++) 
                   2043:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   2044:          /*survp += out[s1][j]; */
                   2045:          lli= log(survp);
                   2046:        }
                   2047:        
                   2048:        else if  (s2==-4) { 
                   2049:          for (j=3,survp=0. ; j<=nlstate; j++)  
                   2050:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   2051:          lli= log(survp); 
                   2052:        } 
                   2053: 
                   2054:        else if  (s2==-5) { 
                   2055:          for (j=1,survp=0. ; j<=2; j++)  
                   2056:            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   2057:          lli= log(survp); 
                   2058:        } 
                   2059:        
                   2060:        else{
                   2061:          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   2062:          /*  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 */
                   2063:        } 
                   2064:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   2065:        /*if(lli ==000.0)*/
                   2066:        /*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); */
                   2067:        ipmx +=1;
                   2068:        sw += weight[i];
                   2069:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183     brouard  2070:        /* if (lli < log(mytinydouble)){ */
                   2071:        /*   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); */
                   2072:        /*   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]); */
                   2073:        /* } */
1.126     brouard  2074:       } /* end of wave */
                   2075:     } /* end of individual */
                   2076:   }  else if(mle==2){
                   2077:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   2078:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   2079:       for(mi=1; mi<= wav[i]-1; mi++){
                   2080:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   2081:          for (j=1;j<=nlstate+ndeath;j++){
                   2082:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2083:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2084:          }
                   2085:        for(d=0; d<=dh[mi][i]; d++){
                   2086:          newm=savm;
                   2087:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   2088:          for (kk=1; kk<=cptcovage;kk++) {
                   2089:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   2090:          }
                   2091:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   2092:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   2093:          savm=oldm;
                   2094:          oldm=newm;
                   2095:        } /* end mult */
                   2096:       
                   2097:        s1=s[mw[mi][i]][i];
                   2098:        s2=s[mw[mi+1][i]][i];
                   2099:        bbh=(double)bh[mi][i]/(double)stepm; 
                   2100:        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 */
                   2101:        ipmx +=1;
                   2102:        sw += weight[i];
                   2103:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   2104:       } /* end of wave */
                   2105:     } /* end of individual */
                   2106:   }  else if(mle==3){  /* exponential inter-extrapolation */
                   2107:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   2108:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   2109:       for(mi=1; mi<= wav[i]-1; mi++){
                   2110:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   2111:          for (j=1;j<=nlstate+ndeath;j++){
                   2112:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2113:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2114:          }
                   2115:        for(d=0; d<dh[mi][i]; d++){
                   2116:          newm=savm;
                   2117:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   2118:          for (kk=1; kk<=cptcovage;kk++) {
                   2119:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   2120:          }
                   2121:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   2122:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   2123:          savm=oldm;
                   2124:          oldm=newm;
                   2125:        } /* end mult */
                   2126:       
                   2127:        s1=s[mw[mi][i]][i];
                   2128:        s2=s[mw[mi+1][i]][i];
                   2129:        bbh=(double)bh[mi][i]/(double)stepm; 
                   2130:        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 */
                   2131:        ipmx +=1;
                   2132:        sw += weight[i];
                   2133:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   2134:       } /* end of wave */
                   2135:     } /* end of individual */
                   2136:   }else if (mle==4){  /* ml=4 no inter-extrapolation */
                   2137:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   2138:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   2139:       for(mi=1; mi<= wav[i]-1; mi++){
                   2140:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   2141:          for (j=1;j<=nlstate+ndeath;j++){
                   2142:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2143:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2144:          }
                   2145:        for(d=0; d<dh[mi][i]; d++){
                   2146:          newm=savm;
                   2147:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   2148:          for (kk=1; kk<=cptcovage;kk++) {
                   2149:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   2150:          }
                   2151:        
                   2152:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   2153:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   2154:          savm=oldm;
                   2155:          oldm=newm;
                   2156:        } /* end mult */
                   2157:       
                   2158:        s1=s[mw[mi][i]][i];
                   2159:        s2=s[mw[mi+1][i]][i];
                   2160:        if( s2 > nlstate){ 
                   2161:          lli=log(out[s1][s2] - savm[s1][s2]);
                   2162:        }else{
                   2163:          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   2164:        }
                   2165:        ipmx +=1;
                   2166:        sw += weight[i];
                   2167:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   2168: /*     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]); */
                   2169:       } /* end of wave */
                   2170:     } /* end of individual */
                   2171:   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                   2172:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   2173:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   2174:       for(mi=1; mi<= wav[i]-1; mi++){
                   2175:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   2176:          for (j=1;j<=nlstate+ndeath;j++){
                   2177:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2178:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2179:          }
                   2180:        for(d=0; d<dh[mi][i]; d++){
                   2181:          newm=savm;
                   2182:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   2183:          for (kk=1; kk<=cptcovage;kk++) {
                   2184:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   2185:          }
                   2186:        
                   2187:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   2188:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   2189:          savm=oldm;
                   2190:          oldm=newm;
                   2191:        } /* end mult */
                   2192:       
                   2193:        s1=s[mw[mi][i]][i];
                   2194:        s2=s[mw[mi+1][i]][i];
                   2195:        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   2196:        ipmx +=1;
                   2197:        sw += weight[i];
                   2198:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   2199:        /*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]);*/
                   2200:       } /* end of wave */
                   2201:     } /* end of individual */
                   2202:   } /* End of if */
                   2203:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   2204:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   2205:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   2206:   return -l;
                   2207: }
                   2208: 
                   2209: /*************** log-likelihood *************/
                   2210: double funcone( double *x)
                   2211: {
                   2212:   /* Same as likeli but slower because of a lot of printf and if */
                   2213:   int i, ii, j, k, mi, d, kk;
1.131     brouard  2214:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126     brouard  2215:   double **out;
                   2216:   double lli; /* Individual log likelihood */
                   2217:   double llt;
                   2218:   int s1, s2;
                   2219:   double bbh, survp;
                   2220:   /*extern weight */
                   2221:   /* We are differentiating ll according to initial status */
                   2222:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   2223:   /*for(i=1;i<imx;i++) 
                   2224:     printf(" %d\n",s[4][i]);
                   2225:   */
                   2226:   cov[1]=1.;
                   2227: 
                   2228:   for(k=1; k<=nlstate; k++) ll[k]=0.;
                   2229: 
                   2230:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   2231:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   2232:     for(mi=1; mi<= wav[i]-1; mi++){
                   2233:       for (ii=1;ii<=nlstate+ndeath;ii++)
                   2234:        for (j=1;j<=nlstate+ndeath;j++){
                   2235:          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2236:          savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   2237:        }
                   2238:       for(d=0; d<dh[mi][i]; d++){
                   2239:        newm=savm;
                   2240:        cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   2241:        for (kk=1; kk<=cptcovage;kk++) {
                   2242:          cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   2243:        }
1.145     brouard  2244:        /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126     brouard  2245:        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   2246:                     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145     brouard  2247:        /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                   2248:        /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126     brouard  2249:        savm=oldm;
                   2250:        oldm=newm;
                   2251:       } /* end mult */
                   2252:       
                   2253:       s1=s[mw[mi][i]][i];
                   2254:       s2=s[mw[mi+1][i]][i];
                   2255:       bbh=(double)bh[mi][i]/(double)stepm; 
                   2256:       /* bias is positive if real duration
                   2257:        * is higher than the multiple of stepm and negative otherwise.
                   2258:        */
                   2259:       if( s2 > nlstate && (mle <5) ){  /* Jackson */
                   2260:        lli=log(out[s1][s2] - savm[s1][s2]);
                   2261:       } else if  (s2==-2) {
                   2262:        for (j=1,survp=0. ; j<=nlstate; j++) 
                   2263:          survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                   2264:        lli= log(survp);
                   2265:       }else if (mle==1){
                   2266:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   2267:       } else if(mle==2){
                   2268:        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 */
                   2269:       } else if(mle==3){  /* exponential inter-extrapolation */
                   2270:        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 */
                   2271:       } else if (mle==4){  /* mle=4 no inter-extrapolation */
                   2272:        lli=log(out[s1][s2]); /* Original formula */
1.136     brouard  2273:       } else{  /* mle=0 back to 1 */
                   2274:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   2275:        /*lli=log(out[s1][s2]); */ /* Original formula */
1.126     brouard  2276:       } /* End of if */
                   2277:       ipmx +=1;
                   2278:       sw += weight[i];
                   2279:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132     brouard  2280:       /*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  2281:       if(globpr){
1.141     brouard  2282:        fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126     brouard  2283:  %11.6f %11.6f %11.6f ", \
                   2284:                num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   2285:                2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                   2286:        for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   2287:          llt +=ll[k]*gipmx/gsw;
                   2288:          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                   2289:        }
                   2290:        fprintf(ficresilk," %10.6f\n", -llt);
                   2291:       }
                   2292:     } /* end of wave */
                   2293:   } /* end of individual */
                   2294:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   2295:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   2296:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                   2297:   if(globpr==0){ /* First time we count the contributions and weights */
                   2298:     gipmx=ipmx;
                   2299:     gsw=sw;
                   2300:   }
                   2301:   return -l;
                   2302: }
                   2303: 
                   2304: 
                   2305: /*************** function likelione ***********/
                   2306: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
                   2307: {
                   2308:   /* This routine should help understanding what is done with 
                   2309:      the selection of individuals/waves and
                   2310:      to check the exact contribution to the likelihood.
                   2311:      Plotting could be done.
                   2312:    */
                   2313:   int k;
                   2314: 
                   2315:   if(*globpri !=0){ /* Just counts and sums, no printings */
                   2316:     strcpy(fileresilk,"ilk"); 
                   2317:     strcat(fileresilk,fileres);
                   2318:     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                   2319:       printf("Problem with resultfile: %s\n", fileresilk);
                   2320:       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
                   2321:     }
                   2322:     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
                   2323:     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
                   2324:     /*         i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                   2325:     for(k=1; k<=nlstate; k++) 
                   2326:       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                   2327:     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
                   2328:   }
                   2329: 
                   2330:   *fretone=(*funcone)(p);
                   2331:   if(*globpri !=0){
                   2332:     fclose(ficresilk);
                   2333:     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
                   2334:     fflush(fichtm); 
                   2335:   } 
                   2336:   return;
                   2337: }
                   2338: 
                   2339: 
                   2340: /*********** Maximum Likelihood Estimation ***************/
                   2341: 
                   2342: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                   2343: {
1.165     brouard  2344:   int i,j, iter=0;
1.126     brouard  2345:   double **xi;
                   2346:   double fret;
                   2347:   double fretone; /* Only one call to likelihood */
                   2348:   /*  char filerespow[FILENAMELENGTH];*/
1.162     brouard  2349: 
                   2350: #ifdef NLOPT
                   2351:   int creturn;
                   2352:   nlopt_opt opt;
                   2353:   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
                   2354:   double *lb;
                   2355:   double minf; /* the minimum objective value, upon return */
                   2356:   double * p1; /* Shifted parameters from 0 instead of 1 */
                   2357:   myfunc_data dinst, *d = &dinst;
                   2358: #endif
                   2359: 
                   2360: 
1.126     brouard  2361:   xi=matrix(1,npar,1,npar);
                   2362:   for (i=1;i<=npar;i++)
                   2363:     for (j=1;j<=npar;j++)
                   2364:       xi[i][j]=(i==j ? 1.0 : 0.0);
                   2365:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
                   2366:   strcpy(filerespow,"pow"); 
                   2367:   strcat(filerespow,fileres);
                   2368:   if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   2369:     printf("Problem with resultfile: %s\n", filerespow);
                   2370:     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   2371:   }
                   2372:   fprintf(ficrespow,"# Powell\n# iter -2*LL");
                   2373:   for (i=1;i<=nlstate;i++)
                   2374:     for(j=1;j<=nlstate+ndeath;j++)
                   2375:       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   2376:   fprintf(ficrespow,"\n");
1.162     brouard  2377: #ifdef POWELL
1.126     brouard  2378:   powell(p,xi,npar,ftol,&iter,&fret,func);
1.162     brouard  2379: #endif
1.126     brouard  2380: 
1.162     brouard  2381: #ifdef NLOPT
                   2382: #ifdef NEWUOA
                   2383:   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
                   2384: #else
                   2385:   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
                   2386: #endif
                   2387:   lb=vector(0,npar-1);
                   2388:   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
                   2389:   nlopt_set_lower_bounds(opt, lb);
                   2390:   nlopt_set_initial_step1(opt, 0.1);
                   2391:   
                   2392:   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
                   2393:   d->function = func;
                   2394:   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
                   2395:   nlopt_set_min_objective(opt, myfunc, d);
                   2396:   nlopt_set_xtol_rel(opt, ftol);
                   2397:   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
                   2398:     printf("nlopt failed! %d\n",creturn); 
                   2399:   }
                   2400:   else {
                   2401:     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
                   2402:     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
                   2403:     iter=1; /* not equal */
                   2404:   }
                   2405:   nlopt_destroy(opt);
                   2406: #endif
1.126     brouard  2407:   free_matrix(xi,1,npar,1,npar);
                   2408:   fclose(ficrespow);
1.180     brouard  2409:   printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   2410:   fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   2411:   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126     brouard  2412: 
                   2413: }
                   2414: 
                   2415: /**** Computes Hessian and covariance matrix ***/
                   2416: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                   2417: {
                   2418:   double  **a,**y,*x,pd;
                   2419:   double **hess;
1.164     brouard  2420:   int i, j;
1.126     brouard  2421:   int *indx;
                   2422: 
                   2423:   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
                   2424:   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
                   2425:   void lubksb(double **a, int npar, int *indx, double b[]) ;
                   2426:   void ludcmp(double **a, int npar, int *indx, double *d) ;
                   2427:   double gompertz(double p[]);
                   2428:   hess=matrix(1,npar,1,npar);
                   2429: 
                   2430:   printf("\nCalculation of the hessian matrix. Wait...\n");
                   2431:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                   2432:   for (i=1;i<=npar;i++){
                   2433:     printf("%d",i);fflush(stdout);
                   2434:     fprintf(ficlog,"%d",i);fflush(ficlog);
                   2435:    
                   2436:      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                   2437:     
                   2438:     /*  printf(" %f ",p[i]);
                   2439:        printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
                   2440:   }
                   2441:   
                   2442:   for (i=1;i<=npar;i++) {
                   2443:     for (j=1;j<=npar;j++)  {
                   2444:       if (j>i) { 
                   2445:        printf(".%d%d",i,j);fflush(stdout);
                   2446:        fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                   2447:        hess[i][j]=hessij(p,delti,i,j,func,npar);
                   2448:        
                   2449:        hess[j][i]=hess[i][j];    
                   2450:        /*printf(" %lf ",hess[i][j]);*/
                   2451:       }
                   2452:     }
                   2453:   }
                   2454:   printf("\n");
                   2455:   fprintf(ficlog,"\n");
                   2456: 
                   2457:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
                   2458:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                   2459:   
                   2460:   a=matrix(1,npar,1,npar);
                   2461:   y=matrix(1,npar,1,npar);
                   2462:   x=vector(1,npar);
                   2463:   indx=ivector(1,npar);
                   2464:   for (i=1;i<=npar;i++)
                   2465:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   2466:   ludcmp(a,npar,indx,&pd);
                   2467: 
                   2468:   for (j=1;j<=npar;j++) {
                   2469:     for (i=1;i<=npar;i++) x[i]=0;
                   2470:     x[j]=1;
                   2471:     lubksb(a,npar,indx,x);
                   2472:     for (i=1;i<=npar;i++){ 
                   2473:       matcov[i][j]=x[i];
                   2474:     }
                   2475:   }
                   2476: 
                   2477:   printf("\n#Hessian matrix#\n");
                   2478:   fprintf(ficlog,"\n#Hessian matrix#\n");
                   2479:   for (i=1;i<=npar;i++) { 
                   2480:     for (j=1;j<=npar;j++) { 
                   2481:       printf("%.3e ",hess[i][j]);
                   2482:       fprintf(ficlog,"%.3e ",hess[i][j]);
                   2483:     }
                   2484:     printf("\n");
                   2485:     fprintf(ficlog,"\n");
                   2486:   }
                   2487: 
                   2488:   /* Recompute Inverse */
                   2489:   for (i=1;i<=npar;i++)
                   2490:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
                   2491:   ludcmp(a,npar,indx,&pd);
                   2492: 
                   2493:   /*  printf("\n#Hessian matrix recomputed#\n");
                   2494: 
                   2495:   for (j=1;j<=npar;j++) {
                   2496:     for (i=1;i<=npar;i++) x[i]=0;
                   2497:     x[j]=1;
                   2498:     lubksb(a,npar,indx,x);
                   2499:     for (i=1;i<=npar;i++){ 
                   2500:       y[i][j]=x[i];
                   2501:       printf("%.3e ",y[i][j]);
                   2502:       fprintf(ficlog,"%.3e ",y[i][j]);
                   2503:     }
                   2504:     printf("\n");
                   2505:     fprintf(ficlog,"\n");
                   2506:   }
                   2507:   */
                   2508: 
                   2509:   free_matrix(a,1,npar,1,npar);
                   2510:   free_matrix(y,1,npar,1,npar);
                   2511:   free_vector(x,1,npar);
                   2512:   free_ivector(indx,1,npar);
                   2513:   free_matrix(hess,1,npar,1,npar);
                   2514: 
                   2515: 
                   2516: }
                   2517: 
                   2518: /*************** hessian matrix ****************/
                   2519: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
                   2520: {
                   2521:   int i;
                   2522:   int l=1, lmax=20;
                   2523:   double k1,k2;
1.132     brouard  2524:   double p2[MAXPARM+1]; /* identical to x */
1.126     brouard  2525:   double res;
                   2526:   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   2527:   double fx;
                   2528:   int k=0,kmax=10;
                   2529:   double l1;
                   2530: 
                   2531:   fx=func(x);
                   2532:   for (i=1;i<=npar;i++) p2[i]=x[i];
1.145     brouard  2533:   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
1.126     brouard  2534:     l1=pow(10,l);
                   2535:     delts=delt;
                   2536:     for(k=1 ; k <kmax; k=k+1){
                   2537:       delt = delta*(l1*k);
                   2538:       p2[theta]=x[theta] +delt;
1.145     brouard  2539:       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
1.126     brouard  2540:       p2[theta]=x[theta]-delt;
                   2541:       k2=func(p2)-fx;
                   2542:       /*res= (k1-2.0*fx+k2)/delt/delt; */
                   2543:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   2544:       
1.132     brouard  2545: #ifdef DEBUGHESS
1.126     brouard  2546:       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);
                   2547:       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);
                   2548: #endif
                   2549:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                   2550:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   2551:        k=kmax;
                   2552:       }
                   2553:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164     brouard  2554:        k=kmax; l=lmax*10;
1.126     brouard  2555:       }
                   2556:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                   2557:        delts=delt;
                   2558:       }
                   2559:     }
                   2560:   }
                   2561:   delti[theta]=delts;
                   2562:   return res; 
                   2563:   
                   2564: }
                   2565: 
                   2566: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
                   2567: {
                   2568:   int i;
1.164     brouard  2569:   int l=1, lmax=20;
1.126     brouard  2570:   double k1,k2,k3,k4,res,fx;
1.132     brouard  2571:   double p2[MAXPARM+1];
1.126     brouard  2572:   int k;
                   2573: 
                   2574:   fx=func(x);
                   2575:   for (k=1; k<=2; k++) {
                   2576:     for (i=1;i<=npar;i++) p2[i]=x[i];
                   2577:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   2578:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   2579:     k1=func(p2)-fx;
                   2580:   
                   2581:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   2582:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   2583:     k2=func(p2)-fx;
                   2584:   
                   2585:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   2586:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   2587:     k3=func(p2)-fx;
                   2588:   
                   2589:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   2590:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   2591:     k4=func(p2)-fx;
                   2592:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                   2593: #ifdef DEBUG
                   2594:     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);
                   2595:     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);
                   2596: #endif
                   2597:   }
                   2598:   return res;
                   2599: }
                   2600: 
                   2601: /************** Inverse of matrix **************/
                   2602: void ludcmp(double **a, int n, int *indx, double *d) 
                   2603: { 
                   2604:   int i,imax,j,k; 
                   2605:   double big,dum,sum,temp; 
                   2606:   double *vv; 
                   2607:  
                   2608:   vv=vector(1,n); 
                   2609:   *d=1.0; 
                   2610:   for (i=1;i<=n;i++) { 
                   2611:     big=0.0; 
                   2612:     for (j=1;j<=n;j++) 
                   2613:       if ((temp=fabs(a[i][j])) > big) big=temp; 
                   2614:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                   2615:     vv[i]=1.0/big; 
                   2616:   } 
                   2617:   for (j=1;j<=n;j++) { 
                   2618:     for (i=1;i<j;i++) { 
                   2619:       sum=a[i][j]; 
                   2620:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                   2621:       a[i][j]=sum; 
                   2622:     } 
                   2623:     big=0.0; 
                   2624:     for (i=j;i<=n;i++) { 
                   2625:       sum=a[i][j]; 
                   2626:       for (k=1;k<j;k++) 
                   2627:        sum -= a[i][k]*a[k][j]; 
                   2628:       a[i][j]=sum; 
                   2629:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   2630:        big=dum; 
                   2631:        imax=i; 
                   2632:       } 
                   2633:     } 
                   2634:     if (j != imax) { 
                   2635:       for (k=1;k<=n;k++) { 
                   2636:        dum=a[imax][k]; 
                   2637:        a[imax][k]=a[j][k]; 
                   2638:        a[j][k]=dum; 
                   2639:       } 
                   2640:       *d = -(*d); 
                   2641:       vv[imax]=vv[j]; 
                   2642:     } 
                   2643:     indx[j]=imax; 
                   2644:     if (a[j][j] == 0.0) a[j][j]=TINY; 
                   2645:     if (j != n) { 
                   2646:       dum=1.0/(a[j][j]); 
                   2647:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                   2648:     } 
                   2649:   } 
                   2650:   free_vector(vv,1,n);  /* Doesn't work */
                   2651: ;
                   2652: } 
                   2653: 
                   2654: void lubksb(double **a, int n, int *indx, double b[]) 
                   2655: { 
                   2656:   int i,ii=0,ip,j; 
                   2657:   double sum; 
                   2658:  
                   2659:   for (i=1;i<=n;i++) { 
                   2660:     ip=indx[i]; 
                   2661:     sum=b[ip]; 
                   2662:     b[ip]=b[i]; 
                   2663:     if (ii) 
                   2664:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                   2665:     else if (sum) ii=i; 
                   2666:     b[i]=sum; 
                   2667:   } 
                   2668:   for (i=n;i>=1;i--) { 
                   2669:     sum=b[i]; 
                   2670:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   2671:     b[i]=sum/a[i][i]; 
                   2672:   } 
                   2673: } 
                   2674: 
                   2675: void pstamp(FILE *fichier)
                   2676: {
                   2677:   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
                   2678: }
                   2679: 
                   2680: /************ Frequencies ********************/
                   2681: void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
                   2682: {  /* Some frequencies */
                   2683:   
1.164     brouard  2684:   int i, m, jk, j1, bool, z1,j;
1.126     brouard  2685:   int first;
                   2686:   double ***freq; /* Frequencies */
                   2687:   double *pp, **prop;
                   2688:   double pos,posprop, k2, dateintsum=0,k2cpt=0;
                   2689:   char fileresp[FILENAMELENGTH];
                   2690:   
                   2691:   pp=vector(1,nlstate);
                   2692:   prop=matrix(1,nlstate,iagemin,iagemax+3);
                   2693:   strcpy(fileresp,"p");
                   2694:   strcat(fileresp,fileres);
                   2695:   if((ficresp=fopen(fileresp,"w"))==NULL) {
                   2696:     printf("Problem with prevalence resultfile: %s\n", fileresp);
                   2697:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                   2698:     exit(0);
                   2699:   }
                   2700:   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
                   2701:   j1=0;
                   2702:   
                   2703:   j=cptcoveff;
                   2704:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   2705: 
                   2706:   first=1;
                   2707: 
1.169     brouard  2708:   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
                   2709:   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
                   2710:   /*    j1++; */
1.145     brouard  2711:   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126     brouard  2712:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                   2713:        scanf("%d", i);*/
                   2714:       for (i=-5; i<=nlstate+ndeath; i++)  
                   2715:        for (jk=-5; jk<=nlstate+ndeath; jk++)  
                   2716:          for(m=iagemin; m <= iagemax+3; m++)
                   2717:            freq[i][jk][m]=0;
1.143     brouard  2718:       
                   2719:       for (i=1; i<=nlstate; i++)  
                   2720:        for(m=iagemin; m <= iagemax+3; m++)
                   2721:          prop[i][m]=0;
1.126     brouard  2722:       
                   2723:       dateintsum=0;
                   2724:       k2cpt=0;
                   2725:       for (i=1; i<=imx; i++) {
                   2726:        bool=1;
1.144     brouard  2727:        if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                   2728:          for (z1=1; z1<=cptcoveff; z1++)       
                   2729:             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145     brouard  2730:                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144     brouard  2731:               bool=0;
1.145     brouard  2732:               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                   2733:                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   2734:                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144     brouard  2735:               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                   2736:             } 
1.126     brouard  2737:        }
1.144     brouard  2738:  
1.126     brouard  2739:        if (bool==1){
                   2740:          for(m=firstpass; m<=lastpass; m++){
                   2741:            k2=anint[m][i]+(mint[m][i]/12.);
                   2742:            /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                   2743:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   2744:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   2745:              if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   2746:              if (m<lastpass) {
                   2747:                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   2748:                freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                   2749:              }
                   2750:              
                   2751:              if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   2752:                dateintsum=dateintsum+k2;
                   2753:                k2cpt++;
                   2754:              }
                   2755:              /*}*/
                   2756:          }
                   2757:        }
1.145     brouard  2758:       } /* end i */
1.126     brouard  2759:        
                   2760:       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                   2761:       pstamp(ficresp);
                   2762:       if  (cptcovn>0) {
                   2763:        fprintf(ficresp, "\n#********** Variable "); 
                   2764:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   2765:        fprintf(ficresp, "**********\n#");
1.143     brouard  2766:        fprintf(ficlog, "\n#********** Variable "); 
                   2767:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   2768:        fprintf(ficlog, "**********\n#");
1.126     brouard  2769:       }
                   2770:       for(i=1; i<=nlstate;i++) 
                   2771:        fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                   2772:       fprintf(ficresp, "\n");
                   2773:       
                   2774:       for(i=iagemin; i <= iagemax+3; i++){
                   2775:        if(i==iagemax+3){
                   2776:          fprintf(ficlog,"Total");
                   2777:        }else{
                   2778:          if(first==1){
                   2779:            first=0;
                   2780:            printf("See log file for details...\n");
                   2781:          }
                   2782:          fprintf(ficlog,"Age %d", i);
                   2783:        }
                   2784:        for(jk=1; jk <=nlstate ; jk++){
                   2785:          for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                   2786:            pp[jk] += freq[jk][m][i]; 
                   2787:        }
                   2788:        for(jk=1; jk <=nlstate ; jk++){
                   2789:          for(m=-1, pos=0; m <=0 ; m++)
                   2790:            pos += freq[jk][m][i];
                   2791:          if(pp[jk]>=1.e-10){
                   2792:            if(first==1){
1.132     brouard  2793:              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126     brouard  2794:            }
                   2795:            fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   2796:          }else{
                   2797:            if(first==1)
                   2798:              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   2799:            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   2800:          }
                   2801:        }
                   2802: 
                   2803:        for(jk=1; jk <=nlstate ; jk++){
                   2804:          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                   2805:            pp[jk] += freq[jk][m][i];
                   2806:        }       
                   2807:        for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                   2808:          pos += pp[jk];
                   2809:          posprop += prop[jk][i];
                   2810:        }
                   2811:        for(jk=1; jk <=nlstate ; jk++){
                   2812:          if(pos>=1.e-5){
                   2813:            if(first==1)
                   2814:              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   2815:            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   2816:          }else{
                   2817:            if(first==1)
                   2818:              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   2819:            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   2820:          }
                   2821:          if( i <= iagemax){
                   2822:            if(pos>=1.e-5){
                   2823:              fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                   2824:              /*probs[i][jk][j1]= pp[jk]/pos;*/
                   2825:              /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                   2826:            }
                   2827:            else
                   2828:              fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                   2829:          }
                   2830:        }
                   2831:        
                   2832:        for(jk=-1; jk <=nlstate+ndeath; jk++)
                   2833:          for(m=-1; m <=nlstate+ndeath; m++)
                   2834:            if(freq[jk][m][i] !=0 ) {
                   2835:            if(first==1)
                   2836:              printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                   2837:              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                   2838:            }
                   2839:        if(i <= iagemax)
                   2840:          fprintf(ficresp,"\n");
                   2841:        if(first==1)
                   2842:          printf("Others in log...\n");
                   2843:        fprintf(ficlog,"\n");
                   2844:       }
1.145     brouard  2845:       /*}*/
1.126     brouard  2846:   }
                   2847:   dateintmean=dateintsum/k2cpt; 
                   2848:  
                   2849:   fclose(ficresp);
                   2850:   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
                   2851:   free_vector(pp,1,nlstate);
                   2852:   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
                   2853:   /* End of Freq */
                   2854: }
                   2855: 
                   2856: /************ Prevalence ********************/
                   2857: 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)
                   2858: {  
                   2859:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   2860:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   2861:      We still use firstpass and lastpass as another selection.
                   2862:   */
                   2863:  
1.164     brouard  2864:   int i, m, jk, j1, bool, z1,j;
                   2865: 
                   2866:   double **prop;
                   2867:   double posprop; 
1.126     brouard  2868:   double  y2; /* in fractional years */
                   2869:   int iagemin, iagemax;
1.145     brouard  2870:   int first; /** to stop verbosity which is redirected to log file */
1.126     brouard  2871: 
                   2872:   iagemin= (int) agemin;
                   2873:   iagemax= (int) agemax;
                   2874:   /*pp=vector(1,nlstate);*/
                   2875:   prop=matrix(1,nlstate,iagemin,iagemax+3); 
                   2876:   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                   2877:   j1=0;
                   2878:   
1.145     brouard  2879:   /*j=cptcoveff;*/
1.126     brouard  2880:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   2881:   
1.145     brouard  2882:   first=1;
                   2883:   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
                   2884:     /*for(i1=1; i1<=ncodemax[k1];i1++){
                   2885:       j1++;*/
1.126     brouard  2886:       
                   2887:       for (i=1; i<=nlstate; i++)  
                   2888:        for(m=iagemin; m <= iagemax+3; m++)
                   2889:          prop[i][m]=0.0;
                   2890:      
                   2891:       for (i=1; i<=imx; i++) { /* Each individual */
                   2892:        bool=1;
                   2893:        if  (cptcovn>0) {
                   2894:          for (z1=1; z1<=cptcoveff; z1++) 
                   2895:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                   2896:              bool=0;
                   2897:        } 
                   2898:        if (bool==1) { 
                   2899:          for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                   2900:            y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   2901:            if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                   2902:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   2903:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   2904:              if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                   2905:              if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   2906:                /*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]]);*/
                   2907:                prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   2908:                prop[s[m][i]][iagemax+3] += weight[i]; 
                   2909:              } 
                   2910:            }
                   2911:          } /* end selection of waves */
                   2912:        }
                   2913:       }
                   2914:       for(i=iagemin; i <= iagemax+3; i++){  
                   2915:        for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   2916:          posprop += prop[jk][i]; 
                   2917:        } 
1.145     brouard  2918:        
1.126     brouard  2919:        for(jk=1; jk <=nlstate ; jk++){     
                   2920:          if( i <=  iagemax){ 
                   2921:            if(posprop>=1.e-5){ 
                   2922:              probs[i][jk][j1]= prop[jk][i]/posprop;
1.145     brouard  2923:            } else{
                   2924:              if(first==1){
                   2925:                first=0;
                   2926:                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                   2927:              }
                   2928:            }
1.126     brouard  2929:          } 
                   2930:        }/* end jk */ 
                   2931:       }/* end i */ 
1.145     brouard  2932:     /*} *//* end i1 */
                   2933:   } /* end j1 */
1.126     brouard  2934:   
                   2935:   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   2936:   /*free_vector(pp,1,nlstate);*/
                   2937:   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                   2938: }  /* End of prevalence */
                   2939: 
                   2940: /************* Waves Concatenation ***************/
                   2941: 
                   2942: 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)
                   2943: {
                   2944:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   2945:      Death is a valid wave (if date is known).
                   2946:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
                   2947:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   2948:      and mw[mi+1][i]. dh depends on stepm.
                   2949:      */
                   2950: 
                   2951:   int i, mi, m;
                   2952:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                   2953:      double sum=0., jmean=0.;*/
                   2954:   int first;
                   2955:   int j, k=0,jk, ju, jl;
                   2956:   double sum=0.;
                   2957:   first=0;
1.164     brouard  2958:   jmin=100000;
1.126     brouard  2959:   jmax=-1;
                   2960:   jmean=0.;
                   2961:   for(i=1; i<=imx; i++){
                   2962:     mi=0;
                   2963:     m=firstpass;
                   2964:     while(s[m][i] <= nlstate){
                   2965:       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
                   2966:        mw[++mi][i]=m;
                   2967:       if(m >=lastpass)
                   2968:        break;
                   2969:       else
                   2970:        m++;
                   2971:     }/* end while */
                   2972:     if (s[m][i] > nlstate){
                   2973:       mi++;    /* Death is another wave */
                   2974:       /* if(mi==0)  never been interviewed correctly before death */
                   2975:         /* Only death is a correct wave */
                   2976:       mw[mi][i]=m;
                   2977:     }
                   2978: 
                   2979:     wav[i]=mi;
                   2980:     if(mi==0){
                   2981:       nbwarn++;
                   2982:       if(first==0){
                   2983:        printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                   2984:        first=1;
                   2985:       }
                   2986:       if(first==1){
                   2987:        fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
                   2988:       }
                   2989:     } /* end mi==0 */
                   2990:   } /* End individuals */
                   2991: 
                   2992:   for(i=1; i<=imx; i++){
                   2993:     for(mi=1; mi<wav[i];mi++){
                   2994:       if (stepm <=0)
                   2995:        dh[mi][i]=1;
                   2996:       else{
                   2997:        if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                   2998:          if (agedc[i] < 2*AGESUP) {
                   2999:            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   3000:            if(j==0) j=1;  /* Survives at least one month after exam */
                   3001:            else if(j<0){
                   3002:              nberr++;
                   3003:              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]);
                   3004:              j=1; /* Temporary Dangerous patch */
                   3005:              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);
                   3006:              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]);
                   3007:              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);
                   3008:            }
                   3009:            k=k+1;
                   3010:            if (j >= jmax){
                   3011:              jmax=j;
                   3012:              ijmax=i;
                   3013:            }
                   3014:            if (j <= jmin){
                   3015:              jmin=j;
                   3016:              ijmin=i;
                   3017:            }
                   3018:            sum=sum+j;
                   3019:            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   3020:            /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                   3021:          }
                   3022:        }
                   3023:        else{
                   3024:          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                   3025: /*       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]); */
                   3026: 
                   3027:          k=k+1;
                   3028:          if (j >= jmax) {
                   3029:            jmax=j;
                   3030:            ijmax=i;
                   3031:          }
                   3032:          else if (j <= jmin){
                   3033:            jmin=j;
                   3034:            ijmin=i;
                   3035:          }
                   3036:          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                   3037:          /*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]);*/
                   3038:          if(j<0){
                   3039:            nberr++;
                   3040:            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]);
                   3041:            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]);
                   3042:          }
                   3043:          sum=sum+j;
                   3044:        }
                   3045:        jk= j/stepm;
                   3046:        jl= j -jk*stepm;
                   3047:        ju= j -(jk+1)*stepm;
                   3048:        if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                   3049:          if(jl==0){
                   3050:            dh[mi][i]=jk;
                   3051:            bh[mi][i]=0;
                   3052:          }else{ /* We want a negative bias in order to only have interpolation ie
1.136     brouard  3053:                  * to avoid the price of an extra matrix product in likelihood */
1.126     brouard  3054:            dh[mi][i]=jk+1;
                   3055:            bh[mi][i]=ju;
                   3056:          }
                   3057:        }else{
                   3058:          if(jl <= -ju){
                   3059:            dh[mi][i]=jk;
                   3060:            bh[mi][i]=jl;       /* bias is positive if real duration
                   3061:                                 * is higher than the multiple of stepm and negative otherwise.
                   3062:                                 */
                   3063:          }
                   3064:          else{
                   3065:            dh[mi][i]=jk+1;
                   3066:            bh[mi][i]=ju;
                   3067:          }
                   3068:          if(dh[mi][i]==0){
                   3069:            dh[mi][i]=1; /* At least one step */
                   3070:            bh[mi][i]=ju; /* At least one step */
                   3071:            /*  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);*/
                   3072:          }
                   3073:        } /* end if mle */
                   3074:       }
                   3075:     } /* end wave */
                   3076:   }
                   3077:   jmean=sum/k;
                   3078:   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  3079:   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);
1.126     brouard  3080:  }
                   3081: 
                   3082: /*********** Tricode ****************************/
1.145     brouard  3083: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126     brouard  3084: {
1.144     brouard  3085:   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
                   3086:   /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
1.169     brouard  3087:    * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145     brouard  3088:    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169     brouard  3089:    * nbcode[Tvar[j]][1]= 
1.144     brouard  3090:   */
1.130     brouard  3091: 
1.145     brouard  3092:   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136     brouard  3093:   int modmaxcovj=0; /* Modality max of covariates j */
1.145     brouard  3094:   int cptcode=0; /* Modality max of covariates j */
                   3095:   int modmincovj=0; /* Modality min of covariates j */
                   3096: 
                   3097: 
1.126     brouard  3098:   cptcoveff=0; 
                   3099:  
1.145     brouard  3100:   for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144     brouard  3101:   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126     brouard  3102: 
1.145     brouard  3103:   /* Loop on covariates without age and products */
                   3104:   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
                   3105:     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
1.136     brouard  3106:                               modality of this covariate Vj*/ 
1.145     brouard  3107:       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                   3108:                                    * If product of Vn*Vm, still boolean *:
                   3109:                                    * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                   3110:                                    * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
                   3111:       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136     brouard  3112:                                      modality of the nth covariate of individual i. */
1.145     brouard  3113:       if (ij > modmaxcovj)
                   3114:         modmaxcovj=ij; 
                   3115:       else if (ij < modmincovj) 
                   3116:        modmincovj=ij; 
                   3117:       if ((ij < -1) && (ij > NCOVMAX)){
                   3118:        printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                   3119:        exit(1);
                   3120:       }else
1.136     brouard  3121:       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145     brouard  3122:       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126     brouard  3123:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136     brouard  3124:       /* getting the maximum value of the modality of the covariate
                   3125:         (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                   3126:         female is 1, then modmaxcovj=1.*/
1.126     brouard  3127:     }
1.145     brouard  3128:     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
                   3129:     cptcode=modmaxcovj;
1.137     brouard  3130:     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145     brouard  3131:    /*for (i=0; i<=cptcode; i++) {*/
                   3132:     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
                   3133:       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
                   3134:       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
                   3135:        ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
                   3136:       }
                   3137:       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
                   3138:         historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131     brouard  3139:     } /* Ndum[-1] number of undefined modalities */
1.126     brouard  3140: 
1.136     brouard  3141:     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145     brouard  3142:     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
                   3143:     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
                   3144:        modmincovj=3; modmaxcovj = 7;
                   3145:        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
                   3146:        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
                   3147:        variables V1_1 and V1_2.
                   3148:        nbcode[Tvar[j]][ij]=k;
                   3149:        nbcode[Tvar[j]][1]=0;
                   3150:        nbcode[Tvar[j]][2]=1;
                   3151:        nbcode[Tvar[j]][3]=2;
                   3152:     */
                   3153:     ij=1; /* ij is similar to i but can jumps over null modalities */
                   3154:     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
                   3155:       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
                   3156:        /*recode from 0 */
1.131     brouard  3157:        if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
                   3158:          nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                   3159:                                     k is a modality. If we have model=V1+V1*sex 
                   3160:                                     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126     brouard  3161:          ij++;
                   3162:        }
                   3163:        if (ij > ncodemax[j]) break; 
1.137     brouard  3164:       }  /* end of loop on */
                   3165:     } /* end of loop on modality */ 
                   3166:   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
                   3167:   
1.145     brouard  3168:  for (k=-1; k< maxncov; k++) Ndum[k]=0; 
1.137     brouard  3169:   
1.145     brouard  3170:   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
                   3171:    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
                   3172:    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
                   3173:    Ndum[ij]++; 
                   3174:  } 
1.126     brouard  3175: 
                   3176:  ij=1;
1.145     brouard  3177:  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
                   3178:    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126     brouard  3179:    if((Ndum[i]!=0) && (i<=ncovcol)){
1.145     brouard  3180:      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
                   3181:      Tvaraff[ij]=i; /*For printing (unclear) */
1.126     brouard  3182:      ij++;
1.145     brouard  3183:    }else
                   3184:        Tvaraff[ij]=0;
1.126     brouard  3185:  }
1.131     brouard  3186:  ij--;
1.144     brouard  3187:  cptcoveff=ij; /*Number of total covariates*/
1.145     brouard  3188: 
1.126     brouard  3189: }
                   3190: 
1.145     brouard  3191: 
1.126     brouard  3192: /*********** Health Expectancies ****************/
                   3193: 
1.127     brouard  3194: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126     brouard  3195: 
                   3196: {
                   3197:   /* Health expectancies, no variances */
1.164     brouard  3198:   int i, j, nhstepm, hstepm, h, nstepm;
1.126     brouard  3199:   int nhstepma, nstepma; /* Decreasing with age */
                   3200:   double age, agelim, hf;
                   3201:   double ***p3mat;
                   3202:   double eip;
                   3203: 
                   3204:   pstamp(ficreseij);
                   3205:   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
                   3206:   fprintf(ficreseij,"# Age");
                   3207:   for(i=1; i<=nlstate;i++){
                   3208:     for(j=1; j<=nlstate;j++){
                   3209:       fprintf(ficreseij," e%1d%1d ",i,j);
                   3210:     }
                   3211:     fprintf(ficreseij," e%1d. ",i);
                   3212:   }
                   3213:   fprintf(ficreseij,"\n");
                   3214: 
                   3215:   
                   3216:   if(estepm < stepm){
                   3217:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   3218:   }
                   3219:   else  hstepm=estepm;   
                   3220:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   3221:    * This is mainly to measure the difference between two models: for example
                   3222:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   3223:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   3224:    * progression in between and thus overestimating or underestimating according
                   3225:    * to the curvature of the survival function. If, for the same date, we 
                   3226:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   3227:    * to compare the new estimate of Life expectancy with the same linear 
                   3228:    * hypothesis. A more precise result, taking into account a more precise
                   3229:    * curvature will be obtained if estepm is as small as stepm. */
                   3230: 
                   3231:   /* For example we decided to compute the life expectancy with the smallest unit */
                   3232:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   3233:      nhstepm is the number of hstepm from age to agelim 
                   3234:      nstepm is the number of stepm from age to agelin. 
                   3235:      Look at hpijx to understand the reason of that which relies in memory size
                   3236:      and note for a fixed period like estepm months */
                   3237:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   3238:      survival function given by stepm (the optimization length). Unfortunately it
                   3239:      means that if the survival funtion is printed only each two years of age and if
                   3240:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   3241:      results. So we changed our mind and took the option of the best precision.
                   3242:   */
                   3243:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   3244: 
                   3245:   agelim=AGESUP;
                   3246:   /* If stepm=6 months */
                   3247:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   3248:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   3249:     
                   3250: /* nhstepm age range expressed in number of stepm */
                   3251:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   3252:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   3253:   /* if (stepm >= YEARM) hstepm=1;*/
                   3254:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   3255:   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3256: 
                   3257:   for (age=bage; age<=fage; age ++){ 
                   3258:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   3259:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   3260:     /* if (stepm >= YEARM) hstepm=1;*/
                   3261:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   3262: 
                   3263:     /* If stepm=6 months */
                   3264:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   3265:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   3266:     
                   3267:     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
                   3268:     
                   3269:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   3270:     
                   3271:     printf("%d|",(int)age);fflush(stdout);
                   3272:     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   3273:     
                   3274:     /* Computing expectancies */
                   3275:     for(i=1; i<=nlstate;i++)
                   3276:       for(j=1; j<=nlstate;j++)
                   3277:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   3278:          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                   3279:          
                   3280:          /* 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]);*/
                   3281: 
                   3282:        }
                   3283: 
                   3284:     fprintf(ficreseij,"%3.0f",age );
                   3285:     for(i=1; i<=nlstate;i++){
                   3286:       eip=0;
                   3287:       for(j=1; j<=nlstate;j++){
                   3288:        eip +=eij[i][j][(int)age];
                   3289:        fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                   3290:       }
                   3291:       fprintf(ficreseij,"%9.4f", eip );
                   3292:     }
                   3293:     fprintf(ficreseij,"\n");
                   3294:     
                   3295:   }
                   3296:   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3297:   printf("\n");
                   3298:   fprintf(ficlog,"\n");
                   3299:   
                   3300: }
                   3301: 
1.127     brouard  3302: 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[] )
1.126     brouard  3303: 
                   3304: {
                   3305:   /* Covariances of health expectancies eij and of total life expectancies according
                   3306:    to initial status i, ei. .
                   3307:   */
                   3308:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
                   3309:   int nhstepma, nstepma; /* Decreasing with age */
                   3310:   double age, agelim, hf;
                   3311:   double ***p3matp, ***p3matm, ***varhe;
                   3312:   double **dnewm,**doldm;
                   3313:   double *xp, *xm;
                   3314:   double **gp, **gm;
                   3315:   double ***gradg, ***trgradg;
                   3316:   int theta;
                   3317: 
                   3318:   double eip, vip;
                   3319: 
                   3320:   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                   3321:   xp=vector(1,npar);
                   3322:   xm=vector(1,npar);
                   3323:   dnewm=matrix(1,nlstate*nlstate,1,npar);
                   3324:   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
                   3325:   
                   3326:   pstamp(ficresstdeij);
                   3327:   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
                   3328:   fprintf(ficresstdeij,"# Age");
                   3329:   for(i=1; i<=nlstate;i++){
                   3330:     for(j=1; j<=nlstate;j++)
                   3331:       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
                   3332:     fprintf(ficresstdeij," e%1d. ",i);
                   3333:   }
                   3334:   fprintf(ficresstdeij,"\n");
                   3335: 
                   3336:   pstamp(ficrescveij);
                   3337:   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
                   3338:   fprintf(ficrescveij,"# Age");
                   3339:   for(i=1; i<=nlstate;i++)
                   3340:     for(j=1; j<=nlstate;j++){
                   3341:       cptj= (j-1)*nlstate+i;
                   3342:       for(i2=1; i2<=nlstate;i2++)
                   3343:        for(j2=1; j2<=nlstate;j2++){
                   3344:          cptj2= (j2-1)*nlstate+i2;
                   3345:          if(cptj2 <= cptj)
                   3346:            fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
                   3347:        }
                   3348:     }
                   3349:   fprintf(ficrescveij,"\n");
                   3350:   
                   3351:   if(estepm < stepm){
                   3352:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   3353:   }
                   3354:   else  hstepm=estepm;   
                   3355:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   3356:    * This is mainly to measure the difference between two models: for example
                   3357:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   3358:    * we are calculating an estimate of the Life Expectancy assuming a linear 
                   3359:    * progression in between and thus overestimating or underestimating according
                   3360:    * to the curvature of the survival function. If, for the same date, we 
                   3361:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   3362:    * to compare the new estimate of Life expectancy with the same linear 
                   3363:    * hypothesis. A more precise result, taking into account a more precise
                   3364:    * curvature will be obtained if estepm is as small as stepm. */
                   3365: 
                   3366:   /* For example we decided to compute the life expectancy with the smallest unit */
                   3367:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   3368:      nhstepm is the number of hstepm from age to agelim 
                   3369:      nstepm is the number of stepm from age to agelin. 
                   3370:      Look at hpijx to understand the reason of that which relies in memory size
                   3371:      and note for a fixed period like estepm months */
                   3372:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   3373:      survival function given by stepm (the optimization length). Unfortunately it
                   3374:      means that if the survival funtion is printed only each two years of age and if
                   3375:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   3376:      results. So we changed our mind and took the option of the best precision.
                   3377:   */
                   3378:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   3379: 
                   3380:   /* If stepm=6 months */
                   3381:   /* nhstepm age range expressed in number of stepm */
                   3382:   agelim=AGESUP;
                   3383:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                   3384:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   3385:   /* if (stepm >= YEARM) hstepm=1;*/
                   3386:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   3387:   
                   3388:   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3389:   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3390:   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                   3391:   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                   3392:   gp=matrix(0,nhstepm,1,nlstate*nlstate);
                   3393:   gm=matrix(0,nhstepm,1,nlstate*nlstate);
                   3394: 
                   3395:   for (age=bage; age<=fage; age ++){ 
                   3396:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                   3397:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   3398:     /* if (stepm >= YEARM) hstepm=1;*/
                   3399:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   3400: 
                   3401:     /* If stepm=6 months */
                   3402:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
                   3403:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                   3404:     
                   3405:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   3406: 
                   3407:     /* Computing  Variances of health expectancies */
                   3408:     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
                   3409:        decrease memory allocation */
                   3410:     for(theta=1; theta <=npar; theta++){
                   3411:       for(i=1; i<=npar; i++){ 
                   3412:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   3413:        xm[i] = x[i] - (i==theta ?delti[theta]:0);
                   3414:       }
                   3415:       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
                   3416:       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                   3417:   
                   3418:       for(j=1; j<= nlstate; j++){
                   3419:        for(i=1; i<=nlstate; i++){
                   3420:          for(h=0; h<=nhstepm-1; h++){
                   3421:            gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                   3422:            gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                   3423:          }
                   3424:        }
                   3425:       }
                   3426:      
                   3427:       for(ij=1; ij<= nlstate*nlstate; ij++)
                   3428:        for(h=0; h<=nhstepm-1; h++){
                   3429:          gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
                   3430:        }
                   3431:     }/* End theta */
                   3432:     
                   3433:     
                   3434:     for(h=0; h<=nhstepm-1; h++)
                   3435:       for(j=1; j<=nlstate*nlstate;j++)
                   3436:        for(theta=1; theta <=npar; theta++)
                   3437:          trgradg[h][j][theta]=gradg[h][theta][j];
                   3438:     
                   3439: 
                   3440:      for(ij=1;ij<=nlstate*nlstate;ij++)
                   3441:       for(ji=1;ji<=nlstate*nlstate;ji++)
                   3442:        varhe[ij][ji][(int)age] =0.;
                   3443: 
                   3444:      printf("%d|",(int)age);fflush(stdout);
                   3445:      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   3446:      for(h=0;h<=nhstepm-1;h++){
                   3447:       for(k=0;k<=nhstepm-1;k++){
                   3448:        matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   3449:        matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                   3450:        for(ij=1;ij<=nlstate*nlstate;ij++)
                   3451:          for(ji=1;ji<=nlstate*nlstate;ji++)
                   3452:            varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
                   3453:       }
                   3454:     }
                   3455: 
                   3456:     /* Computing expectancies */
                   3457:     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
                   3458:     for(i=1; i<=nlstate;i++)
                   3459:       for(j=1; j<=nlstate;j++)
                   3460:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   3461:          eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                   3462:          
                   3463:          /* 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]);*/
                   3464: 
                   3465:        }
                   3466: 
                   3467:     fprintf(ficresstdeij,"%3.0f",age );
                   3468:     for(i=1; i<=nlstate;i++){
                   3469:       eip=0.;
                   3470:       vip=0.;
                   3471:       for(j=1; j<=nlstate;j++){
                   3472:        eip += eij[i][j][(int)age];
                   3473:        for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                   3474:          vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                   3475:        fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
                   3476:       }
                   3477:       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
                   3478:     }
                   3479:     fprintf(ficresstdeij,"\n");
                   3480: 
                   3481:     fprintf(ficrescveij,"%3.0f",age );
                   3482:     for(i=1; i<=nlstate;i++)
                   3483:       for(j=1; j<=nlstate;j++){
                   3484:        cptj= (j-1)*nlstate+i;
                   3485:        for(i2=1; i2<=nlstate;i2++)
                   3486:          for(j2=1; j2<=nlstate;j2++){
                   3487:            cptj2= (j2-1)*nlstate+i2;
                   3488:            if(cptj2 <= cptj)
                   3489:              fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                   3490:          }
                   3491:       }
                   3492:     fprintf(ficrescveij,"\n");
                   3493:    
                   3494:   }
                   3495:   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   3496:   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   3497:   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   3498:   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                   3499:   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3500:   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3501:   printf("\n");
                   3502:   fprintf(ficlog,"\n");
                   3503: 
                   3504:   free_vector(xm,1,npar);
                   3505:   free_vector(xp,1,npar);
                   3506:   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   3507:   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   3508:   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                   3509: }
                   3510: 
                   3511: /************ Variance ******************/
                   3512: 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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
                   3513: {
                   3514:   /* Variance of health expectancies */
                   3515:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                   3516:   /* double **newm;*/
1.169     brouard  3517:   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
                   3518:   
                   3519:   int movingaverage();
1.126     brouard  3520:   double **dnewm,**doldm;
                   3521:   double **dnewmp,**doldmp;
                   3522:   int i, j, nhstepm, hstepm, h, nstepm ;
1.164     brouard  3523:   int k;
1.126     brouard  3524:   double *xp;
                   3525:   double **gp, **gm;  /* for var eij */
                   3526:   double ***gradg, ***trgradg; /*for var eij */
                   3527:   double **gradgp, **trgradgp; /* for var p point j */
                   3528:   double *gpp, *gmp; /* for var p point j */
                   3529:   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                   3530:   double ***p3mat;
                   3531:   double age,agelim, hf;
                   3532:   double ***mobaverage;
                   3533:   int theta;
                   3534:   char digit[4];
                   3535:   char digitp[25];
                   3536: 
                   3537:   char fileresprobmorprev[FILENAMELENGTH];
                   3538: 
                   3539:   if(popbased==1){
                   3540:     if(mobilav!=0)
                   3541:       strcpy(digitp,"-populbased-mobilav-");
                   3542:     else strcpy(digitp,"-populbased-nomobil-");
                   3543:   }
                   3544:   else 
                   3545:     strcpy(digitp,"-stablbased-");
                   3546: 
                   3547:   if (mobilav!=0) {
                   3548:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3549:     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   3550:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   3551:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   3552:     }
                   3553:   }
                   3554: 
                   3555:   strcpy(fileresprobmorprev,"prmorprev"); 
                   3556:   sprintf(digit,"%-d",ij);
                   3557:   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   3558:   strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   3559:   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   3560:   strcat(fileresprobmorprev,fileres);
                   3561:   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   3562:     printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   3563:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   3564:   }
                   3565:   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   3566:  
                   3567:   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   3568:   pstamp(ficresprobmorprev);
                   3569:   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);
                   3570:   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   3571:   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   3572:     fprintf(ficresprobmorprev," p.%-d SE",j);
                   3573:     for(i=1; i<=nlstate;i++)
                   3574:       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   3575:   }  
                   3576:   fprintf(ficresprobmorprev,"\n");
                   3577:   fprintf(ficgp,"\n# Routine varevsij");
                   3578:   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
                   3579:   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");
                   3580:   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   3581: /*   } */
                   3582:   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3583:   pstamp(ficresvij);
                   3584:   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
                   3585:   if(popbased==1)
1.128     brouard  3586:     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);
1.126     brouard  3587:   else
                   3588:     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
                   3589:   fprintf(ficresvij,"# Age");
                   3590:   for(i=1; i<=nlstate;i++)
                   3591:     for(j=1; j<=nlstate;j++)
                   3592:       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
                   3593:   fprintf(ficresvij,"\n");
                   3594: 
                   3595:   xp=vector(1,npar);
                   3596:   dnewm=matrix(1,nlstate,1,npar);
                   3597:   doldm=matrix(1,nlstate,1,nlstate);
                   3598:   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   3599:   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3600: 
                   3601:   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                   3602:   gpp=vector(nlstate+1,nlstate+ndeath);
                   3603:   gmp=vector(nlstate+1,nlstate+ndeath);
                   3604:   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   3605:   
                   3606:   if(estepm < stepm){
                   3607:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   3608:   }
                   3609:   else  hstepm=estepm;   
                   3610:   /* For example we decided to compute the life expectancy with the smallest unit */
                   3611:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   3612:      nhstepm is the number of hstepm from age to agelim 
                   3613:      nstepm is the number of stepm from age to agelin. 
1.128     brouard  3614:      Look at function hpijx to understand why (it is linked to memory size questions) */
1.126     brouard  3615:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   3616:      survival function given by stepm (the optimization length). Unfortunately it
                   3617:      means that if the survival funtion is printed every two years of age and if
                   3618:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   3619:      results. So we changed our mind and took the option of the best precision.
                   3620:   */
                   3621:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   3622:   agelim = AGESUP;
                   3623:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   3624:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   3625:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   3626:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3627:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                   3628:     gp=matrix(0,nhstepm,1,nlstate);
                   3629:     gm=matrix(0,nhstepm,1,nlstate);
                   3630: 
                   3631: 
                   3632:     for(theta=1; theta <=npar; theta++){
                   3633:       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                   3634:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   3635:       }
                   3636:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   3637:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3638: 
                   3639:       if (popbased==1) {
                   3640:        if(mobilav ==0){
                   3641:          for(i=1; i<=nlstate;i++)
                   3642:            prlim[i][i]=probs[(int)age][i][ij];
                   3643:        }else{ /* mobilav */ 
                   3644:          for(i=1; i<=nlstate;i++)
                   3645:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   3646:        }
                   3647:       }
                   3648:   
                   3649:       for(j=1; j<= nlstate; j++){
                   3650:        for(h=0; h<=nhstepm; h++){
                   3651:          for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                   3652:            gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   3653:        }
                   3654:       }
                   3655:       /* This for computing probability of death (h=1 means
                   3656:          computed over hstepm matrices product = hstepm*stepm months) 
                   3657:          as a weighted average of prlim.
                   3658:       */
                   3659:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   3660:        for(i=1,gpp[j]=0.; i<= nlstate; i++)
                   3661:          gpp[j] += prlim[i][i]*p3mat[i][j][1];
                   3662:       }    
                   3663:       /* end probability of death */
                   3664: 
                   3665:       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                   3666:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   3667:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   3668:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3669:  
                   3670:       if (popbased==1) {
                   3671:        if(mobilav ==0){
                   3672:          for(i=1; i<=nlstate;i++)
                   3673:            prlim[i][i]=probs[(int)age][i][ij];
                   3674:        }else{ /* mobilav */ 
                   3675:          for(i=1; i<=nlstate;i++)
                   3676:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   3677:        }
                   3678:       }
                   3679: 
1.128     brouard  3680:       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
1.126     brouard  3681:        for(h=0; h<=nhstepm; h++){
                   3682:          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   3683:            gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                   3684:        }
                   3685:       }
                   3686:       /* This for computing probability of death (h=1 means
                   3687:          computed over hstepm matrices product = hstepm*stepm months) 
                   3688:          as a weighted average of prlim.
                   3689:       */
                   3690:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   3691:        for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   3692:          gmp[j] += prlim[i][i]*p3mat[i][j][1];
                   3693:       }    
                   3694:       /* end probability of death */
                   3695: 
                   3696:       for(j=1; j<= nlstate; j++) /* vareij */
                   3697:        for(h=0; h<=nhstepm; h++){
                   3698:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   3699:        }
                   3700: 
                   3701:       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                   3702:        gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                   3703:       }
                   3704: 
                   3705:     } /* End theta */
                   3706: 
                   3707:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   3708: 
                   3709:     for(h=0; h<=nhstepm; h++) /* veij */
                   3710:       for(j=1; j<=nlstate;j++)
                   3711:        for(theta=1; theta <=npar; theta++)
                   3712:          trgradg[h][j][theta]=gradg[h][theta][j];
                   3713: 
                   3714:     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                   3715:       for(theta=1; theta <=npar; theta++)
                   3716:        trgradgp[j][theta]=gradgp[theta][j];
                   3717:   
                   3718: 
                   3719:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   3720:     for(i=1;i<=nlstate;i++)
                   3721:       for(j=1;j<=nlstate;j++)
                   3722:        vareij[i][j][(int)age] =0.;
                   3723: 
                   3724:     for(h=0;h<=nhstepm;h++){
                   3725:       for(k=0;k<=nhstepm;k++){
                   3726:        matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                   3727:        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                   3728:        for(i=1;i<=nlstate;i++)
                   3729:          for(j=1;j<=nlstate;j++)
                   3730:            vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                   3731:       }
                   3732:     }
                   3733:   
                   3734:     /* pptj */
                   3735:     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                   3736:     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                   3737:     for(j=nlstate+1;j<=nlstate+ndeath;j++)
                   3738:       for(i=nlstate+1;i<=nlstate+ndeath;i++)
                   3739:        varppt[j][i]=doldmp[j][i];
                   3740:     /* end ppptj */
                   3741:     /*  x centered again */
                   3742:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                   3743:     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                   3744:  
                   3745:     if (popbased==1) {
                   3746:       if(mobilav ==0){
                   3747:        for(i=1; i<=nlstate;i++)
                   3748:          prlim[i][i]=probs[(int)age][i][ij];
                   3749:       }else{ /* mobilav */ 
                   3750:        for(i=1; i<=nlstate;i++)
                   3751:          prlim[i][i]=mobaverage[(int)age][i][ij];
                   3752:       }
                   3753:     }
                   3754:              
                   3755:     /* This for computing probability of death (h=1 means
                   3756:        computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   3757:        as a weighted average of prlim.
                   3758:     */
                   3759:     for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   3760:       for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                   3761:        gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   3762:     }    
                   3763:     /* end probability of death */
                   3764: 
                   3765:     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   3766:     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   3767:       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                   3768:       for(i=1; i<=nlstate;i++){
                   3769:        fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   3770:       }
                   3771:     } 
                   3772:     fprintf(ficresprobmorprev,"\n");
                   3773: 
                   3774:     fprintf(ficresvij,"%.0f ",age );
                   3775:     for(i=1; i<=nlstate;i++)
                   3776:       for(j=1; j<=nlstate;j++){
                   3777:        fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                   3778:       }
                   3779:     fprintf(ficresvij,"\n");
                   3780:     free_matrix(gp,0,nhstepm,1,nlstate);
                   3781:     free_matrix(gm,0,nhstepm,1,nlstate);
                   3782:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                   3783:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                   3784:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3785:   } /* End age */
                   3786:   free_vector(gpp,nlstate+1,nlstate+ndeath);
                   3787:   free_vector(gmp,nlstate+1,nlstate+ndeath);
                   3788:   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                   3789:   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145     brouard  3790:   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126     brouard  3791:   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131     brouard  3792:   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126     brouard  3793: /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                   3794: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   3795: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145     brouard  3796:   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170     brouard  3797:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145     brouard  3798:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126     brouard  3799:   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
                   3800:   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
                   3801:   /*  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.png\"> <br>\n", stepm,YEARM,digitp,digit);
                   3802: */
                   3803: /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
                   3804:   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
                   3805: 
                   3806:   free_vector(xp,1,npar);
                   3807:   free_matrix(doldm,1,nlstate,1,nlstate);
                   3808:   free_matrix(dnewm,1,nlstate,1,npar);
                   3809:   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3810:   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   3811:   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   3812:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3813:   fclose(ficresprobmorprev);
                   3814:   fflush(ficgp);
                   3815:   fflush(fichtm); 
                   3816: }  /* end varevsij */
                   3817: 
                   3818: /************ Variance of prevlim ******************/
                   3819: 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 ij, char strstart[])
                   3820: {
                   3821:   /* Variance of prevalence limit */
                   3822:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164     brouard  3823: 
1.126     brouard  3824:   double **dnewm,**doldm;
                   3825:   int i, j, nhstepm, hstepm;
                   3826:   double *xp;
                   3827:   double *gp, *gm;
                   3828:   double **gradg, **trgradg;
                   3829:   double age,agelim;
                   3830:   int theta;
                   3831:   
                   3832:   pstamp(ficresvpl);
                   3833:   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
                   3834:   fprintf(ficresvpl,"# Age");
                   3835:   for(i=1; i<=nlstate;i++)
                   3836:       fprintf(ficresvpl," %1d-%1d",i,i);
                   3837:   fprintf(ficresvpl,"\n");
                   3838: 
                   3839:   xp=vector(1,npar);
                   3840:   dnewm=matrix(1,nlstate,1,npar);
                   3841:   doldm=matrix(1,nlstate,1,nlstate);
                   3842:   
                   3843:   hstepm=1*YEARM; /* Every year of age */
                   3844:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                   3845:   agelim = AGESUP;
                   3846:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   3847:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   3848:     if (stepm >= YEARM) hstepm=1;
                   3849:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   3850:     gradg=matrix(1,npar,1,nlstate);
                   3851:     gp=vector(1,nlstate);
                   3852:     gm=vector(1,nlstate);
                   3853: 
                   3854:     for(theta=1; theta <=npar; theta++){
                   3855:       for(i=1; i<=npar; i++){ /* Computes gradient */
                   3856:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   3857:       }
                   3858:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3859:       for(i=1;i<=nlstate;i++)
                   3860:        gp[i] = prlim[i][i];
                   3861:     
                   3862:       for(i=1; i<=npar; i++) /* Computes gradient */
                   3863:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   3864:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   3865:       for(i=1;i<=nlstate;i++)
                   3866:        gm[i] = prlim[i][i];
                   3867: 
                   3868:       for(i=1;i<=nlstate;i++)
                   3869:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                   3870:     } /* End theta */
                   3871: 
                   3872:     trgradg =matrix(1,nlstate,1,npar);
                   3873: 
                   3874:     for(j=1; j<=nlstate;j++)
                   3875:       for(theta=1; theta <=npar; theta++)
                   3876:        trgradg[j][theta]=gradg[theta][j];
                   3877: 
                   3878:     for(i=1;i<=nlstate;i++)
                   3879:       varpl[i][(int)age] =0.;
                   3880:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   3881:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   3882:     for(i=1;i<=nlstate;i++)
                   3883:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   3884: 
                   3885:     fprintf(ficresvpl,"%.0f ",age );
                   3886:     for(i=1; i<=nlstate;i++)
                   3887:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                   3888:     fprintf(ficresvpl,"\n");
                   3889:     free_vector(gp,1,nlstate);
                   3890:     free_vector(gm,1,nlstate);
                   3891:     free_matrix(gradg,1,npar,1,nlstate);
                   3892:     free_matrix(trgradg,1,nlstate,1,npar);
                   3893:   } /* End age */
                   3894: 
                   3895:   free_vector(xp,1,npar);
                   3896:   free_matrix(doldm,1,nlstate,1,npar);
                   3897:   free_matrix(dnewm,1,nlstate,1,nlstate);
                   3898: 
                   3899: }
                   3900: 
                   3901: /************ Variance of one-step probabilities  ******************/
                   3902: 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[])
                   3903: {
1.164     brouard  3904:   int i, j=0,  k1, l1, tj;
1.126     brouard  3905:   int k2, l2, j1,  z1;
1.164     brouard  3906:   int k=0, l;
1.145     brouard  3907:   int first=1, first1, first2;
1.126     brouard  3908:   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                   3909:   double **dnewm,**doldm;
                   3910:   double *xp;
                   3911:   double *gp, *gm;
                   3912:   double **gradg, **trgradg;
                   3913:   double **mu;
1.164     brouard  3914:   double age, cov[NCOVMAX+1];
1.126     brouard  3915:   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   3916:   int theta;
                   3917:   char fileresprob[FILENAMELENGTH];
                   3918:   char fileresprobcov[FILENAMELENGTH];
                   3919:   char fileresprobcor[FILENAMELENGTH];
                   3920:   double ***varpij;
                   3921: 
                   3922:   strcpy(fileresprob,"prob"); 
                   3923:   strcat(fileresprob,fileres);
                   3924:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                   3925:     printf("Problem with resultfile: %s\n", fileresprob);
                   3926:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   3927:   }
                   3928:   strcpy(fileresprobcov,"probcov"); 
                   3929:   strcat(fileresprobcov,fileres);
                   3930:   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   3931:     printf("Problem with resultfile: %s\n", fileresprobcov);
                   3932:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   3933:   }
                   3934:   strcpy(fileresprobcor,"probcor"); 
                   3935:   strcat(fileresprobcor,fileres);
                   3936:   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                   3937:     printf("Problem with resultfile: %s\n", fileresprobcor);
                   3938:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   3939:   }
                   3940:   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   3941:   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   3942:   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   3943:   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   3944:   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   3945:   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   3946:   pstamp(ficresprob);
                   3947:   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
                   3948:   fprintf(ficresprob,"# Age");
                   3949:   pstamp(ficresprobcov);
                   3950:   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
                   3951:   fprintf(ficresprobcov,"# Age");
                   3952:   pstamp(ficresprobcor);
                   3953:   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
                   3954:   fprintf(ficresprobcor,"# Age");
                   3955: 
                   3956: 
                   3957:   for(i=1; i<=nlstate;i++)
                   3958:     for(j=1; j<=(nlstate+ndeath);j++){
                   3959:       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                   3960:       fprintf(ficresprobcov," p%1d-%1d ",i,j);
                   3961:       fprintf(ficresprobcor," p%1d-%1d ",i,j);
                   3962:     }  
                   3963:  /* fprintf(ficresprob,"\n");
                   3964:   fprintf(ficresprobcov,"\n");
                   3965:   fprintf(ficresprobcor,"\n");
                   3966:  */
1.131     brouard  3967:   xp=vector(1,npar);
1.126     brouard  3968:   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   3969:   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   3970:   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                   3971:   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                   3972:   first=1;
                   3973:   fprintf(ficgp,"\n# Routine varprob");
                   3974:   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   3975:   fprintf(fichtm,"\n");
                   3976: 
                   3977:   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
                   3978:   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
                   3979:   file %s<br>\n",optionfilehtmcov);
                   3980:   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
                   3981: and drawn. It helps understanding how is the covariance between two incidences.\
                   3982:  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
                   3983:   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. \
                   3984: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
                   3985: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
                   3986: standard deviations wide on each axis. <br>\
                   3987:  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
                   3988:  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
                   3989: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
                   3990: 
                   3991:   cov[1]=1;
1.145     brouard  3992:   /* tj=cptcoveff; */
                   3993:   tj = (int) pow(2,cptcoveff);
1.126     brouard  3994:   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   3995:   j1=0;
1.145     brouard  3996:   for(j1=1; j1<=tj;j1++){
                   3997:     /*for(i1=1; i1<=ncodemax[t];i1++){ */
                   3998:     /*j1++;*/
1.126     brouard  3999:       if  (cptcovn>0) {
                   4000:        fprintf(ficresprob, "\n#********** Variable "); 
                   4001:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   4002:        fprintf(ficresprob, "**********\n#\n");
                   4003:        fprintf(ficresprobcov, "\n#********** Variable "); 
                   4004:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   4005:        fprintf(ficresprobcov, "**********\n#\n");
                   4006:        
                   4007:        fprintf(ficgp, "\n#********** Variable "); 
                   4008:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   4009:        fprintf(ficgp, "**********\n#\n");
                   4010:        
                   4011:        
                   4012:        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                   4013:        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   4014:        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                   4015:        
                   4016:        fprintf(ficresprobcor, "\n#********** Variable ");    
                   4017:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   4018:        fprintf(ficresprobcor, "**********\n#");    
                   4019:       }
                   4020:       
1.145     brouard  4021:       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                   4022:       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   4023:       gp=vector(1,(nlstate)*(nlstate+ndeath));
                   4024:       gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126     brouard  4025:       for (age=bage; age<=fage; age ++){ 
                   4026:        cov[2]=age;
                   4027:        for (k=1; k<=cptcovn;k++) {
1.145     brouard  4028:          cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                   4029:                                                         * 1  1 1 1 1
                   4030:                                                         * 2  2 1 1 1
                   4031:                                                         * 3  1 2 1 1
                   4032:                                                         */
                   4033:          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126     brouard  4034:        }
                   4035:        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   4036:        for (k=1; k<=cptcovprod;k++)
                   4037:          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   4038:        
                   4039:     
                   4040:        for(theta=1; theta <=npar; theta++){
                   4041:          for(i=1; i<=npar; i++)
                   4042:            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                   4043:          
                   4044:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   4045:          
                   4046:          k=0;
                   4047:          for(i=1; i<= (nlstate); i++){
                   4048:            for(j=1; j<=(nlstate+ndeath);j++){
                   4049:              k=k+1;
                   4050:              gp[k]=pmmij[i][j];
                   4051:            }
                   4052:          }
                   4053:          
                   4054:          for(i=1; i<=npar; i++)
                   4055:            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                   4056:     
                   4057:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   4058:          k=0;
                   4059:          for(i=1; i<=(nlstate); i++){
                   4060:            for(j=1; j<=(nlstate+ndeath);j++){
                   4061:              k=k+1;
                   4062:              gm[k]=pmmij[i][j];
                   4063:            }
                   4064:          }
                   4065:      
                   4066:          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                   4067:            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
                   4068:        }
                   4069: 
                   4070:        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   4071:          for(theta=1; theta <=npar; theta++)
                   4072:            trgradg[j][theta]=gradg[theta][j];
                   4073:        
                   4074:        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   4075:        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                   4076: 
                   4077:        pmij(pmmij,cov,ncovmodel,x,nlstate);
                   4078:        
                   4079:        k=0;
                   4080:        for(i=1; i<=(nlstate); i++){
                   4081:          for(j=1; j<=(nlstate+ndeath);j++){
                   4082:            k=k+1;
                   4083:            mu[k][(int) age]=pmmij[i][j];
                   4084:          }
                   4085:        }
                   4086:        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                   4087:          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   4088:            varpij[i][j][(int)age] = doldm[i][j];
                   4089: 
                   4090:        /*printf("\n%d ",(int)age);
                   4091:          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   4092:          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   4093:          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   4094:          }*/
                   4095: 
                   4096:        fprintf(ficresprob,"\n%d ",(int)age);
                   4097:        fprintf(ficresprobcov,"\n%d ",(int)age);
                   4098:        fprintf(ficresprobcor,"\n%d ",(int)age);
                   4099: 
                   4100:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   4101:          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                   4102:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   4103:          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                   4104:          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                   4105:        }
                   4106:        i=0;
                   4107:        for (k=1; k<=(nlstate);k++){
                   4108:          for (l=1; l<=(nlstate+ndeath);l++){ 
1.145     brouard  4109:            i++;
1.126     brouard  4110:            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   4111:            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                   4112:            for (j=1; j<=i;j++){
1.145     brouard  4113:              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126     brouard  4114:              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                   4115:              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   4116:            }
                   4117:          }
                   4118:        }/* end of loop for state */
                   4119:       } /* end of loop for age */
1.145     brouard  4120:       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                   4121:       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                   4122:       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   4123:       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   4124:       
1.126     brouard  4125:       /* Confidence intervalle of pij  */
                   4126:       /*
1.131     brouard  4127:        fprintf(ficgp,"\nunset parametric;unset label");
1.126     brouard  4128:        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                   4129:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                   4130:        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);
                   4131:        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                   4132:        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                   4133:        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                   4134:       */
                   4135: 
                   4136:       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145     brouard  4137:       first1=1;first2=2;
1.126     brouard  4138:       for (k2=1; k2<=(nlstate);k2++){
                   4139:        for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                   4140:          if(l2==k2) continue;
                   4141:          j=(k2-1)*(nlstate+ndeath)+l2;
                   4142:          for (k1=1; k1<=(nlstate);k1++){
                   4143:            for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                   4144:              if(l1==k1) continue;
                   4145:              i=(k1-1)*(nlstate+ndeath)+l1;
                   4146:              if(i<=j) continue;
                   4147:              for (age=bage; age<=fage; age ++){ 
                   4148:                if ((int)age %5==0){
                   4149:                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                   4150:                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   4151:                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   4152:                  mu1=mu[i][(int) age]/stepm*YEARM ;
                   4153:                  mu2=mu[j][(int) age]/stepm*YEARM;
                   4154:                  c12=cv12/sqrt(v1*v2);
                   4155:                  /* Computing eigen value of matrix of covariance */
                   4156:                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   4157:                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135     brouard  4158:                  if ((lc2 <0) || (lc1 <0) ){
1.145     brouard  4159:                    if(first2==1){
                   4160:                      first1=0;
                   4161:                    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);
                   4162:                    }
                   4163:                    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);
                   4164:                    /* lc1=fabs(lc1); */ /* If we want to have them positive */
                   4165:                    /* lc2=fabs(lc2); */
1.135     brouard  4166:                  }
                   4167: 
1.126     brouard  4168:                  /* Eigen vectors */
                   4169:                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   4170:                  /*v21=sqrt(1.-v11*v11); *//* error */
                   4171:                  v21=(lc1-v1)/cv12*v11;
                   4172:                  v12=-v21;
                   4173:                  v22=v11;
                   4174:                  tnalp=v21/v11;
                   4175:                  if(first1==1){
                   4176:                    first1=0;
                   4177:                    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);
                   4178:                  }
                   4179:                  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);
                   4180:                  /*printf(fignu*/
                   4181:                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                   4182:                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   4183:                  if(first==1){
                   4184:                    first=0;
                   4185:                    fprintf(ficgp,"\nset parametric;unset label");
                   4186:                    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);
1.145     brouard  4187:                    fprintf(ficgp,"\nset ter png small size 320, 240");
1.126     brouard  4188:                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
                   4189:  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
                   4190: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                   4191:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                   4192:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   4193:                    fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   4194:                    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                   4195:                    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   4196:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   4197:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   4198:                    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",\
                   4199:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   4200:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   4201:                  }else{
                   4202:                    first=0;
                   4203:                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                   4204:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   4205:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   4206:                    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",\
                   4207:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   4208:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   4209:                  }/* if first */
                   4210:                } /* age mod 5 */
                   4211:              } /* end loop age */
                   4212:              fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   4213:              first=1;
                   4214:            } /*l12 */
                   4215:          } /* k12 */
                   4216:        } /*l1 */
                   4217:       }/* k1 */
1.169     brouard  4218:       /* } */ /* loop covariates */
1.126     brouard  4219:   }
                   4220:   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
                   4221:   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
                   4222:   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   4223:   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
                   4224:   free_vector(xp,1,npar);
                   4225:   fclose(ficresprob);
                   4226:   fclose(ficresprobcov);
                   4227:   fclose(ficresprobcor);
                   4228:   fflush(ficgp);
                   4229:   fflush(fichtmcov);
                   4230: }
                   4231: 
                   4232: 
                   4233: /******************* Printing html file ***********/
                   4234: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                   4235:                  int lastpass, int stepm, int weightopt, char model[],\
                   4236:                  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   4237:                  int popforecast, int estepm ,\
                   4238:                  double jprev1, double mprev1,double anprev1, \
                   4239:                  double jprev2, double mprev2,double anprev2){
                   4240:   int jj1, k1, i1, cpt;
                   4241: 
                   4242:    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
                   4243:    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
                   4244: </ul>");
                   4245:    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
                   4246:  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
                   4247:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
                   4248:    fprintf(fichtm,"\
                   4249:  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
                   4250:           stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
                   4251:    fprintf(fichtm,"\
                   4252:  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
                   4253:           subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
                   4254:    fprintf(fichtm,"\
1.128     brouard  4255:  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . 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  4256:    <a href=\"%s\">%s</a> <br>\n",
                   4257:           estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
                   4258:    fprintf(fichtm,"\
                   4259:  - Population projections by age and states: \
                   4260:    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
                   4261: 
                   4262: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
                   4263: 
1.145     brouard  4264:  m=pow(2,cptcoveff);
1.126     brouard  4265:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   4266: 
                   4267:  jj1=0;
                   4268:  for(k1=1; k1<=m;k1++){
                   4269:    for(i1=1; i1<=ncodemax[k1];i1++){
                   4270:      jj1++;
                   4271:      if (cptcovn > 0) {
                   4272:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   4273:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   4274:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   4275:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   4276:      }
                   4277:      /* Pij */
1.145     brouard  4278:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
                   4279: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
1.126     brouard  4280:      /* Quasi-incidences */
                   4281:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145     brouard  4282:  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
                   4283: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
1.126     brouard  4284:        /* Period (stable) prevalence in each health state */
1.154     brouard  4285:        for(cpt=1; cpt<=nlstate;cpt++){
1.166     brouard  4286:         fprintf(fichtm,"<br>- 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.png\">%s%d_%d.png</a><br> \
                   4287: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126     brouard  4288:        }
                   4289:      for(cpt=1; cpt<=nlstate;cpt++) {
1.154     brouard  4290:         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) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
                   4291: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126     brouard  4292:      }
                   4293:    } /* end i1 */
                   4294:  }/* End k1 */
                   4295:  fprintf(fichtm,"</ul>");
                   4296: 
                   4297: 
                   4298:  fprintf(fichtm,"\
                   4299: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
                   4300:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
                   4301: 
                   4302:  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   4303:         subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
                   4304:  fprintf(fichtm,"\
                   4305:  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   4306:         subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
                   4307: 
                   4308:  fprintf(fichtm,"\
                   4309:  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   4310:         subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
                   4311:  fprintf(fichtm,"\
                   4312:  - 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): \
                   4313:    <a href=\"%s\">%s</a> <br>\n</li>",
                   4314:           estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
                   4315:  fprintf(fichtm,"\
                   4316:  - (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): \
                   4317:    <a href=\"%s\">%s</a> <br>\n</li>",
                   4318:           estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
                   4319:  fprintf(fichtm,"\
1.128     brouard  4320:  - 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",
1.126     brouard  4321:         estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
                   4322:  fprintf(fichtm,"\
1.128     brouard  4323:  - 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",
                   4324:         estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126     brouard  4325:  fprintf(fichtm,"\
                   4326:  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
                   4327:         subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
                   4328: 
                   4329: /*  if(popforecast==1) fprintf(fichtm,"\n */
                   4330: /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                   4331: /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                   4332: /*     <br>",fileres,fileres,fileres,fileres); */
                   4333: /*  else  */
                   4334: /*    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); */
                   4335:  fflush(fichtm);
                   4336:  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
                   4337: 
1.145     brouard  4338:  m=pow(2,cptcoveff);
1.126     brouard  4339:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   4340: 
                   4341:  jj1=0;
                   4342:  for(k1=1; k1<=m;k1++){
                   4343:    for(i1=1; i1<=ncodemax[k1];i1++){
                   4344:      jj1++;
                   4345:      if (cptcovn > 0) {
                   4346:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   4347:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   4348:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   4349:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   4350:      }
                   4351:      for(cpt=1; cpt<=nlstate;cpt++) {
                   4352:        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145     brouard  4353: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
                   4354: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
1.126     brouard  4355:      }
                   4356:      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128     brouard  4357: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
                   4358: true period expectancies (those weighted with period prevalences are also\
                   4359:  drawn in addition to the population based expectancies computed using\
                   4360:  observed and cahotic prevalences: %s%d.png<br>\
1.126     brouard  4361: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
                   4362:    } /* end i1 */
                   4363:  }/* End k1 */
                   4364:  fprintf(fichtm,"</ul>");
                   4365:  fflush(fichtm);
                   4366: }
                   4367: 
                   4368: /******************* Gnuplot file **************/
                   4369: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
                   4370: 
                   4371:   char dirfileres[132],optfileres[132];
1.164     brouard  4372:   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130     brouard  4373:   int ng=0;
1.126     brouard  4374: /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
                   4375: /*     printf("Problem with file %s",optionfilegnuplot); */
                   4376: /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
                   4377: /*   } */
                   4378: 
                   4379:   /*#ifdef windows */
                   4380:   fprintf(ficgp,"cd \"%s\" \n",pathc);
                   4381:     /*#endif */
                   4382:   m=pow(2,cptcoveff);
                   4383: 
                   4384:   strcpy(dirfileres,optionfilefiname);
                   4385:   strcpy(optfileres,"vpl");
                   4386:  /* 1eme*/
1.153     brouard  4387:   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126     brouard  4388:   for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145     brouard  4389:     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
                   4390:      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
                   4391:      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126     brouard  4392:      fprintf(ficgp,"set xlabel \"Age\" \n\
                   4393: set ylabel \"Probability\" \n\
1.145     brouard  4394: set ter png small size 320, 240\n\
1.170     brouard  4395: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126     brouard  4396: 
                   4397:      for (i=1; i<= nlstate ; i ++) {
1.170     brouard  4398:        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   4399:        else        fprintf(ficgp," %%*lf (%%*lf)");
1.126     brouard  4400:      }
1.170     brouard  4401:      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126     brouard  4402:      for (i=1; i<= nlstate ; i ++) {
1.170     brouard  4403:        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   4404:        else fprintf(ficgp," %%*lf (%%*lf)");
1.126     brouard  4405:      } 
1.170     brouard  4406:      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
1.126     brouard  4407:      for (i=1; i<= nlstate ; i ++) {
1.170     brouard  4408:        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                   4409:        else fprintf(ficgp," %%*lf (%%*lf)");
1.126     brouard  4410:      }  
1.145     brouard  4411:      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126     brouard  4412:    }
                   4413:   }
                   4414:   /*2 eme*/
1.153     brouard  4415:   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126     brouard  4416:   for (k1=1; k1<= m ; k1 ++) { 
                   4417:     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145     brouard  4418:     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126     brouard  4419:     
                   4420:     for (i=1; i<= nlstate+1 ; i ++) {
                   4421:       k=2*i;
1.170     brouard  4422:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126     brouard  4423:       for (j=1; j<= nlstate+1 ; j ++) {
1.170     brouard  4424:        if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   4425:        else fprintf(ficgp," %%*lf (%%*lf)");
1.126     brouard  4426:       }   
                   4427:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
                   4428:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170     brouard  4429:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126     brouard  4430:       for (j=1; j<= nlstate+1 ; j ++) {
1.170     brouard  4431:        if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   4432:        else fprintf(ficgp," %%*lf (%%*lf)");
1.126     brouard  4433:       }   
1.145     brouard  4434:       fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170     brouard  4435:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126     brouard  4436:       for (j=1; j<= nlstate+1 ; j ++) {
1.170     brouard  4437:        if (j==i) fprintf(ficgp," %%lf (%%lf)");
                   4438:        else fprintf(ficgp," %%*lf (%%*lf)");
1.126     brouard  4439:       }   
1.145     brouard  4440:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
                   4441:       else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126     brouard  4442:     }
                   4443:   }
                   4444:   
                   4445:   /*3eme*/
                   4446:   
                   4447:   for (k1=1; k1<= m ; k1 ++) { 
                   4448:     for (cpt=1; cpt<= nlstate ; cpt ++) {
                   4449:       /*       k=2+nlstate*(2*cpt-2); */
                   4450:       k=2+(nlstate+1)*(cpt-1);
                   4451:       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145     brouard  4452:       fprintf(ficgp,"set ter png small size 320, 240\n\
1.126     brouard  4453: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
                   4454:       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   4455:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   4456:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   4457:        fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   4458:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   4459:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   4460:        
                   4461:       */
                   4462:       for (i=1; i< nlstate ; i ++) {
                   4463:        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
                   4464:        /*      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);*/
                   4465:        
                   4466:       } 
                   4467:       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
                   4468:     }
                   4469:   }
                   4470:   
                   4471:   /* CV preval stable (period) */
1.153     brouard  4472:   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
                   4473:     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126     brouard  4474:       k=3;
1.153     brouard  4475:       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145     brouard  4476:       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126     brouard  4477:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145     brouard  4478: set ter png small size 320, 240\n\
1.126     brouard  4479: unset log y\n\
1.153     brouard  4480: plot [%.f:%.f]  ", ageminpar, agemaxpar);
                   4481:       for (i=1; i<= nlstate ; i ++){
                   4482:        if(i==1)
                   4483:          fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
                   4484:        else
                   4485:          fprintf(ficgp,", '' ");
1.154     brouard  4486:        l=(nlstate+ndeath)*(i-1)+1;
                   4487:        fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153     brouard  4488:        for (j=1; j<= (nlstate-1) ; j ++)
                   4489:          fprintf(ficgp,"+$%d",k+l+j);
                   4490:        fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
                   4491:       } /* nlstate */
                   4492:       fprintf(ficgp,"\n");
                   4493:     } /* end cpt state*/ 
                   4494:   } /* end covariate */  
1.126     brouard  4495:   
                   4496:   /* proba elementaires */
                   4497:   for(i=1,jk=1; i <=nlstate; i++){
                   4498:     for(k=1; k <=(nlstate+ndeath); k++){
                   4499:       if (k != i) {
                   4500:        for(j=1; j <=ncovmodel; j++){
                   4501:          fprintf(ficgp,"p%d=%f ",jk,p[jk]);
                   4502:          jk++; 
                   4503:          fprintf(ficgp,"\n");
                   4504:        }
                   4505:       }
                   4506:     }
                   4507:    }
1.145     brouard  4508:   /*goto avoid;*/
1.126     brouard  4509:    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
                   4510:      for(jk=1; jk <=m; jk++) {
1.145     brouard  4511:        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
1.126     brouard  4512:        if (ng==2)
                   4513:         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
                   4514:        else
                   4515:         fprintf(ficgp,"\nset title \"Probability\"\n");
1.145     brouard  4516:        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
1.126     brouard  4517:        i=1;
                   4518:        for(k2=1; k2<=nlstate; k2++) {
                   4519:         k3=i;
                   4520:         for(k=1; k<=(nlstate+ndeath); k++) {
                   4521:           if (k != k2){
                   4522:             if(ng==2)
                   4523:               fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                   4524:             else
                   4525:               fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141     brouard  4526:             ij=1;/* To be checked else nbcode[0][0] wrong */
1.126     brouard  4527:             for(j=3; j <=ncovmodel; j++) {
1.145     brouard  4528:               /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                   4529:               /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                   4530:               /*        ij++; */
                   4531:               /* } */
                   4532:               /* else */
1.126     brouard  4533:                 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   4534:             }
                   4535:             fprintf(ficgp,")/(1");
                   4536:             
                   4537:             for(k1=1; k1 <=nlstate; k1++){   
                   4538:               fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   4539:               ij=1;
                   4540:               for(j=3; j <=ncovmodel; j++){
1.145     brouard  4541:                 /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                   4542:                 /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                   4543:                 /*   ij++; */
                   4544:                 /* } */
                   4545:                 /* else */
1.126     brouard  4546:                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   4547:               }
                   4548:               fprintf(ficgp,")");
                   4549:             }
                   4550:             fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                   4551:             if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                   4552:             i=i+ncovmodel;
                   4553:           }
                   4554:         } /* end k */
                   4555:        } /* end k2 */
                   4556:      } /* end jk */
                   4557:    } /* end ng */
1.164     brouard  4558:  /* avoid: */
1.126     brouard  4559:    fflush(ficgp); 
                   4560: }  /* end gnuplot */
                   4561: 
                   4562: 
                   4563: /*************** Moving average **************/
                   4564: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
                   4565: 
                   4566:   int i, cpt, cptcod;
                   4567:   int modcovmax =1;
                   4568:   int mobilavrange, mob;
                   4569:   double age;
                   4570: 
                   4571:   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                   4572:                           a covariate has 2 modalities */
                   4573:   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
                   4574: 
                   4575:   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
                   4576:     if(mobilav==1) mobilavrange=5; /* default */
                   4577:     else mobilavrange=mobilav;
                   4578:     for (age=bage; age<=fage; age++)
                   4579:       for (i=1; i<=nlstate;i++)
                   4580:        for (cptcod=1;cptcod<=modcovmax;cptcod++)
                   4581:          mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   4582:     /* We keep the original values on the extreme ages bage, fage and for 
                   4583:        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
                   4584:        we use a 5 terms etc. until the borders are no more concerned. 
                   4585:     */ 
                   4586:     for (mob=3;mob <=mobilavrange;mob=mob+2){
                   4587:       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                   4588:        for (i=1; i<=nlstate;i++){
                   4589:          for (cptcod=1;cptcod<=modcovmax;cptcod++){
                   4590:            mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                   4591:              for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   4592:                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   4593:                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                   4594:              }
                   4595:            mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                   4596:          }
                   4597:        }
                   4598:       }/* end age */
                   4599:     }/* end mob */
                   4600:   }else return -1;
                   4601:   return 0;
                   4602: }/* End movingaverage */
                   4603: 
                   4604: 
                   4605: /************** Forecasting ******************/
1.169     brouard  4606: 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  4607:   /* proj1, year, month, day of starting projection 
                   4608:      agemin, agemax range of age
                   4609:      dateprev1 dateprev2 range of dates during which prevalence is computed
                   4610:      anproj2 year of en of projection (same day and month as proj1).
                   4611:   */
1.164     brouard  4612:   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126     brouard  4613:   double agec; /* generic age */
                   4614:   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
                   4615:   double *popeffectif,*popcount;
                   4616:   double ***p3mat;
                   4617:   double ***mobaverage;
                   4618:   char fileresf[FILENAMELENGTH];
                   4619: 
                   4620:   agelim=AGESUP;
                   4621:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
                   4622:  
                   4623:   strcpy(fileresf,"f"); 
                   4624:   strcat(fileresf,fileres);
                   4625:   if((ficresf=fopen(fileresf,"w"))==NULL) {
                   4626:     printf("Problem with forecast resultfile: %s\n", fileresf);
                   4627:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
                   4628:   }
                   4629:   printf("Computing forecasting: result on file '%s' \n", fileresf);
                   4630:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
                   4631: 
                   4632:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   4633: 
                   4634:   if (mobilav!=0) {
                   4635:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4636:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   4637:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   4638:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   4639:     }
                   4640:   }
                   4641: 
                   4642:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   4643:   if (stepm<=12) stepsize=1;
                   4644:   if(estepm < stepm){
                   4645:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   4646:   }
                   4647:   else  hstepm=estepm;   
                   4648: 
                   4649:   hstepm=hstepm/stepm; 
                   4650:   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                   4651:                                fractional in yp1 */
                   4652:   anprojmean=yp;
                   4653:   yp2=modf((yp1*12),&yp);
                   4654:   mprojmean=yp;
                   4655:   yp1=modf((yp2*30.5),&yp);
                   4656:   jprojmean=yp;
                   4657:   if(jprojmean==0) jprojmean=1;
                   4658:   if(mprojmean==0) jprojmean=1;
                   4659: 
                   4660:   i1=cptcoveff;
                   4661:   if (cptcovn < 1){i1=1;}
                   4662:   
                   4663:   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
                   4664:   
                   4665:   fprintf(ficresf,"#****** Routine prevforecast **\n");
                   4666: 
                   4667: /*           if (h==(int)(YEARM*yearp)){ */
                   4668:   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
                   4669:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   4670:       k=k+1;
                   4671:       fprintf(ficresf,"\n#******");
                   4672:       for(j=1;j<=cptcoveff;j++) {
                   4673:        fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4674:       }
                   4675:       fprintf(ficresf,"******\n");
                   4676:       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
                   4677:       for(j=1; j<=nlstate+ndeath;j++){ 
                   4678:        for(i=1; i<=nlstate;i++)              
                   4679:           fprintf(ficresf," p%d%d",i,j);
                   4680:        fprintf(ficresf," p.%d",j);
                   4681:       }
                   4682:       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
                   4683:        fprintf(ficresf,"\n");
                   4684:        fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
                   4685: 
                   4686:        for (agec=fage; agec>=(ageminpar-1); agec--){ 
                   4687:          nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                   4688:          nhstepm = nhstepm/hstepm; 
                   4689:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4690:          oldm=oldms;savm=savms;
                   4691:          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   4692:        
                   4693:          for (h=0; h<=nhstepm; h++){
                   4694:            if (h*hstepm/YEARM*stepm ==yearp) {
                   4695:               fprintf(ficresf,"\n");
                   4696:               for(j=1;j<=cptcoveff;j++) 
                   4697:                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4698:              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                   4699:            } 
                   4700:            for(j=1; j<=nlstate+ndeath;j++) {
                   4701:              ppij=0.;
                   4702:              for(i=1; i<=nlstate;i++) {
                   4703:                if (mobilav==1) 
                   4704:                  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   4705:                else {
                   4706:                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   4707:                }
                   4708:                if (h*hstepm/YEARM*stepm== yearp) {
                   4709:                  fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   4710:                }
                   4711:              } /* end i */
                   4712:              if (h*hstepm/YEARM*stepm==yearp) {
                   4713:                fprintf(ficresf," %.3f", ppij);
                   4714:              }
                   4715:            }/* end j */
                   4716:          } /* end h */
                   4717:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4718:        } /* end agec */
                   4719:       } /* end yearp */
                   4720:     } /* end cptcod */
                   4721:   } /* end  cptcov */
                   4722:        
                   4723:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4724: 
                   4725:   fclose(ficresf);
                   4726: }
                   4727: 
                   4728: /************** Forecasting *****not tested NB*************/
1.169     brouard  4729: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
1.126     brouard  4730:   
                   4731:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
                   4732:   int *popage;
                   4733:   double calagedatem, agelim, kk1, kk2;
                   4734:   double *popeffectif,*popcount;
                   4735:   double ***p3mat,***tabpop,***tabpopprev;
                   4736:   double ***mobaverage;
                   4737:   char filerespop[FILENAMELENGTH];
                   4738: 
                   4739:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4740:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4741:   agelim=AGESUP;
                   4742:   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
                   4743:   
                   4744:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
                   4745:   
                   4746:   
                   4747:   strcpy(filerespop,"pop"); 
                   4748:   strcat(filerespop,fileres);
                   4749:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
                   4750:     printf("Problem with forecast resultfile: %s\n", filerespop);
                   4751:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
                   4752:   }
                   4753:   printf("Computing forecasting: result on file '%s' \n", filerespop);
                   4754:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
                   4755: 
                   4756:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   4757: 
                   4758:   if (mobilav!=0) {
                   4759:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4760:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   4761:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   4762:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   4763:     }
                   4764:   }
                   4765: 
                   4766:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   4767:   if (stepm<=12) stepsize=1;
                   4768:   
                   4769:   agelim=AGESUP;
                   4770:   
                   4771:   hstepm=1;
                   4772:   hstepm=hstepm/stepm; 
                   4773:   
                   4774:   if (popforecast==1) {
                   4775:     if((ficpop=fopen(popfile,"r"))==NULL) {
                   4776:       printf("Problem with population file : %s\n",popfile);exit(0);
                   4777:       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
                   4778:     } 
                   4779:     popage=ivector(0,AGESUP);
                   4780:     popeffectif=vector(0,AGESUP);
                   4781:     popcount=vector(0,AGESUP);
                   4782:     
                   4783:     i=1;   
                   4784:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
                   4785:    
                   4786:     imx=i;
                   4787:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
                   4788:   }
                   4789: 
                   4790:   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
                   4791:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   4792:       k=k+1;
                   4793:       fprintf(ficrespop,"\n#******");
                   4794:       for(j=1;j<=cptcoveff;j++) {
                   4795:        fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4796:       }
                   4797:       fprintf(ficrespop,"******\n");
                   4798:       fprintf(ficrespop,"# Age");
                   4799:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
                   4800:       if (popforecast==1)  fprintf(ficrespop," [Population]");
                   4801:       
                   4802:       for (cpt=0; cpt<=0;cpt++) { 
                   4803:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                   4804:        
                   4805:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
                   4806:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   4807:          nhstepm = nhstepm/hstepm; 
                   4808:          
                   4809:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4810:          oldm=oldms;savm=savms;
                   4811:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   4812:        
                   4813:          for (h=0; h<=nhstepm; h++){
                   4814:            if (h==(int) (calagedatem+YEARM*cpt)) {
                   4815:              fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   4816:            } 
                   4817:            for(j=1; j<=nlstate+ndeath;j++) {
                   4818:              kk1=0.;kk2=0;
                   4819:              for(i=1; i<=nlstate;i++) {              
                   4820:                if (mobilav==1) 
                   4821:                  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   4822:                else {
                   4823:                  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   4824:                }
                   4825:              }
                   4826:              if (h==(int)(calagedatem+12*cpt)){
                   4827:                tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   4828:                  /*fprintf(ficrespop," %.3f", kk1);
                   4829:                    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                   4830:              }
                   4831:            }
                   4832:            for(i=1; i<=nlstate;i++){
                   4833:              kk1=0.;
                   4834:                for(j=1; j<=nlstate;j++){
                   4835:                  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   4836:                }
                   4837:                  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
                   4838:            }
                   4839: 
                   4840:            if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                   4841:              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
                   4842:          }
                   4843:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4844:        }
                   4845:       }
                   4846:  
                   4847:   /******/
                   4848: 
                   4849:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
                   4850:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                   4851:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
                   4852:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   4853:          nhstepm = nhstepm/hstepm; 
                   4854:          
                   4855:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4856:          oldm=oldms;savm=savms;
                   4857:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   4858:          for (h=0; h<=nhstepm; h++){
                   4859:            if (h==(int) (calagedatem+YEARM*cpt)) {
                   4860:              fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   4861:            } 
                   4862:            for(j=1; j<=nlstate+ndeath;j++) {
                   4863:              kk1=0.;kk2=0;
                   4864:              for(i=1; i<=nlstate;i++) {              
                   4865:                kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                   4866:              }
                   4867:              if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
                   4868:            }
                   4869:          }
                   4870:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4871:        }
                   4872:       }
                   4873:    } 
                   4874:   }
                   4875:  
                   4876:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4877: 
                   4878:   if (popforecast==1) {
                   4879:     free_ivector(popage,0,AGESUP);
                   4880:     free_vector(popeffectif,0,AGESUP);
                   4881:     free_vector(popcount,0,AGESUP);
                   4882:   }
                   4883:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4884:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   4885:   fclose(ficrespop);
                   4886: } /* End of popforecast */
                   4887: 
                   4888: int fileappend(FILE *fichier, char *optionfich)
                   4889: {
                   4890:   if((fichier=fopen(optionfich,"a"))==NULL) {
                   4891:     printf("Problem with file: %s\n", optionfich);
                   4892:     fprintf(ficlog,"Problem with file: %s\n", optionfich);
                   4893:     return (0);
                   4894:   }
                   4895:   fflush(fichier);
                   4896:   return (1);
                   4897: }
                   4898: 
                   4899: 
                   4900: /**************** function prwizard **********************/
                   4901: void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
                   4902: {
                   4903: 
                   4904:   /* Wizard to print covariance matrix template */
                   4905: 
1.164     brouard  4906:   char ca[32], cb[32];
                   4907:   int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126     brouard  4908:   int numlinepar;
                   4909: 
                   4910:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4911:   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4912:   for(i=1; i <=nlstate; i++){
                   4913:     jj=0;
                   4914:     for(j=1; j <=nlstate+ndeath; j++){
                   4915:       if(j==i) continue;
                   4916:       jj++;
                   4917:       /*ca[0]= k+'a'-1;ca[1]='\0';*/
                   4918:       printf("%1d%1d",i,j);
                   4919:       fprintf(ficparo,"%1d%1d",i,j);
                   4920:       for(k=1; k<=ncovmodel;k++){
                   4921:        /*        printf(" %lf",param[i][j][k]); */
                   4922:        /*        fprintf(ficparo," %lf",param[i][j][k]); */
                   4923:        printf(" 0.");
                   4924:        fprintf(ficparo," 0.");
                   4925:       }
                   4926:       printf("\n");
                   4927:       fprintf(ficparo,"\n");
                   4928:     }
                   4929:   }
                   4930:   printf("# Scales (for hessian or gradient estimation)\n");
                   4931:   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
                   4932:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
                   4933:   for(i=1; i <=nlstate; i++){
                   4934:     jj=0;
                   4935:     for(j=1; j <=nlstate+ndeath; j++){
                   4936:       if(j==i) continue;
                   4937:       jj++;
                   4938:       fprintf(ficparo,"%1d%1d",i,j);
                   4939:       printf("%1d%1d",i,j);
                   4940:       fflush(stdout);
                   4941:       for(k=1; k<=ncovmodel;k++){
                   4942:        /*      printf(" %le",delti3[i][j][k]); */
                   4943:        /*      fprintf(ficparo," %le",delti3[i][j][k]); */
                   4944:        printf(" 0.");
                   4945:        fprintf(ficparo," 0.");
                   4946:       }
                   4947:       numlinepar++;
                   4948:       printf("\n");
                   4949:       fprintf(ficparo,"\n");
                   4950:     }
                   4951:   }
                   4952:   printf("# Covariance matrix\n");
                   4953: /* # 121 Var(a12)\n\ */
                   4954: /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   4955: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   4956: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   4957: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   4958: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   4959: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   4960: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   4961:   fflush(stdout);
                   4962:   fprintf(ficparo,"# Covariance matrix\n");
                   4963:   /* # 121 Var(a12)\n\ */
                   4964:   /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   4965:   /* #   ...\n\ */
                   4966:   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
                   4967:   
                   4968:   for(itimes=1;itimes<=2;itimes++){
                   4969:     jj=0;
                   4970:     for(i=1; i <=nlstate; i++){
                   4971:       for(j=1; j <=nlstate+ndeath; j++){
                   4972:        if(j==i) continue;
                   4973:        for(k=1; k<=ncovmodel;k++){
                   4974:          jj++;
                   4975:          ca[0]= k+'a'-1;ca[1]='\0';
                   4976:          if(itimes==1){
                   4977:            printf("#%1d%1d%d",i,j,k);
                   4978:            fprintf(ficparo,"#%1d%1d%d",i,j,k);
                   4979:          }else{
                   4980:            printf("%1d%1d%d",i,j,k);
                   4981:            fprintf(ficparo,"%1d%1d%d",i,j,k);
                   4982:            /*  printf(" %.5le",matcov[i][j]); */
                   4983:          }
                   4984:          ll=0;
                   4985:          for(li=1;li <=nlstate; li++){
                   4986:            for(lj=1;lj <=nlstate+ndeath; lj++){
                   4987:              if(lj==li) continue;
                   4988:              for(lk=1;lk<=ncovmodel;lk++){
                   4989:                ll++;
                   4990:                if(ll<=jj){
                   4991:                  cb[0]= lk +'a'-1;cb[1]='\0';
                   4992:                  if(ll<jj){
                   4993:                    if(itimes==1){
                   4994:                      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   4995:                      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   4996:                    }else{
                   4997:                      printf(" 0.");
                   4998:                      fprintf(ficparo," 0.");
                   4999:                    }
                   5000:                  }else{
                   5001:                    if(itimes==1){
                   5002:                      printf(" Var(%s%1d%1d)",ca,i,j);
                   5003:                      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                   5004:                    }else{
                   5005:                      printf(" 0.");
                   5006:                      fprintf(ficparo," 0.");
                   5007:                    }
                   5008:                  }
                   5009:                }
                   5010:              } /* end lk */
                   5011:            } /* end lj */
                   5012:          } /* end li */
                   5013:          printf("\n");
                   5014:          fprintf(ficparo,"\n");
                   5015:          numlinepar++;
                   5016:        } /* end k*/
                   5017:       } /*end j */
                   5018:     } /* end i */
                   5019:   } /* end itimes */
                   5020: 
                   5021: } /* end of prwizard */
                   5022: /******************* Gompertz Likelihood ******************************/
                   5023: double gompertz(double x[])
                   5024: { 
                   5025:   double A,B,L=0.0,sump=0.,num=0.;
                   5026:   int i,n=0; /* n is the size of the sample */
                   5027: 
                   5028:   for (i=0;i<=imx-1 ; i++) {
                   5029:     sump=sump+weight[i];
                   5030:     /*    sump=sump+1;*/
                   5031:     num=num+1;
                   5032:   }
                   5033:  
                   5034:  
                   5035:   /* for (i=0; i<=imx; i++) 
                   5036:      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]);*/
                   5037: 
                   5038:   for (i=1;i<=imx ; i++)
                   5039:     {
                   5040:       if (cens[i] == 1 && wav[i]>1)
                   5041:        A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
                   5042:       
                   5043:       if (cens[i] == 0 && wav[i]>1)
                   5044:        A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                   5045:             +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
                   5046:       
                   5047:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
                   5048:       if (wav[i] > 1 ) { /* ??? */
                   5049:        L=L+A*weight[i];
                   5050:        /*      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]);*/
                   5051:       }
                   5052:     }
                   5053: 
                   5054:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
                   5055:  
                   5056:   return -2*L*num/sump;
                   5057: }
                   5058: 
1.136     brouard  5059: #ifdef GSL
                   5060: /******************* Gompertz_f Likelihood ******************************/
                   5061: double gompertz_f(const gsl_vector *v, void *params)
                   5062: { 
                   5063:   double A,B,LL=0.0,sump=0.,num=0.;
                   5064:   double *x= (double *) v->data;
                   5065:   int i,n=0; /* n is the size of the sample */
                   5066: 
                   5067:   for (i=0;i<=imx-1 ; i++) {
                   5068:     sump=sump+weight[i];
                   5069:     /*    sump=sump+1;*/
                   5070:     num=num+1;
                   5071:   }
                   5072:  
                   5073:  
                   5074:   /* for (i=0; i<=imx; i++) 
                   5075:      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]);*/
                   5076:   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
                   5077:   for (i=1;i<=imx ; i++)
                   5078:     {
                   5079:       if (cens[i] == 1 && wav[i]>1)
                   5080:        A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
                   5081:       
                   5082:       if (cens[i] == 0 && wav[i]>1)
                   5083:        A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                   5084:             +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
                   5085:       
                   5086:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
                   5087:       if (wav[i] > 1 ) { /* ??? */
                   5088:        LL=LL+A*weight[i];
                   5089:        /*      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]);*/
                   5090:       }
                   5091:     }
                   5092: 
                   5093:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
                   5094:   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
                   5095:  
                   5096:   return -2*LL*num/sump;
                   5097: }
                   5098: #endif
                   5099: 
1.126     brouard  5100: /******************* Printing html file ***********/
                   5101: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                   5102:                  int lastpass, int stepm, int weightopt, char model[],\
                   5103:                  int imx,  double p[],double **matcov,double agemortsup){
                   5104:   int i,k;
                   5105: 
                   5106:   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
                   5107:   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
                   5108:   for (i=1;i<=2;i++) 
                   5109:     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]));
                   5110:   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
                   5111:   fprintf(fichtm,"</ul>");
                   5112: 
                   5113: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
                   5114: 
                   5115:  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>");
                   5116: 
                   5117:  for (k=agegomp;k<(agemortsup-2);k++) 
                   5118:    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]);
                   5119: 
                   5120:  
                   5121:   fflush(fichtm);
                   5122: }
                   5123: 
                   5124: /******************* Gnuplot file **************/
                   5125: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
                   5126: 
                   5127:   char dirfileres[132],optfileres[132];
1.164     brouard  5128: 
1.126     brouard  5129:   int ng;
                   5130: 
                   5131: 
                   5132:   /*#ifdef windows */
                   5133:   fprintf(ficgp,"cd \"%s\" \n",pathc);
                   5134:     /*#endif */
                   5135: 
                   5136: 
                   5137:   strcpy(dirfileres,optionfilefiname);
                   5138:   strcpy(optfileres,"vpl");
                   5139:   fprintf(ficgp,"set out \"graphmort.png\"\n "); 
                   5140:   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
1.145     brouard  5141:   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
                   5142:   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126     brouard  5143:   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
                   5144: 
                   5145: } 
                   5146: 
1.136     brouard  5147: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
                   5148: {
1.126     brouard  5149: 
1.136     brouard  5150:   /*-------- data file ----------*/
                   5151:   FILE *fic;
                   5152:   char dummy[]="                         ";
1.164     brouard  5153:   int i=0, j=0, n=0;
1.136     brouard  5154:   int linei, month, year,iout;
                   5155:   char line[MAXLINE], linetmp[MAXLINE];
1.164     brouard  5156:   char stra[MAXLINE], strb[MAXLINE];
1.136     brouard  5157:   char *stratrunc;
                   5158:   int lstra;
1.126     brouard  5159: 
                   5160: 
1.136     brouard  5161:   if((fic=fopen(datafile,"r"))==NULL)    {
                   5162:     printf("Problem while opening datafile: %s\n", datafile);return 1;
                   5163:     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
                   5164:   }
1.126     brouard  5165: 
1.136     brouard  5166:   i=1;
                   5167:   linei=0;
                   5168:   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
                   5169:     linei=linei+1;
                   5170:     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
                   5171:       if(line[j] == '\t')
                   5172:        line[j] = ' ';
                   5173:     }
                   5174:     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
                   5175:       ;
                   5176:     };
                   5177:     line[j+1]=0;  /* Trims blanks at end of line */
                   5178:     if(line[0]=='#'){
                   5179:       fprintf(ficlog,"Comment line\n%s\n",line);
                   5180:       printf("Comment line\n%s\n",line);
                   5181:       continue;
                   5182:     }
                   5183:     trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164     brouard  5184:     strcpy(line, linetmp);
1.136     brouard  5185:   
1.126     brouard  5186: 
1.136     brouard  5187:     for (j=maxwav;j>=1;j--){
1.137     brouard  5188:       cutv(stra, strb, line, ' '); 
1.136     brouard  5189:       if(strb[0]=='.') { /* Missing status */
                   5190:        lval=-1;
                   5191:       }else{
                   5192:        errno=0;
                   5193:        lval=strtol(strb,&endptr,10); 
                   5194:       /*       if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                   5195:        if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  5196:          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);
                   5197:          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);
1.136     brouard  5198:          return 1;
                   5199:        }
                   5200:       }
                   5201:       s[j][i]=lval;
                   5202:       
                   5203:       strcpy(line,stra);
                   5204:       cutv(stra, strb,line,' ');
1.169     brouard  5205:       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  5206:       }
1.169     brouard  5207:       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136     brouard  5208:        month=99;
                   5209:        year=9999;
                   5210:       }else{
1.141     brouard  5211:        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);
                   5212:        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);
1.136     brouard  5213:        return 1;
                   5214:       }
                   5215:       anint[j][i]= (double) year; 
                   5216:       mint[j][i]= (double)month; 
                   5217:       strcpy(line,stra);
                   5218:     } /* ENd Waves */
                   5219:     
                   5220:     cutv(stra, strb,line,' '); 
1.169     brouard  5221:     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  5222:     }
1.169     brouard  5223:     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136     brouard  5224:       month=99;
                   5225:       year=9999;
                   5226:     }else{
1.141     brouard  5227:       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);
                   5228:        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);
1.136     brouard  5229:        return 1;
                   5230:     }
                   5231:     andc[i]=(double) year; 
                   5232:     moisdc[i]=(double) month; 
                   5233:     strcpy(line,stra);
                   5234:     
                   5235:     cutv(stra, strb,line,' '); 
1.169     brouard  5236:     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136     brouard  5237:     }
1.169     brouard  5238:     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136     brouard  5239:       month=99;
                   5240:       year=9999;
                   5241:     }else{
1.141     brouard  5242:       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);
                   5243:       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);
1.136     brouard  5244:        return 1;
                   5245:     }
                   5246:     if (year==9999) {
1.141     brouard  5247:       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);
                   5248:       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);
1.136     brouard  5249:        return 1;
1.126     brouard  5250: 
1.136     brouard  5251:     }
                   5252:     annais[i]=(double)(year);
                   5253:     moisnais[i]=(double)(month); 
                   5254:     strcpy(line,stra);
                   5255:     
                   5256:     cutv(stra, strb,line,' '); 
                   5257:     errno=0;
                   5258:     dval=strtod(strb,&endptr); 
                   5259:     if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  5260:       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
                   5261:       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  5262:       fflush(ficlog);
                   5263:       return 1;
                   5264:     }
                   5265:     weight[i]=dval; 
                   5266:     strcpy(line,stra);
                   5267:     
                   5268:     for (j=ncovcol;j>=1;j--){
                   5269:       cutv(stra, strb,line,' '); 
                   5270:       if(strb[0]=='.') { /* Missing status */
                   5271:        lval=-1;
                   5272:       }else{
                   5273:        errno=0;
                   5274:        lval=strtol(strb,&endptr,10); 
                   5275:        if( strb[0]=='\0' || (*endptr != '\0')){
1.141     brouard  5276:          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);
                   5277:          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);
1.136     brouard  5278:          return 1;
                   5279:        }
                   5280:       }
                   5281:       if(lval <-1 || lval >1){
1.141     brouard  5282:        printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  5283:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   5284:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
                   5285:  For example, for multinomial values like 1, 2 and 3,\n \
                   5286:  build V1=0 V2=0 for the reference value (1),\n \
                   5287:         V1=1 V2=0 for (2) \n \
                   5288:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
                   5289:  output of IMaCh is often meaningless.\n \
                   5290:  Exiting.\n",lval,linei, i,line,j);
1.141     brouard  5291:        fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136     brouard  5292:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
                   5293:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
                   5294:  For example, for multinomial values like 1, 2 and 3,\n \
                   5295:  build V1=0 V2=0 for the reference value (1),\n \
                   5296:         V1=1 V2=0 for (2) \n \
                   5297:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
                   5298:  output of IMaCh is often meaningless.\n \
                   5299:  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
                   5300:        return 1;
                   5301:       }
                   5302:       covar[j][i]=(double)(lval);
                   5303:       strcpy(line,stra);
                   5304:     }  
                   5305:     lstra=strlen(stra);
                   5306:      
                   5307:     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
                   5308:       stratrunc = &(stra[lstra-9]);
                   5309:       num[i]=atol(stratrunc);
                   5310:     }
                   5311:     else
                   5312:       num[i]=atol(stra);
                   5313:     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
                   5314:       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;}*/
                   5315:     
                   5316:     i=i+1;
                   5317:   } /* End loop reading  data */
1.126     brouard  5318: 
1.136     brouard  5319:   *imax=i-1; /* Number of individuals */
                   5320:   fclose(fic);
                   5321:  
                   5322:   return (0);
1.164     brouard  5323:   /* endread: */
1.136     brouard  5324:     printf("Exiting readdata: ");
                   5325:     fclose(fic);
                   5326:     return (1);
1.126     brouard  5327: 
                   5328: 
                   5329: 
1.136     brouard  5330: }
1.145     brouard  5331: void removespace(char *str) {
                   5332:   char *p1 = str, *p2 = str;
                   5333:   do
                   5334:     while (*p2 == ' ')
                   5335:       p2++;
1.169     brouard  5336:   while (*p1++ == *p2++);
1.145     brouard  5337: }
                   5338: 
                   5339: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
                   5340:    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
                   5341:    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
                   5342:    * - cptcovn or number of covariates k of the models excluding age*products =6
                   5343:    * - cptcovage number of covariates with age*products =2
                   5344:    * - cptcovs number of simple covariates
                   5345:    * - 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
                   5346:    *     which is a new column after the 9 (ncovcol) variables. 
                   5347:    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
                   5348:    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
                   5349:    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
                   5350:    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
                   5351:  */
1.136     brouard  5352: {
1.145     brouard  5353:   int i, j, k, ks;
1.164     brouard  5354:   int  j1, k1, k2;
1.136     brouard  5355:   char modelsav[80];
1.145     brouard  5356:   char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136     brouard  5357: 
1.145     brouard  5358:   /*removespace(model);*/
1.136     brouard  5359:   if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145     brouard  5360:     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
                   5361:     j=nbocc(model,'+'); /**< j=Number of '+' */
                   5362:     j1=nbocc(model,'*'); /**< j1=Number of '*' */
                   5363:     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
                   5364:     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                   5365:                   /* including age products which are counted in cptcovage.
1.169     brouard  5366:                  * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
1.145     brouard  5367:     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
                   5368:     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
1.136     brouard  5369:     strcpy(modelsav,model); 
1.137     brouard  5370:     if (strstr(model,"AGE") !=0){
                   5371:       printf("Error. AGE must be in lower case 'age' model=%s ",model);
                   5372:       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136     brouard  5373:       return 1;
                   5374:     }
1.141     brouard  5375:     if (strstr(model,"v") !=0){
                   5376:       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
                   5377:       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
                   5378:       return 1;
                   5379:     }
1.136     brouard  5380:     
1.145     brouard  5381:     /*   Design
                   5382:      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
                   5383:      *  <          ncovcol=8                >
                   5384:      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
                   5385:      *   k=  1    2      3       4     5       6      7        8
                   5386:      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
                   5387:      *  covar[k,i], value of kth covariate if not including age for individual i:
                   5388:      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
                   5389:      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
                   5390:      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
                   5391:      *  Tage[++cptcovage]=k
                   5392:      *       if products, new covar are created after ncovcol with k1
                   5393:      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
                   5394:      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
                   5395:      *  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
                   5396:      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
                   5397:      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
                   5398:      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
                   5399:      *  <          ncovcol=8                >
                   5400:      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
                   5401:      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
                   5402:      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
                   5403:      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
                   5404:      * p Tprod[1]@2={                         6, 5}
                   5405:      *p Tvard[1][1]@4= {7, 8, 5, 6}
                   5406:      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
                   5407:      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   5408:      *How to reorganize?
                   5409:      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
                   5410:      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
                   5411:      *       {2,   1,     4,      8,    5,      6,     3,       7}
                   5412:      * Struct []
                   5413:      */
                   5414: 
1.136     brouard  5415:     /* This loop fills the array Tvar from the string 'model'.*/
                   5416:     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137     brouard  5417:     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
                   5418:     /*         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
                   5419:     /*         k=3 V4 Tvar[k=3]= 4 (from V4) */
                   5420:     /*         k=2 V1 Tvar[k=2]= 1 (from V1) */
                   5421:     /*         k=1 Tvar[1]=2 (from V2) */
                   5422:     /*         k=5 Tvar[5] */
                   5423:     /* for (k=1; k<=cptcovn;k++) { */
                   5424:     /*         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
                   5425:     /*         } */
                   5426:     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145     brouard  5427:     /*
                   5428:      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
                   5429:     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
                   5430:         Tvar[k]=0;
                   5431:     cptcovage=0;
                   5432:     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
                   5433:       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                   5434:                                     modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
1.137     brouard  5435:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136     brouard  5436:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
                   5437:       /*scanf("%d",i);*/
1.145     brouard  5438:       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
                   5439:        cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
                   5440:        if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
                   5441:          /* covar is not filled and then is empty */
1.136     brouard  5442:          cptcovprod--;
1.145     brouard  5443:          cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
                   5444:          Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136     brouard  5445:          cptcovage++; /* Sums the number of covariates which include age as a product */
1.137     brouard  5446:          Tage[cptcovage]=k;  /* Tage[1] = 4 */
1.136     brouard  5447:          /*printf("stre=%s ", stre);*/
1.137     brouard  5448:        } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136     brouard  5449:          cptcovprod--;
1.145     brouard  5450:          cutl(stre,strb,strc,'V');
1.136     brouard  5451:          Tvar[k]=atoi(stre);
                   5452:          cptcovage++;
                   5453:          Tage[cptcovage]=k;
1.137     brouard  5454:        } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
                   5455:          /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145     brouard  5456:          cptcovn++;
                   5457:          cptcovprodnoage++;k1++;
                   5458:          cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
                   5459:          Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137     brouard  5460:                                  because this model-covariate is a construction we invent a new column
                   5461:                                  ncovcol + k1
                   5462:                                  If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                   5463:                                  Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145     brouard  5464:          cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137     brouard  5465:          Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
1.145     brouard  5466:          Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
                   5467:          Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
                   5468:          k2=k2+2;
                   5469:          Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
                   5470:          Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137     brouard  5471:          for (i=1; i<=lastobs;i++){
                   5472:            /* Computes the new covariate which is a product of
1.145     brouard  5473:               covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136     brouard  5474:            covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137     brouard  5475:          }
                   5476:        } /* End age is not in the model */
                   5477:       } /* End if model includes a product */
1.136     brouard  5478:       else { /* no more sum */
                   5479:        /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
                   5480:        /*  scanf("%d",i);*/
1.145     brouard  5481:        cutl(strd,strc,strb,'V');
                   5482:        ks++; /**< Number of simple covariates */
                   5483:        cptcovn++;
                   5484:        Tvar[k]=atoi(strd);
1.136     brouard  5485:       }
1.137     brouard  5486:       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
1.136     brouard  5487:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                   5488:        scanf("%d",i);*/
                   5489:     } /* end of loop + */
                   5490:   } /* end model */
                   5491:   
                   5492:   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
                   5493:     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
                   5494: 
                   5495:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
                   5496:   printf("cptcovprod=%d ", cptcovprod);
                   5497:   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
                   5498: 
                   5499:   scanf("%d ",i);*/
                   5500: 
                   5501: 
1.137     brouard  5502:   return (0); /* with covar[new additional covariate if product] and Tage if age */ 
1.164     brouard  5503:   /*endread:*/
1.136     brouard  5504:     printf("Exiting decodemodel: ");
                   5505:     return (1);
                   5506: }
                   5507: 
1.169     brouard  5508: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136     brouard  5509: {
                   5510:   int i, m;
                   5511: 
                   5512:   for (i=1; i<=imx; i++) {
                   5513:     for(m=2; (m<= maxwav); m++) {
                   5514:       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
                   5515:        anint[m][i]=9999;
                   5516:        s[m][i]=-1;
                   5517:       }
                   5518:       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169     brouard  5519:        *nberr = *nberr + 1;
                   5520:        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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
                   5521:        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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
1.136     brouard  5522:        s[m][i]=-1;
                   5523:       }
                   5524:       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169     brouard  5525:        (*nberr)++;
1.136     brouard  5526:        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]); 
                   5527:        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]); 
                   5528:        s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
                   5529:       }
                   5530:     }
                   5531:   }
                   5532: 
                   5533:   for (i=1; i<=imx; i++)  {
                   5534:     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
                   5535:     for(m=firstpass; (m<= lastpass); m++){
                   5536:       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
                   5537:        if (s[m][i] >= nlstate+1) {
1.169     brouard  5538:          if(agedc[i]>0){
                   5539:            if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136     brouard  5540:              agev[m][i]=agedc[i];
                   5541:          /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169     brouard  5542:            }else {
1.136     brouard  5543:              if ((int)andc[i]!=9999){
                   5544:                nbwarn++;
                   5545:                printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   5546:                fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   5547:                agev[m][i]=-1;
                   5548:              }
                   5549:            }
1.169     brouard  5550:          } /* agedc > 0 */
1.136     brouard  5551:        }
                   5552:        else if(s[m][i] !=9){ /* Standard case, age in fractional
                   5553:                                 years but with the precision of a month */
                   5554:          agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
                   5555:          if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
                   5556:            agev[m][i]=1;
                   5557:          else if(agev[m][i] < *agemin){ 
                   5558:            *agemin=agev[m][i];
                   5559:            printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
                   5560:          }
                   5561:          else if(agev[m][i] >*agemax){
                   5562:            *agemax=agev[m][i];
1.156     brouard  5563:            /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136     brouard  5564:          }
                   5565:          /*agev[m][i]=anint[m][i]-annais[i];*/
                   5566:          /*     agev[m][i] = age[i]+2*m;*/
                   5567:        }
                   5568:        else { /* =9 */
                   5569:          agev[m][i]=1;
                   5570:          s[m][i]=-1;
                   5571:        }
                   5572:       }
                   5573:       else /*= 0 Unknown */
                   5574:        agev[m][i]=1;
                   5575:     }
                   5576:     
                   5577:   }
                   5578:   for (i=1; i<=imx; i++)  {
                   5579:     for(m=firstpass; (m<=lastpass); m++){
                   5580:       if (s[m][i] > (nlstate+ndeath)) {
1.169     brouard  5581:        (*nberr)++;
1.136     brouard  5582:        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);     
                   5583:        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);     
                   5584:        return 1;
                   5585:       }
                   5586:     }
                   5587:   }
                   5588: 
                   5589:   /*for (i=1; i<=imx; i++){
                   5590:   for (m=firstpass; (m<lastpass); m++){
                   5591:      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
                   5592: }
                   5593: 
                   5594: }*/
                   5595: 
                   5596: 
1.139     brouard  5597:   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
                   5598:   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
1.136     brouard  5599: 
                   5600:   return (0);
1.164     brouard  5601:  /* endread:*/
1.136     brouard  5602:     printf("Exiting calandcheckages: ");
                   5603:     return (1);
                   5604: }
                   5605: 
1.172     brouard  5606: #if defined(_MSC_VER)
                   5607: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
                   5608: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
                   5609: //#include "stdafx.h"
                   5610: //#include <stdio.h>
                   5611: //#include <tchar.h>
                   5612: //#include <windows.h>
                   5613: //#include <iostream>
                   5614: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
                   5615: 
                   5616: LPFN_ISWOW64PROCESS fnIsWow64Process;
                   5617: 
                   5618: BOOL IsWow64()
                   5619: {
                   5620:        BOOL bIsWow64 = FALSE;
                   5621: 
                   5622:        //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
                   5623:        //  (HANDLE, PBOOL);
                   5624: 
                   5625:        //LPFN_ISWOW64PROCESS fnIsWow64Process;
                   5626: 
                   5627:        HMODULE module = GetModuleHandle(_T("kernel32"));
                   5628:        const char funcName[] = "IsWow64Process";
                   5629:        fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   5630:                GetProcAddress(module, funcName);
                   5631: 
                   5632:        if (NULL != fnIsWow64Process)
                   5633:        {
                   5634:                if (!fnIsWow64Process(GetCurrentProcess(),
                   5635:                        &bIsWow64))
                   5636:                        //throw std::exception("Unknown error");
                   5637:                        printf("Unknown error\n");
                   5638:        }
                   5639:        return bIsWow64 != FALSE;
                   5640: }
                   5641: #endif
1.177     brouard  5642: 
1.169     brouard  5643: void syscompilerinfo()
1.167     brouard  5644:  {
                   5645:    /* #include "syscompilerinfo.h"*/
1.184   ! brouard  5646:        /* command line Intel compiler 64bit windows:
        !          5647:        /GS /W3 /Gy /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        !          5648:        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        !          5649:        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo 
        !          5650:        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
        !          5651:        /*
        !          5652:        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        !          5653:        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        !          5654:        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        !          5655:        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
1.177     brouard  5656: #if defined __INTEL_COMPILER
1.178     brouard  5657: #if defined(__GNUC__)
                   5658:        struct utsname sysInfo;  /* For Intel on Linux and OS/X */
                   5659: #endif
1.177     brouard  5660: #elif defined(__GNUC__) 
1.179     brouard  5661: #ifndef  __APPLE__
1.174     brouard  5662: #include <gnu/libc-version.h>  /* Only on gnu */
1.179     brouard  5663: #endif
1.177     brouard  5664:    struct utsname sysInfo;
1.178     brouard  5665:    int cross = CROSS;
                   5666:    if (cross){
                   5667:           printf("Cross-");
                   5668:           fprintf(ficlog, "Cross-");
                   5669:    }
1.174     brouard  5670: #endif
                   5671: 
1.171     brouard  5672: #include <stdint.h>
1.178     brouard  5673: 
1.169     brouard  5674:    printf("Compiled with:");fprintf(ficlog,"Compiled with:");
                   5675: #if defined(__clang__)
                   5676:    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM");        /* Clang/LLVM. ---------------------------------------------- */
                   5677: #endif
                   5678: #if defined(__ICC) || defined(__INTEL_COMPILER)
                   5679:    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
                   5680: #endif
                   5681: #if defined(__GNUC__) || defined(__GNUG__)
                   5682:    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
                   5683: #endif
                   5684: #if defined(__HP_cc) || defined(__HP_aCC)
                   5685:    printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
                   5686: #endif
                   5687: #if defined(__IBMC__) || defined(__IBMCPP__)
                   5688:    printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
                   5689: #endif
                   5690: #if defined(_MSC_VER)
                   5691:    printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
                   5692: #endif
                   5693: #if defined(__PGI)
                   5694:    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
                   5695: #endif
                   5696: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
                   5697:    printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167     brouard  5698: #endif
1.174     brouard  5699:    printf(" for ");fprintf(ficlog," for ");
1.169     brouard  5700:    
1.167     brouard  5701: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
                   5702: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
                   5703:     // Windows (x64 and x86)
1.174     brouard  5704:    printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
1.167     brouard  5705: #elif __unix__ // all unices, not all compilers
                   5706:     // Unix
1.174     brouard  5707:    printf("Unix ");fprintf(ficlog,"Unix ");
1.167     brouard  5708: #elif __linux__
                   5709:     // linux
1.174     brouard  5710:    printf("linux ");fprintf(ficlog,"linux ");
1.167     brouard  5711: #elif __APPLE__
1.174     brouard  5712:     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
                   5713:    printf("Mac OS ");fprintf(ficlog,"Mac OS ");
1.167     brouard  5714: #endif
                   5715: 
                   5716: /*  __MINGW32__          */
                   5717: /*  __CYGWIN__  */
                   5718: /* __MINGW64__  */
                   5719: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
                   5720: /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
                   5721: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
                   5722: /* _WIN64  // Defined for applications for Win64. */
                   5723: /* _M_X64 // Defined for compilations that target x64 processors. */
                   5724: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171     brouard  5725: 
1.167     brouard  5726: #if UINTPTR_MAX == 0xffffffff
1.174     brouard  5727:    printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
1.167     brouard  5728: #elif UINTPTR_MAX == 0xffffffffffffffff
1.174     brouard  5729:    printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
1.167     brouard  5730: #else
1.174     brouard  5731:    printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
1.167     brouard  5732: #endif
                   5733: 
1.169     brouard  5734: #if defined(__GNUC__)
                   5735: # if defined(__GNUC_PATCHLEVEL__)
                   5736: #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                   5737:                             + __GNUC_MINOR__ * 100 \
                   5738:                             + __GNUC_PATCHLEVEL__)
                   5739: # else
                   5740: #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                   5741:                             + __GNUC_MINOR__ * 100)
                   5742: # endif
1.174     brouard  5743:    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
                   5744:    fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176     brouard  5745: 
                   5746:    if (uname(&sysInfo) != -1) {
                   5747:      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
                   5748:      fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
                   5749:    }
                   5750:    else
                   5751:       perror("uname() error");
1.179     brouard  5752:    //#ifndef __INTEL_COMPILER 
                   5753: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174     brouard  5754:    printf("GNU libc version: %s\n", gnu_get_libc_version()); 
1.179     brouard  5755:    fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177     brouard  5756: #endif
1.169     brouard  5757: #endif
1.172     brouard  5758: 
                   5759:    //   void main()
                   5760:    //   {
1.169     brouard  5761: #if defined(_MSC_VER)
1.174     brouard  5762:    if (IsWow64()){
1.176     brouard  5763:           printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
                   5764:           fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174     brouard  5765:    }
                   5766:    else{
1.176     brouard  5767:           printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.178     brouard  5768:           fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174     brouard  5769:    }
1.172     brouard  5770:    //     printf("\nPress Enter to continue...");
                   5771:    //     getchar();
                   5772:    //   }
                   5773: 
1.169     brouard  5774: #endif
                   5775:    
1.167     brouard  5776: 
                   5777:  }
1.136     brouard  5778: 
1.180     brouard  5779: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
                   5780:   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
                   5781:   int i, j, k, i1 ;
                   5782:   double ftolpl = 1.e-10;
                   5783:   double age, agebase, agelim;
                   5784: 
                   5785:     strcpy(filerespl,"pl");
                   5786:     strcat(filerespl,fileres);
                   5787:     if((ficrespl=fopen(filerespl,"w"))==NULL) {
                   5788:       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
                   5789:       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
                   5790:     }
                   5791:     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
                   5792:     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
                   5793:     pstamp(ficrespl);
                   5794:     fprintf(ficrespl,"# Period (stable) prevalence \n");
                   5795:     fprintf(ficrespl,"#Age ");
                   5796:     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
                   5797:     fprintf(ficrespl,"\n");
                   5798:   
                   5799:     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
                   5800: 
                   5801:     agebase=ageminpar;
                   5802:     agelim=agemaxpar;
                   5803: 
                   5804:     i1=pow(2,cptcoveff);
                   5805:     if (cptcovn < 1){i1=1;}
                   5806: 
                   5807:     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   5808:     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
                   5809:       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   5810:        k=k+1;
                   5811:        /* to clean */
                   5812:        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
                   5813:        fprintf(ficrespl,"\n#******");
                   5814:        printf("\n#******");
                   5815:        fprintf(ficlog,"\n#******");
                   5816:        for(j=1;j<=cptcoveff;j++) {
                   5817:          fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5818:          printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5819:          fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5820:        }
                   5821:        fprintf(ficrespl,"******\n");
                   5822:        printf("******\n");
                   5823:        fprintf(ficlog,"******\n");
                   5824: 
                   5825:        fprintf(ficrespl,"#Age ");
                   5826:        for(j=1;j<=cptcoveff;j++) {
                   5827:          fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5828:        }
                   5829:        for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
                   5830:        fprintf(ficrespl,"\n");
                   5831:        
                   5832:        for (age=agebase; age<=agelim; age++){
                   5833:        /* for (age=agebase; age<=agebase; age++){ */
                   5834:          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
                   5835:          fprintf(ficrespl,"%.0f ",age );
                   5836:          for(j=1;j<=cptcoveff;j++)
                   5837:            fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5838:          for(i=1; i<=nlstate;i++)
                   5839:            fprintf(ficrespl," %.5f", prlim[i][i]);
                   5840:          fprintf(ficrespl,"\n");
                   5841:        } /* Age */
                   5842:        /* was end of cptcod */
                   5843:     } /* cptcov */
1.184   ! brouard  5844:        return 0;
1.180     brouard  5845: }
                   5846: 
                   5847: int hPijx(double *p, int bage, int fage){
                   5848:     /*------------- h Pij x at various ages ------------*/
                   5849: 
                   5850:   int stepsize;
                   5851:   int agelim;
                   5852:   int hstepm;
                   5853:   int nhstepm;
                   5854:   int h, i, i1, j, k;
                   5855: 
                   5856:   double agedeb;
                   5857:   double ***p3mat;
                   5858: 
                   5859:     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
                   5860:     if((ficrespij=fopen(filerespij,"w"))==NULL) {
                   5861:       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
                   5862:       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
                   5863:     }
                   5864:     printf("Computing pij: result on file '%s' \n", filerespij);
                   5865:     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
                   5866:   
                   5867:     stepsize=(int) (stepm+YEARM-1)/YEARM;
                   5868:     /*if (stepm<=24) stepsize=2;*/
                   5869: 
                   5870:     agelim=AGESUP;
                   5871:     hstepm=stepsize*YEARM; /* Every year of age */
                   5872:     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                   5873: 
                   5874:     /* hstepm=1;   aff par mois*/
                   5875:     pstamp(ficrespij);
                   5876:     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
                   5877:     i1= pow(2,cptcoveff);
1.183     brouard  5878:    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                   5879:    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                   5880:    /*          k=k+1;  */
                   5881:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
                   5882:       fprintf(ficrespij,"\n#****** ");
                   5883:       for(j=1;j<=cptcoveff;j++) 
                   5884:        fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5885:       fprintf(ficrespij,"******\n");
                   5886:       
                   5887:       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
                   5888:        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   5889:        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   5890:        
                   5891:        /*        nhstepm=nhstepm*YEARM; aff par mois*/
1.180     brouard  5892:        
1.183     brouard  5893:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5894:        oldm=oldms;savm=savms;
                   5895:        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   5896:        fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
                   5897:        for(i=1; i<=nlstate;i++)
                   5898:          for(j=1; j<=nlstate+ndeath;j++)
                   5899:            fprintf(ficrespij," %1d-%1d",i,j);
                   5900:        fprintf(ficrespij,"\n");
                   5901:        for (h=0; h<=nhstepm; h++){
                   5902:          /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
                   5903:          fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180     brouard  5904:          for(i=1; i<=nlstate;i++)
                   5905:            for(j=1; j<=nlstate+ndeath;j++)
1.183     brouard  5906:              fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180     brouard  5907:          fprintf(ficrespij,"\n");
                   5908:        }
1.183     brouard  5909:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   5910:        fprintf(ficrespij,"\n");
                   5911:       }
1.180     brouard  5912:       /*}*/
                   5913:     }
1.184   ! brouard  5914:        return 0;
1.180     brouard  5915: }
                   5916: 
                   5917: 
1.136     brouard  5918: /***********************************************/
                   5919: /**************** Main Program *****************/
                   5920: /***********************************************/
                   5921: 
                   5922: int main(int argc, char *argv[])
                   5923: {
                   5924: #ifdef GSL
                   5925:   const gsl_multimin_fminimizer_type *T;
                   5926:   size_t iteri = 0, it;
                   5927:   int rval = GSL_CONTINUE;
                   5928:   int status = GSL_SUCCESS;
                   5929:   double ssval;
                   5930: #endif
                   5931:   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164     brouard  5932:   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
                   5933: 
                   5934:   int jj, ll, li, lj, lk;
1.136     brouard  5935:   int numlinepar=0; /* Current linenumber of parameter file */
                   5936:   int itimes;
                   5937:   int NDIM=2;
                   5938:   int vpopbased=0;
                   5939: 
1.164     brouard  5940:   char ca[32], cb[32];
1.136     brouard  5941:   /*  FILE *fichtm; *//* Html File */
                   5942:   /* FILE *ficgp;*/ /*Gnuplot File */
                   5943:   struct stat info;
1.164     brouard  5944:   double agedeb;
1.136     brouard  5945:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
                   5946: 
1.165     brouard  5947:   double fret;
1.136     brouard  5948:   double dum; /* Dummy variable */
                   5949:   double ***p3mat;
                   5950:   double ***mobaverage;
1.164     brouard  5951: 
                   5952:   char line[MAXLINE];
1.136     brouard  5953:   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
                   5954:   char pathr[MAXLINE], pathimach[MAXLINE]; 
1.164     brouard  5955:   char *tok, *val; /* pathtot */
1.136     brouard  5956:   int firstobs=1, lastobs=10;
1.164     brouard  5957:   int c,  h , cpt;
                   5958:   int jl;
                   5959:   int i1, j1, jk, stepsize;
                   5960:   int *tab; 
1.136     brouard  5961:   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
                   5962:   int mobilav=0,popforecast=0;
                   5963:   int hstepm, nhstepm;
                   5964:   int agemortsup;
                   5965:   float  sumlpop=0.;
                   5966:   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
                   5967:   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
                   5968: 
1.164     brouard  5969:   double bage=0, fage=110, age, agelim, agebase;
1.136     brouard  5970:   double ftolpl=FTOL;
                   5971:   double **prlim;
                   5972:   double ***param; /* Matrix of parameters */
                   5973:   double  *p;
                   5974:   double **matcov; /* Matrix of covariance */
                   5975:   double ***delti3; /* Scale */
                   5976:   double *delti; /* Scale */
                   5977:   double ***eij, ***vareij;
                   5978:   double **varpl; /* Variances of prevalence limits by age */
                   5979:   double *epj, vepp;
1.164     brouard  5980: 
1.136     brouard  5981:   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
                   5982:   double **ximort;
1.145     brouard  5983:   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136     brouard  5984:   int *dcwave;
                   5985: 
1.164     brouard  5986:   char z[1]="c";
1.136     brouard  5987: 
                   5988:   /*char  *strt;*/
                   5989:   char strtend[80];
1.126     brouard  5990: 
1.164     brouard  5991: 
1.126     brouard  5992: /*   setlocale (LC_ALL, ""); */
                   5993: /*   bindtextdomain (PACKAGE, LOCALEDIR); */
                   5994: /*   textdomain (PACKAGE); */
                   5995: /*   setlocale (LC_CTYPE, ""); */
                   5996: /*   setlocale (LC_MESSAGES, ""); */
                   5997: 
                   5998:   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157     brouard  5999:   rstart_time = time(NULL);  
                   6000:   /*  (void) gettimeofday(&start_time,&tzp);*/
                   6001:   start_time = *localtime(&rstart_time);
1.126     brouard  6002:   curr_time=start_time;
1.157     brouard  6003:   /*tml = *localtime(&start_time.tm_sec);*/
                   6004:   /* strcpy(strstart,asctime(&tml)); */
                   6005:   strcpy(strstart,asctime(&start_time));
1.126     brouard  6006: 
                   6007: /*  printf("Localtime (at start)=%s",strstart); */
1.157     brouard  6008: /*  tp.tm_sec = tp.tm_sec +86400; */
                   6009: /*  tm = *localtime(&start_time.tm_sec); */
1.126     brouard  6010: /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
                   6011: /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
                   6012: /*   tmg.tm_hour=tmg.tm_hour + 1; */
1.157     brouard  6013: /*   tp.tm_sec = mktime(&tmg); */
1.126     brouard  6014: /*   strt=asctime(&tmg); */
                   6015: /*   printf("Time(after) =%s",strstart);  */
                   6016: /*  (void) time (&time_value);
                   6017: *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
                   6018: *  tm = *localtime(&time_value);
                   6019: *  strstart=asctime(&tm);
                   6020: *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
                   6021: */
                   6022: 
                   6023:   nberr=0; /* Number of errors and warnings */
                   6024:   nbwarn=0;
1.184   ! brouard  6025: #ifdef WIN32
        !          6026:   _getcwd(pathcd, size);
        !          6027: #else
1.126     brouard  6028:   getcwd(pathcd, size);
1.184   ! brouard  6029: #endif
1.126     brouard  6030: 
                   6031:   printf("\n%s\n%s",version,fullversion);
                   6032:   if(argc <=1){
                   6033:     printf("\nEnter the parameter file name: ");
                   6034:     fgets(pathr,FILENAMELENGTH,stdin);
                   6035:     i=strlen(pathr);
                   6036:     if(pathr[i-1]=='\n')
                   6037:       pathr[i-1]='\0';
1.156     brouard  6038:     i=strlen(pathr);
                   6039:     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
                   6040:       pathr[i-1]='\0';
1.126     brouard  6041:    for (tok = pathr; tok != NULL; ){
                   6042:       printf("Pathr |%s|\n",pathr);
                   6043:       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
                   6044:       printf("val= |%s| pathr=%s\n",val,pathr);
                   6045:       strcpy (pathtot, val);
                   6046:       if(pathr[0] == '\0') break; /* Dirty */
                   6047:     }
                   6048:   }
                   6049:   else{
                   6050:     strcpy(pathtot,argv[1]);
                   6051:   }
                   6052:   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
                   6053:   /*cygwin_split_path(pathtot,path,optionfile);
                   6054:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
                   6055:   /* cutv(path,optionfile,pathtot,'\\');*/
                   6056: 
                   6057:   /* Split argv[0], imach program to get pathimach */
                   6058:   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
                   6059:   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   6060:   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
                   6061:  /*   strcpy(pathimach,argv[0]); */
                   6062:   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
                   6063:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
                   6064:   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184   ! brouard  6065: #ifdef WIN32
        !          6066:   _chdir(path); /* Can be a relative path */
        !          6067:   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
        !          6068: #else
1.126     brouard  6069:   chdir(path); /* Can be a relative path */
1.184   ! brouard  6070:   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
        !          6071: #endif
        !          6072:   printf("Current directory %s!\n",pathcd);
1.126     brouard  6073:   strcpy(command,"mkdir ");
                   6074:   strcat(command,optionfilefiname);
                   6075:   if((outcmd=system(command)) != 0){
1.169     brouard  6076:     printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126     brouard  6077:     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
                   6078:     /* fclose(ficlog); */
                   6079: /*     exit(1); */
                   6080:   }
                   6081: /*   if((imk=mkdir(optionfilefiname))<0){ */
                   6082: /*     perror("mkdir"); */
                   6083: /*   } */
                   6084: 
                   6085:   /*-------- arguments in the command line --------*/
                   6086: 
                   6087:   /* Log file */
                   6088:   strcat(filelog, optionfilefiname);
                   6089:   strcat(filelog,".log");    /* */
                   6090:   if((ficlog=fopen(filelog,"w"))==NULL)    {
                   6091:     printf("Problem with logfile %s\n",filelog);
                   6092:     goto end;
                   6093:   }
                   6094:   fprintf(ficlog,"Log filename:%s\n",filelog);
                   6095:   fprintf(ficlog,"\n%s\n%s",version,fullversion);
                   6096:   fprintf(ficlog,"\nEnter the parameter file name: \n");
                   6097:   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
                   6098:  path=%s \n\
                   6099:  optionfile=%s\n\
                   6100:  optionfilext=%s\n\
1.156     brouard  6101:  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126     brouard  6102: 
1.167     brouard  6103:   syscompilerinfo();
                   6104: 
1.126     brouard  6105:   printf("Local time (at start):%s",strstart);
                   6106:   fprintf(ficlog,"Local time (at start): %s",strstart);
                   6107:   fflush(ficlog);
                   6108: /*   (void) gettimeofday(&curr_time,&tzp); */
1.157     brouard  6109: /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126     brouard  6110: 
                   6111:   /* */
                   6112:   strcpy(fileres,"r");
                   6113:   strcat(fileres, optionfilefiname);
                   6114:   strcat(fileres,".txt");    /* Other files have txt extension */
                   6115: 
                   6116:   /*---------arguments file --------*/
                   6117: 
                   6118:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
1.155     brouard  6119:     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
                   6120:     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126     brouard  6121:     fflush(ficlog);
1.149     brouard  6122:     /* goto end; */
                   6123:     exit(70); 
1.126     brouard  6124:   }
                   6125: 
                   6126: 
                   6127: 
                   6128:   strcpy(filereso,"o");
                   6129:   strcat(filereso,fileres);
                   6130:   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
                   6131:     printf("Problem with Output resultfile: %s\n", filereso);
                   6132:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
                   6133:     fflush(ficlog);
                   6134:     goto end;
                   6135:   }
                   6136: 
                   6137:   /* Reads comments: lines beginning with '#' */
                   6138:   numlinepar=0;
                   6139:   while((c=getc(ficpar))=='#' && c!= EOF){
                   6140:     ungetc(c,ficpar);
                   6141:     fgets(line, MAXLINE, ficpar);
                   6142:     numlinepar++;
1.141     brouard  6143:     fputs(line,stdout);
1.126     brouard  6144:     fputs(line,ficparo);
                   6145:     fputs(line,ficlog);
                   6146:   }
                   6147:   ungetc(c,ficpar);
                   6148: 
                   6149:   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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
                   6150:   numlinepar++;
                   6151:   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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
                   6152:   fprintf(ficparo,"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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
                   6153:   fprintf(ficlog,"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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
                   6154:   fflush(ficlog);
                   6155:   while((c=getc(ficpar))=='#' && c!= EOF){
                   6156:     ungetc(c,ficpar);
                   6157:     fgets(line, MAXLINE, ficpar);
                   6158:     numlinepar++;
1.141     brouard  6159:     fputs(line, stdout);
                   6160:     //puts(line);
1.126     brouard  6161:     fputs(line,ficparo);
                   6162:     fputs(line,ficlog);
                   6163:   }
                   6164:   ungetc(c,ficpar);
                   6165: 
                   6166:    
1.145     brouard  6167:   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
1.136     brouard  6168:   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
                   6169:   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
                   6170:      v1+v2*age+v2*v3 makes cptcovn = 3
                   6171:   */
                   6172:   if (strlen(model)>1) 
1.145     brouard  6173:     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*/
                   6174:   else
                   6175:     ncovmodel=2;
1.126     brouard  6176:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133     brouard  6177:   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
                   6178:   npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131     brouard  6179:   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
                   6180:     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);
                   6181:     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);
                   6182:     fflush(stdout);
                   6183:     fclose (ficlog);
                   6184:     goto end;
                   6185:   }
1.126     brouard  6186:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   6187:   delti=delti3[1][1];
                   6188:   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
                   6189:   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
                   6190:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
                   6191:     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   6192:     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   6193:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   6194:     fclose (ficparo);
                   6195:     fclose (ficlog);
                   6196:     goto end;
                   6197:     exit(0);
                   6198:   }
                   6199:   else if(mle==-3) {
                   6200:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
                   6201:     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
                   6202:     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
                   6203:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   6204:     matcov=matrix(1,npar,1,npar);
                   6205:   }
                   6206:   else{
1.145     brouard  6207:     /* Read guessed parameters */
1.126     brouard  6208:     /* Reads comments: lines beginning with '#' */
                   6209:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6210:       ungetc(c,ficpar);
                   6211:       fgets(line, MAXLINE, ficpar);
                   6212:       numlinepar++;
1.141     brouard  6213:       fputs(line,stdout);
1.126     brouard  6214:       fputs(line,ficparo);
                   6215:       fputs(line,ficlog);
                   6216:     }
                   6217:     ungetc(c,ficpar);
                   6218:     
                   6219:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
                   6220:     for(i=1; i <=nlstate; i++){
                   6221:       j=0;
                   6222:       for(jj=1; jj <=nlstate+ndeath; jj++){
                   6223:        if(jj==i) continue;
                   6224:        j++;
                   6225:        fscanf(ficpar,"%1d%1d",&i1,&j1);
                   6226:        if ((i1 != i) && (j1 != j)){
                   6227:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
                   6228: It might be a problem of design; if ncovcol and the model are correct\n \
                   6229: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
                   6230:          exit(1);
                   6231:        }
                   6232:        fprintf(ficparo,"%1d%1d",i1,j1);
                   6233:        if(mle==1)
                   6234:          printf("%1d%1d",i,j);
                   6235:        fprintf(ficlog,"%1d%1d",i,j);
                   6236:        for(k=1; k<=ncovmodel;k++){
                   6237:          fscanf(ficpar," %lf",&param[i][j][k]);
                   6238:          if(mle==1){
                   6239:            printf(" %lf",param[i][j][k]);
                   6240:            fprintf(ficlog," %lf",param[i][j][k]);
                   6241:          }
                   6242:          else
                   6243:            fprintf(ficlog," %lf",param[i][j][k]);
                   6244:          fprintf(ficparo," %lf",param[i][j][k]);
                   6245:        }
                   6246:        fscanf(ficpar,"\n");
                   6247:        numlinepar++;
                   6248:        if(mle==1)
                   6249:          printf("\n");
                   6250:        fprintf(ficlog,"\n");
                   6251:        fprintf(ficparo,"\n");
                   6252:       }
                   6253:     }  
                   6254:     fflush(ficlog);
                   6255: 
1.145     brouard  6256:     /* Reads scales values */
1.126     brouard  6257:     p=param[1][1];
                   6258:     
                   6259:     /* Reads comments: lines beginning with '#' */
                   6260:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6261:       ungetc(c,ficpar);
                   6262:       fgets(line, MAXLINE, ficpar);
                   6263:       numlinepar++;
1.141     brouard  6264:       fputs(line,stdout);
1.126     brouard  6265:       fputs(line,ficparo);
                   6266:       fputs(line,ficlog);
                   6267:     }
                   6268:     ungetc(c,ficpar);
                   6269: 
                   6270:     for(i=1; i <=nlstate; i++){
                   6271:       for(j=1; j <=nlstate+ndeath-1; j++){
                   6272:        fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164     brouard  6273:        if ( (i1-i) * (j1-j) != 0){
1.126     brouard  6274:          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   6275:          exit(1);
                   6276:        }
                   6277:        printf("%1d%1d",i,j);
                   6278:        fprintf(ficparo,"%1d%1d",i1,j1);
                   6279:        fprintf(ficlog,"%1d%1d",i1,j1);
                   6280:        for(k=1; k<=ncovmodel;k++){
                   6281:          fscanf(ficpar,"%le",&delti3[i][j][k]);
                   6282:          printf(" %le",delti3[i][j][k]);
                   6283:          fprintf(ficparo," %le",delti3[i][j][k]);
                   6284:          fprintf(ficlog," %le",delti3[i][j][k]);
                   6285:        }
                   6286:        fscanf(ficpar,"\n");
                   6287:        numlinepar++;
                   6288:        printf("\n");
                   6289:        fprintf(ficparo,"\n");
                   6290:        fprintf(ficlog,"\n");
                   6291:       }
                   6292:     }
                   6293:     fflush(ficlog);
                   6294: 
1.145     brouard  6295:     /* Reads covariance matrix */
1.126     brouard  6296:     delti=delti3[1][1];
                   6297: 
                   6298: 
                   6299:     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
                   6300:   
                   6301:     /* Reads comments: lines beginning with '#' */
                   6302:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6303:       ungetc(c,ficpar);
                   6304:       fgets(line, MAXLINE, ficpar);
                   6305:       numlinepar++;
1.141     brouard  6306:       fputs(line,stdout);
1.126     brouard  6307:       fputs(line,ficparo);
                   6308:       fputs(line,ficlog);
                   6309:     }
                   6310:     ungetc(c,ficpar);
                   6311:   
                   6312:     matcov=matrix(1,npar,1,npar);
1.131     brouard  6313:     for(i=1; i <=npar; i++)
                   6314:       for(j=1; j <=npar; j++) matcov[i][j]=0.;
                   6315:       
1.126     brouard  6316:     for(i=1; i <=npar; i++){
1.145     brouard  6317:       fscanf(ficpar,"%s",str);
1.126     brouard  6318:       if(mle==1)
                   6319:        printf("%s",str);
                   6320:       fprintf(ficlog,"%s",str);
                   6321:       fprintf(ficparo,"%s",str);
                   6322:       for(j=1; j <=i; j++){
                   6323:        fscanf(ficpar," %le",&matcov[i][j]);
                   6324:        if(mle==1){
                   6325:          printf(" %.5le",matcov[i][j]);
                   6326:        }
                   6327:        fprintf(ficlog," %.5le",matcov[i][j]);
                   6328:        fprintf(ficparo," %.5le",matcov[i][j]);
                   6329:       }
                   6330:       fscanf(ficpar,"\n");
                   6331:       numlinepar++;
                   6332:       if(mle==1)
                   6333:        printf("\n");
                   6334:       fprintf(ficlog,"\n");
                   6335:       fprintf(ficparo,"\n");
                   6336:     }
                   6337:     for(i=1; i <=npar; i++)
                   6338:       for(j=i+1;j<=npar;j++)
                   6339:        matcov[i][j]=matcov[j][i];
                   6340:     
                   6341:     if(mle==1)
                   6342:       printf("\n");
                   6343:     fprintf(ficlog,"\n");
                   6344:     
                   6345:     fflush(ficlog);
                   6346:     
                   6347:     /*-------- Rewriting parameter file ----------*/
                   6348:     strcpy(rfileres,"r");    /* "Rparameterfile */
                   6349:     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
                   6350:     strcat(rfileres,".");    /* */
                   6351:     strcat(rfileres,optionfilext);    /* Other files have txt extension */
                   6352:     if((ficres =fopen(rfileres,"w"))==NULL) {
                   6353:       printf("Problem writing new parameter file: %s\n", fileres);goto end;
                   6354:       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
                   6355:     }
                   6356:     fprintf(ficres,"#%s\n",version);
                   6357:   }    /* End of mle != -3 */
                   6358: 
                   6359: 
                   6360:   n= lastobs;
                   6361:   num=lvector(1,n);
                   6362:   moisnais=vector(1,n);
                   6363:   annais=vector(1,n);
                   6364:   moisdc=vector(1,n);
                   6365:   andc=vector(1,n);
                   6366:   agedc=vector(1,n);
                   6367:   cod=ivector(1,n);
                   6368:   weight=vector(1,n);
                   6369:   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
                   6370:   mint=matrix(1,maxwav,1,n);
                   6371:   anint=matrix(1,maxwav,1,n);
1.131     brouard  6372:   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
1.126     brouard  6373:   tab=ivector(1,NCOVMAX);
1.144     brouard  6374:   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126     brouard  6375: 
1.136     brouard  6376:   /* Reads data from file datafile */
                   6377:   if (readdata(datafile, firstobs, lastobs, &imx)==1)
                   6378:     goto end;
                   6379: 
                   6380:   /* Calculation of the number of parameters from char model */
1.137     brouard  6381:     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
                   6382:        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
                   6383:        k=3 V4 Tvar[k=3]= 4 (from V4)
                   6384:        k=2 V1 Tvar[k=2]= 1 (from V1)
                   6385:        k=1 Tvar[1]=2 (from V2)
                   6386:     */
                   6387:   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
                   6388:   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
                   6389:       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
                   6390:       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
                   6391:   */
                   6392:   /* For model-covariate k tells which data-covariate to use but
                   6393:     because this model-covariate is a construction we invent a new column
                   6394:     ncovcol + k1
                   6395:     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
                   6396:     Tvar[3=V1*V4]=4+1 etc */
1.145     brouard  6397:   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137     brouard  6398:   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
                   6399:      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
                   6400:   */
1.145     brouard  6401:   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
                   6402:   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  6403:                            * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                   6404:                            * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145     brouard  6405:   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137     brouard  6406:                         4 covariates (3 plus signs)
                   6407:                         Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                   6408:                      */  
1.136     brouard  6409: 
                   6410:   if(decodemodel(model, lastobs) == 1)
                   6411:     goto end;
                   6412: 
1.137     brouard  6413:   if((double)(lastobs-imx)/(double)imx > 1.10){
                   6414:     nbwarn++;
                   6415:     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); 
                   6416:     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); 
                   6417:   }
1.136     brouard  6418:     /*  if(mle==1){*/
1.137     brouard  6419:   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
                   6420:     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136     brouard  6421:   }
                   6422: 
                   6423:     /*-calculation of age at interview from date of interview and age at death -*/
                   6424:   agev=matrix(1,maxwav,1,imx);
                   6425: 
                   6426:   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
                   6427:     goto end;
                   6428: 
1.126     brouard  6429: 
1.136     brouard  6430:   agegomp=(int)agemin;
                   6431:   free_vector(moisnais,1,n);
                   6432:   free_vector(annais,1,n);
1.126     brouard  6433:   /* free_matrix(mint,1,maxwav,1,n);
                   6434:      free_matrix(anint,1,maxwav,1,n);*/
                   6435:   free_vector(moisdc,1,n);
                   6436:   free_vector(andc,1,n);
1.145     brouard  6437:   /* */
                   6438:   
1.126     brouard  6439:   wav=ivector(1,imx);
                   6440:   dh=imatrix(1,lastpass-firstpass+1,1,imx);
                   6441:   bh=imatrix(1,lastpass-firstpass+1,1,imx);
                   6442:   mw=imatrix(1,lastpass-firstpass+1,1,imx);
                   6443:    
                   6444:   /* Concatenates waves */
                   6445:   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
1.145     brouard  6446:   /* */
                   6447:  
1.126     brouard  6448:   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
                   6449: 
                   6450:   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
                   6451:   ncodemax[1]=1;
1.145     brouard  6452:   Ndum =ivector(-1,NCOVMAX);  
                   6453:   if (ncovmodel > 2)
                   6454:     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
                   6455: 
                   6456:   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
                   6457:   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
                   6458:   h=0;
                   6459: 
                   6460: 
                   6461:   /*if (cptcovn > 0) */
1.126     brouard  6462:       
1.145     brouard  6463:  
1.126     brouard  6464:   m=pow(2,cptcoveff);
                   6465:  
1.131     brouard  6466:   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143     brouard  6467:     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
                   6468:       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
                   6469:        for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
1.126     brouard  6470:          h++;
1.141     brouard  6471:          if (h>m) 
1.136     brouard  6472:            h=1;
1.144     brouard  6473:          /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143     brouard  6474:           *     h     1     2     3     4
                   6475:           *______________________________  
                   6476:           *     1 i=1 1 i=1 1 i=1 1 i=1 1
                   6477:           *     2     2     1     1     1
                   6478:           *     3 i=2 1     2     1     1
                   6479:           *     4     2     2     1     1
                   6480:           *     5 i=3 1 i=2 1     2     1
                   6481:           *     6     2     1     2     1
                   6482:           *     7 i=4 1     2     2     1
                   6483:           *     8     2     2     2     1
                   6484:           *     9 i=5 1 i=3 1 i=2 1     1
                   6485:           *    10     2     1     1     1
                   6486:           *    11 i=6 1     2     1     1
                   6487:           *    12     2     2     1     1
                   6488:           *    13 i=7 1 i=4 1     2     1    
                   6489:           *    14     2     1     2     1
                   6490:           *    15 i=8 1     2     2     1
                   6491:           *    16     2     2     2     1
                   6492:           */
1.141     brouard  6493:          codtab[h][k]=j;
1.145     brouard  6494:          /*codtab[h][Tvar[k]]=j;*/
1.130     brouard  6495:          printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
1.126     brouard  6496:        } 
                   6497:       }
                   6498:     }
                   6499:   } 
                   6500:   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
                   6501:      codtab[1][2]=1;codtab[2][2]=2; */
                   6502:   /* for(i=1; i <=m ;i++){ 
                   6503:      for(k=1; k <=cptcovn; k++){
1.131     brouard  6504:        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126     brouard  6505:      }
                   6506:      printf("\n");
                   6507:      }
                   6508:      scanf("%d",i);*/
1.145     brouard  6509: 
                   6510:  free_ivector(Ndum,-1,NCOVMAX);
                   6511: 
                   6512: 
1.126     brouard  6513:     
                   6514:   /*------------ gnuplot -------------*/
                   6515:   strcpy(optionfilegnuplot,optionfilefiname);
                   6516:   if(mle==-3)
                   6517:     strcat(optionfilegnuplot,"-mort");
                   6518:   strcat(optionfilegnuplot,".gp");
                   6519: 
                   6520:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
                   6521:     printf("Problem with file %s",optionfilegnuplot);
                   6522:   }
                   6523:   else{
                   6524:     fprintf(ficgp,"\n# %s\n", version); 
                   6525:     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
1.141     brouard  6526:     //fprintf(ficgp,"set missing 'NaNq'\n");
                   6527:     fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126     brouard  6528:   }
                   6529:   /*  fclose(ficgp);*/
                   6530:   /*--------- index.htm --------*/
                   6531: 
                   6532:   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
                   6533:   if(mle==-3)
                   6534:     strcat(optionfilehtm,"-mort");
                   6535:   strcat(optionfilehtm,".htm");
                   6536:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
1.131     brouard  6537:     printf("Problem with %s \n",optionfilehtm);
                   6538:     exit(0);
1.126     brouard  6539:   }
                   6540: 
                   6541:   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
                   6542:   strcat(optionfilehtmcov,"-cov.htm");
                   6543:   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
                   6544:     printf("Problem with %s \n",optionfilehtmcov), exit(0);
                   6545:   }
                   6546:   else{
                   6547:   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                   6548: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   6549: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
                   6550:          optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   6551:   }
                   6552: 
                   6553:   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                   6554: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   6555: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
                   6556: \n\
                   6557: <hr  size=\"2\" color=\"#EC5E5E\">\
                   6558:  <ul><li><h4>Parameter files</h4>\n\
                   6559:  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
                   6560:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
                   6561:  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
                   6562:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
                   6563:  - Date and time at start: %s</ul>\n",\
                   6564:          optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
                   6565:          optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
                   6566:          fileres,fileres,\
                   6567:          filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
                   6568:   fflush(fichtm);
                   6569: 
                   6570:   strcpy(pathr,path);
                   6571:   strcat(pathr,optionfilefiname);
1.184   ! brouard  6572: #ifdef WIN32
        !          6573:   _chdir(optionfilefiname); /* Move to directory named optionfile */
        !          6574: #else
1.126     brouard  6575:   chdir(optionfilefiname); /* Move to directory named optionfile */
1.184   ! brouard  6576: #endif
        !          6577:          
1.126     brouard  6578:   
                   6579:   /* Calculates basic frequencies. Computes observed prevalence at single age
                   6580:      and prints on file fileres'p'. */
                   6581:   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
                   6582: 
                   6583:   fprintf(fichtm,"\n");
                   6584:   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
                   6585: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
                   6586: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
                   6587:          imx,agemin,agemax,jmin,jmax,jmean);
                   6588:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   6589:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   6590:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   6591:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   6592:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
                   6593:     
                   6594:    
                   6595:   /* For Powell, parameters are in a vector p[] starting at p[1]
                   6596:      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
                   6597:   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
                   6598: 
                   6599:   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
                   6600: 
                   6601:   if (mle==-3){
1.136     brouard  6602:     ximort=matrix(1,NDIM,1,NDIM); 
                   6603: /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126     brouard  6604:     cens=ivector(1,n);
                   6605:     ageexmed=vector(1,n);
                   6606:     agecens=vector(1,n);
                   6607:     dcwave=ivector(1,n);
                   6608:  
                   6609:     for (i=1; i<=imx; i++){
                   6610:       dcwave[i]=-1;
                   6611:       for (m=firstpass; m<=lastpass; m++)
                   6612:        if (s[m][i]>nlstate) {
                   6613:          dcwave[i]=m;
                   6614:          /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                   6615:          break;
                   6616:        }
                   6617:     }
                   6618: 
                   6619:     for (i=1; i<=imx; i++) {
                   6620:       if (wav[i]>0){
                   6621:        ageexmed[i]=agev[mw[1][i]][i];
                   6622:        j=wav[i];
                   6623:        agecens[i]=1.; 
                   6624: 
                   6625:        if (ageexmed[i]> 1 && wav[i] > 0){
                   6626:          agecens[i]=agev[mw[j][i]][i];
                   6627:          cens[i]= 1;
                   6628:        }else if (ageexmed[i]< 1) 
                   6629:          cens[i]= -1;
                   6630:        if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                   6631:          cens[i]=0 ;
                   6632:       }
                   6633:       else cens[i]=-1;
                   6634:     }
                   6635:     
                   6636:     for (i=1;i<=NDIM;i++) {
                   6637:       for (j=1;j<=NDIM;j++)
                   6638:        ximort[i][j]=(i == j ? 1.0 : 0.0);
                   6639:     }
                   6640:     
1.145     brouard  6641:     /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126     brouard  6642:     /*printf("%lf %lf", p[1], p[2]);*/
                   6643:     
                   6644:     
1.136     brouard  6645: #ifdef GSL
                   6646:     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
1.162     brouard  6647: #else
1.126     brouard  6648:     printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.136     brouard  6649: #endif
1.126     brouard  6650:     strcpy(filerespow,"pow-mort"); 
                   6651:     strcat(filerespow,fileres);
                   6652:     if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   6653:       printf("Problem with resultfile: %s\n", filerespow);
                   6654:       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   6655:     }
1.136     brouard  6656: #ifdef GSL
                   6657:     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162     brouard  6658: #else
1.126     brouard  6659:     fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136     brouard  6660: #endif
1.126     brouard  6661:     /*  for (i=1;i<=nlstate;i++)
                   6662:        for(j=1;j<=nlstate+ndeath;j++)
                   6663:        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   6664:     */
                   6665:     fprintf(ficrespow,"\n");
1.136     brouard  6666: #ifdef GSL
                   6667:     /* gsl starts here */ 
                   6668:     T = gsl_multimin_fminimizer_nmsimplex;
                   6669:     gsl_multimin_fminimizer *sfm = NULL;
                   6670:     gsl_vector *ss, *x;
                   6671:     gsl_multimin_function minex_func;
                   6672: 
                   6673:     /* Initial vertex size vector */
                   6674:     ss = gsl_vector_alloc (NDIM);
                   6675:     
                   6676:     if (ss == NULL){
                   6677:       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
                   6678:     }
                   6679:     /* Set all step sizes to 1 */
                   6680:     gsl_vector_set_all (ss, 0.001);
                   6681: 
                   6682:     /* Starting point */
1.126     brouard  6683:     
1.136     brouard  6684:     x = gsl_vector_alloc (NDIM);
                   6685:     
                   6686:     if (x == NULL){
                   6687:       gsl_vector_free(ss);
                   6688:       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
                   6689:     }
                   6690:   
                   6691:     /* Initialize method and iterate */
                   6692:     /*     p[1]=0.0268; p[NDIM]=0.083; */
                   6693: /*     gsl_vector_set(x, 0, 0.0268); */
                   6694: /*     gsl_vector_set(x, 1, 0.083); */
                   6695:     gsl_vector_set(x, 0, p[1]);
                   6696:     gsl_vector_set(x, 1, p[2]);
                   6697: 
                   6698:     minex_func.f = &gompertz_f;
                   6699:     minex_func.n = NDIM;
                   6700:     minex_func.params = (void *)&p; /* ??? */
                   6701:     
                   6702:     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
                   6703:     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
                   6704:     
                   6705:     printf("Iterations beginning .....\n\n");
                   6706:     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
                   6707: 
                   6708:     iteri=0;
                   6709:     while (rval == GSL_CONTINUE){
                   6710:       iteri++;
                   6711:       status = gsl_multimin_fminimizer_iterate(sfm);
                   6712:       
                   6713:       if (status) printf("error: %s\n", gsl_strerror (status));
                   6714:       fflush(0);
                   6715:       
                   6716:       if (status) 
                   6717:         break;
                   6718:       
                   6719:       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
                   6720:       ssval = gsl_multimin_fminimizer_size (sfm);
                   6721:       
                   6722:       if (rval == GSL_SUCCESS)
                   6723:         printf ("converged to a local maximum at\n");
                   6724:       
                   6725:       printf("%5d ", iteri);
                   6726:       for (it = 0; it < NDIM; it++){
                   6727:        printf ("%10.5f ", gsl_vector_get (sfm->x, it));
                   6728:       }
                   6729:       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
                   6730:     }
                   6731:     
                   6732:     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
                   6733:     
                   6734:     gsl_vector_free(x); /* initial values */
                   6735:     gsl_vector_free(ss); /* inital step size */
                   6736:     for (it=0; it<NDIM; it++){
                   6737:       p[it+1]=gsl_vector_get(sfm->x,it);
                   6738:       fprintf(ficrespow," %.12lf", p[it]);
                   6739:     }
                   6740:     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
                   6741: #endif
                   6742: #ifdef POWELL
                   6743:      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
                   6744: #endif  
1.126     brouard  6745:     fclose(ficrespow);
                   6746:     
                   6747:     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
                   6748: 
                   6749:     for(i=1; i <=NDIM; i++)
                   6750:       for(j=i+1;j<=NDIM;j++)
                   6751:        matcov[i][j]=matcov[j][i];
                   6752:     
                   6753:     printf("\nCovariance matrix\n ");
                   6754:     for(i=1; i <=NDIM; i++) {
                   6755:       for(j=1;j<=NDIM;j++){ 
                   6756:        printf("%f ",matcov[i][j]);
                   6757:       }
                   6758:       printf("\n ");
                   6759:     }
                   6760:     
                   6761:     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
                   6762:     for (i=1;i<=NDIM;i++) 
                   6763:       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
                   6764: 
                   6765:     lsurv=vector(1,AGESUP);
                   6766:     lpop=vector(1,AGESUP);
                   6767:     tpop=vector(1,AGESUP);
                   6768:     lsurv[agegomp]=100000;
                   6769:     
                   6770:     for (k=agegomp;k<=AGESUP;k++) {
                   6771:       agemortsup=k;
                   6772:       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
                   6773:     }
                   6774:     
                   6775:     for (k=agegomp;k<agemortsup;k++)
                   6776:       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
                   6777:     
                   6778:     for (k=agegomp;k<agemortsup;k++){
                   6779:       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
                   6780:       sumlpop=sumlpop+lpop[k];
                   6781:     }
                   6782:     
                   6783:     tpop[agegomp]=sumlpop;
                   6784:     for (k=agegomp;k<(agemortsup-3);k++){
                   6785:       /*  tpop[k+1]=2;*/
                   6786:       tpop[k+1]=tpop[k]-lpop[k];
                   6787:     }
                   6788:     
                   6789:     
                   6790:     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
                   6791:     for (k=agegomp;k<(agemortsup-2);k++) 
                   6792:       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]);
                   6793:     
                   6794:     
                   6795:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   6796:     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   6797:     
                   6798:     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                   6799:                     stepm, weightopt,\
                   6800:                     model,imx,p,matcov,agemortsup);
                   6801:     
                   6802:     free_vector(lsurv,1,AGESUP);
                   6803:     free_vector(lpop,1,AGESUP);
                   6804:     free_vector(tpop,1,AGESUP);
1.136     brouard  6805: #ifdef GSL
                   6806:     free_ivector(cens,1,n);
                   6807:     free_vector(agecens,1,n);
                   6808:     free_ivector(dcwave,1,n);
                   6809:     free_matrix(ximort,1,NDIM,1,NDIM);
                   6810: #endif
1.126     brouard  6811:   } /* Endof if mle==-3 */
                   6812:   
                   6813:   else{ /* For mle >=1 */
1.132     brouard  6814:     globpr=0;/* debug */
                   6815:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126     brouard  6816:     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   6817:     for (k=1; k<=npar;k++)
                   6818:       printf(" %d %8.5f",k,p[k]);
                   6819:     printf("\n");
                   6820:     globpr=1; /* to print the contributions */
                   6821:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   6822:     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   6823:     for (k=1; k<=npar;k++)
                   6824:       printf(" %d %8.5f",k,p[k]);
                   6825:     printf("\n");
                   6826:     if(mle>=1){ /* Could be 1 or 2 */
                   6827:       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
                   6828:     }
                   6829:     
                   6830:     /*--------- results files --------------*/
                   6831:     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
                   6832:     
                   6833:     
                   6834:     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   6835:     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   6836:     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   6837:     for(i=1,jk=1; i <=nlstate; i++){
                   6838:       for(k=1; k <=(nlstate+ndeath); k++){
                   6839:        if (k != i) {
                   6840:          printf("%d%d ",i,k);
                   6841:          fprintf(ficlog,"%d%d ",i,k);
                   6842:          fprintf(ficres,"%1d%1d ",i,k);
                   6843:          for(j=1; j <=ncovmodel; j++){
                   6844:            printf("%lf ",p[jk]);
                   6845:            fprintf(ficlog,"%lf ",p[jk]);
                   6846:            fprintf(ficres,"%lf ",p[jk]);
                   6847:            jk++; 
                   6848:          }
                   6849:          printf("\n");
                   6850:          fprintf(ficlog,"\n");
                   6851:          fprintf(ficres,"\n");
                   6852:        }
                   6853:       }
                   6854:     }
                   6855:     if(mle!=0){
                   6856:       /* Computing hessian and covariance matrix */
                   6857:       ftolhess=ftol; /* Usually correct */
                   6858:       hesscov(matcov, p, npar, delti, ftolhess, func);
                   6859:     }
                   6860:     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
                   6861:     printf("# Scales (for hessian or gradient estimation)\n");
                   6862:     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
                   6863:     for(i=1,jk=1; i <=nlstate; i++){
                   6864:       for(j=1; j <=nlstate+ndeath; j++){
                   6865:        if (j!=i) {
                   6866:          fprintf(ficres,"%1d%1d",i,j);
                   6867:          printf("%1d%1d",i,j);
                   6868:          fprintf(ficlog,"%1d%1d",i,j);
                   6869:          for(k=1; k<=ncovmodel;k++){
                   6870:            printf(" %.5e",delti[jk]);
                   6871:            fprintf(ficlog," %.5e",delti[jk]);
                   6872:            fprintf(ficres," %.5e",delti[jk]);
                   6873:            jk++;
                   6874:          }
                   6875:          printf("\n");
                   6876:          fprintf(ficlog,"\n");
                   6877:          fprintf(ficres,"\n");
                   6878:        }
                   6879:       }
                   6880:     }
                   6881:     
                   6882:     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");
                   6883:     if(mle>=1)
                   6884:       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");
                   6885:     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");
                   6886:     /* # 121 Var(a12)\n\ */
                   6887:     /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   6888:     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   6889:     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   6890:     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   6891:     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   6892:     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   6893:     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   6894:     
                   6895:     
                   6896:     /* Just to have a covariance matrix which will be more understandable
                   6897:        even is we still don't want to manage dictionary of variables
                   6898:     */
                   6899:     for(itimes=1;itimes<=2;itimes++){
                   6900:       jj=0;
                   6901:       for(i=1; i <=nlstate; i++){
                   6902:        for(j=1; j <=nlstate+ndeath; j++){
                   6903:          if(j==i) continue;
                   6904:          for(k=1; k<=ncovmodel;k++){
                   6905:            jj++;
                   6906:            ca[0]= k+'a'-1;ca[1]='\0';
                   6907:            if(itimes==1){
                   6908:              if(mle>=1)
                   6909:                printf("#%1d%1d%d",i,j,k);
                   6910:              fprintf(ficlog,"#%1d%1d%d",i,j,k);
                   6911:              fprintf(ficres,"#%1d%1d%d",i,j,k);
                   6912:            }else{
                   6913:              if(mle>=1)
                   6914:                printf("%1d%1d%d",i,j,k);
                   6915:              fprintf(ficlog,"%1d%1d%d",i,j,k);
                   6916:              fprintf(ficres,"%1d%1d%d",i,j,k);
                   6917:            }
                   6918:            ll=0;
                   6919:            for(li=1;li <=nlstate; li++){
                   6920:              for(lj=1;lj <=nlstate+ndeath; lj++){
                   6921:                if(lj==li) continue;
                   6922:                for(lk=1;lk<=ncovmodel;lk++){
                   6923:                  ll++;
                   6924:                  if(ll<=jj){
                   6925:                    cb[0]= lk +'a'-1;cb[1]='\0';
                   6926:                    if(ll<jj){
                   6927:                      if(itimes==1){
                   6928:                        if(mle>=1)
                   6929:                          printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   6930:                        fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   6931:                        fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   6932:                      }else{
                   6933:                        if(mle>=1)
                   6934:                          printf(" %.5e",matcov[jj][ll]); 
                   6935:                        fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   6936:                        fprintf(ficres," %.5e",matcov[jj][ll]); 
                   6937:                      }
                   6938:                    }else{
                   6939:                      if(itimes==1){
                   6940:                        if(mle>=1)
                   6941:                          printf(" Var(%s%1d%1d)",ca,i,j);
                   6942:                        fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                   6943:                        fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                   6944:                      }else{
                   6945:                        if(mle>=1)
                   6946:                          printf(" %.5e",matcov[jj][ll]); 
                   6947:                        fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   6948:                        fprintf(ficres," %.5e",matcov[jj][ll]); 
                   6949:                      }
                   6950:                    }
                   6951:                  }
                   6952:                } /* end lk */
                   6953:              } /* end lj */
                   6954:            } /* end li */
                   6955:            if(mle>=1)
                   6956:              printf("\n");
                   6957:            fprintf(ficlog,"\n");
                   6958:            fprintf(ficres,"\n");
                   6959:            numlinepar++;
                   6960:          } /* end k*/
                   6961:        } /*end j */
                   6962:       } /* end i */
                   6963:     } /* end itimes */
                   6964:     
                   6965:     fflush(ficlog);
                   6966:     fflush(ficres);
                   6967:     
                   6968:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6969:       ungetc(c,ficpar);
                   6970:       fgets(line, MAXLINE, ficpar);
1.141     brouard  6971:       fputs(line,stdout);
1.126     brouard  6972:       fputs(line,ficparo);
                   6973:     }
                   6974:     ungetc(c,ficpar);
                   6975:     
                   6976:     estepm=0;
                   6977:     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
                   6978:     if (estepm==0 || estepm < stepm) estepm=stepm;
                   6979:     if (fage <= 2) {
                   6980:       bage = ageminpar;
                   6981:       fage = agemaxpar;
                   6982:     }
                   6983:     
                   6984:     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
                   6985:     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
                   6986:     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
                   6987:     
                   6988:     while((c=getc(ficpar))=='#' && c!= EOF){
                   6989:       ungetc(c,ficpar);
                   6990:       fgets(line, MAXLINE, ficpar);
1.141     brouard  6991:       fputs(line,stdout);
1.126     brouard  6992:       fputs(line,ficparo);
                   6993:     }
                   6994:     ungetc(c,ficpar);
                   6995:     
                   6996:     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);
                   6997:     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);
                   6998:     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);
                   6999:     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   7000:     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);
                   7001:     
                   7002:     while((c=getc(ficpar))=='#' && c!= EOF){
                   7003:       ungetc(c,ficpar);
                   7004:       fgets(line, MAXLINE, ficpar);
1.141     brouard  7005:       fputs(line,stdout);
1.126     brouard  7006:       fputs(line,ficparo);
                   7007:     }
                   7008:     ungetc(c,ficpar);
                   7009:     
                   7010:     
                   7011:     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
                   7012:     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
                   7013:     
                   7014:     fscanf(ficpar,"pop_based=%d\n",&popbased);
                   7015:     fprintf(ficparo,"pop_based=%d\n",popbased);   
                   7016:     fprintf(ficres,"pop_based=%d\n",popbased);   
                   7017:     
                   7018:     while((c=getc(ficpar))=='#' && c!= EOF){
                   7019:       ungetc(c,ficpar);
                   7020:       fgets(line, MAXLINE, ficpar);
1.141     brouard  7021:       fputs(line,stdout);
1.126     brouard  7022:       fputs(line,ficparo);
                   7023:     }
                   7024:     ungetc(c,ficpar);
                   7025:     
                   7026:     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);
                   7027:     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);
                   7028:     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);
                   7029:     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);
                   7030:     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);
                   7031:     /* day and month of proj2 are not used but only year anproj2.*/
                   7032:     
                   7033:     
                   7034:     
1.145     brouard  7035:      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
                   7036:     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126     brouard  7037:     
                   7038:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   7039:     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   7040:     
                   7041:     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                   7042:                 model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                   7043:                 jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
                   7044:       
                   7045:    /*------------ free_vector  -------------*/
                   7046:    /*  chdir(path); */
                   7047:  
                   7048:     free_ivector(wav,1,imx);
                   7049:     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
                   7050:     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
                   7051:     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
                   7052:     free_lvector(num,1,n);
                   7053:     free_vector(agedc,1,n);
                   7054:     /*free_matrix(covar,0,NCOVMAX,1,n);*/
                   7055:     /*free_matrix(covar,1,NCOVMAX,1,n);*/
                   7056:     fclose(ficparo);
                   7057:     fclose(ficres);
                   7058: 
                   7059: 
                   7060:     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
1.180     brouard  7061:     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
                   7062:     prlim=matrix(1,nlstate,1,nlstate);
                   7063:     prevalence_limit(p, prlim,  ageminpar, agemaxpar);
1.126     brouard  7064:     fclose(ficrespl);
                   7065: 
1.145     brouard  7066: #ifdef FREEEXIT2
                   7067: #include "freeexit2.h"
                   7068: #endif
                   7069: 
1.126     brouard  7070:     /*------------- h Pij x at various ages ------------*/
1.180     brouard  7071:     /*#include "hpijx.h"*/
                   7072:     hPijx(p, bage, fage);
1.145     brouard  7073:     fclose(ficrespij);
1.126     brouard  7074: 
1.145     brouard  7075:   /*-------------- Variance of one-step probabilities---*/
                   7076:     k=1;
1.126     brouard  7077:     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
                   7078: 
                   7079: 
                   7080:     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   7081:     for(i=1;i<=AGESUP;i++)
                   7082:       for(j=1;j<=NCOVMAX;j++)
                   7083:        for(k=1;k<=NCOVMAX;k++)
                   7084:          probs[i][j][k]=0.;
                   7085: 
                   7086:     /*---------- Forecasting ------------------*/
                   7087:     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
                   7088:     if(prevfcast==1){
                   7089:       /*    if(stepm ==1){*/
                   7090:       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
                   7091:       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
                   7092:       /*      }  */
                   7093:       /*      else{ */
                   7094:       /*        erreur=108; */
                   7095:       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
                   7096:       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
                   7097:       /*      } */
                   7098:     }
                   7099:   
                   7100: 
1.127     brouard  7101:     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
                   7102: 
                   7103:     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
                   7104:     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
                   7105:        ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
                   7106:     */
1.126     brouard  7107: 
1.127     brouard  7108:     if (mobilav!=0) {
                   7109:       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   7110:       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   7111:        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   7112:        printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   7113:       }
1.126     brouard  7114:     }
                   7115: 
                   7116: 
1.127     brouard  7117:     /*---------- Health expectancies, no variances ------------*/
                   7118: 
1.126     brouard  7119:     strcpy(filerese,"e");
                   7120:     strcat(filerese,fileres);
                   7121:     if((ficreseij=fopen(filerese,"w"))==NULL) {
                   7122:       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   7123:       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   7124:     }
                   7125:     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
                   7126:     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145     brouard  7127:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   7128:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   7129:           
                   7130:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127     brouard  7131:        fprintf(ficreseij,"\n#****** ");
                   7132:        for(j=1;j<=cptcoveff;j++) {
                   7133:          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   7134:        }
                   7135:        fprintf(ficreseij,"******\n");
                   7136: 
                   7137:        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   7138:        oldm=oldms;savm=savms;
                   7139:        evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
                   7140:       
                   7141:        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145     brouard  7142:       /*}*/
1.127     brouard  7143:     }
                   7144:     fclose(ficreseij);
                   7145: 
                   7146: 
                   7147:     /*---------- Health expectancies and variances ------------*/
                   7148: 
                   7149: 
                   7150:     strcpy(filerest,"t");
                   7151:     strcat(filerest,fileres);
                   7152:     if((ficrest=fopen(filerest,"w"))==NULL) {
                   7153:       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
                   7154:       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
                   7155:     }
                   7156:     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
                   7157:     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
                   7158: 
1.126     brouard  7159: 
                   7160:     strcpy(fileresstde,"stde");
                   7161:     strcat(fileresstde,fileres);
                   7162:     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
                   7163:       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
                   7164:       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
                   7165:     }
                   7166:     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
                   7167:     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
                   7168: 
                   7169:     strcpy(filerescve,"cve");
                   7170:     strcat(filerescve,fileres);
                   7171:     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
                   7172:       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
                   7173:       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
                   7174:     }
                   7175:     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
                   7176:     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
                   7177: 
                   7178:     strcpy(fileresv,"v");
                   7179:     strcat(fileresv,fileres);
                   7180:     if((ficresvij=fopen(fileresv,"w"))==NULL) {
                   7181:       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
                   7182:       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
                   7183:     }
                   7184:     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
                   7185:     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
                   7186: 
1.145     brouard  7187:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   7188:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   7189:           
                   7190:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
                   7191:        fprintf(ficrest,"\n#****** ");
1.126     brouard  7192:        for(j=1;j<=cptcoveff;j++) 
                   7193:          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   7194:        fprintf(ficrest,"******\n");
                   7195: 
                   7196:        fprintf(ficresstdeij,"\n#****** ");
                   7197:        fprintf(ficrescveij,"\n#****** ");
                   7198:        for(j=1;j<=cptcoveff;j++) {
                   7199:          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   7200:          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   7201:        }
                   7202:        fprintf(ficresstdeij,"******\n");
                   7203:        fprintf(ficrescveij,"******\n");
                   7204: 
                   7205:        fprintf(ficresvij,"\n#****** ");
                   7206:        for(j=1;j<=cptcoveff;j++) 
                   7207:          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   7208:        fprintf(ficresvij,"******\n");
                   7209: 
                   7210:        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   7211:        oldm=oldms;savm=savms;
1.127     brouard  7212:        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
1.145     brouard  7213:        /*
                   7214:         */
                   7215:        /* goto endfree; */
1.126     brouard  7216:  
                   7217:        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   7218:        pstamp(ficrest);
1.145     brouard  7219: 
                   7220: 
1.128     brouard  7221:        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145     brouard  7222:          oldm=oldms;savm=savms; /* Segmentation fault */
1.161     brouard  7223:          cptcod= 0; /* To be deleted */
                   7224:          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145     brouard  7225:          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 ");
1.128     brouard  7226:          if(vpopbased==1)
                   7227:            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);
                   7228:          else
                   7229:            fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
                   7230:          fprintf(ficrest,"# Age e.. (std) ");
                   7231:          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                   7232:          fprintf(ficrest,"\n");
1.126     brouard  7233: 
1.128     brouard  7234:          epj=vector(1,nlstate+1);
                   7235:          for(age=bage; age <=fage ;age++){
                   7236:            prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
                   7237:            if (vpopbased==1) {
                   7238:              if(mobilav ==0){
                   7239:                for(i=1; i<=nlstate;i++)
                   7240:                  prlim[i][i]=probs[(int)age][i][k];
                   7241:              }else{ /* mobilav */ 
                   7242:                for(i=1; i<=nlstate;i++)
                   7243:                  prlim[i][i]=mobaverage[(int)age][i][k];
                   7244:              }
1.126     brouard  7245:            }
                   7246:        
1.128     brouard  7247:            fprintf(ficrest," %4.0f",age);
                   7248:            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                   7249:              for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   7250:                epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   7251:                /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                   7252:              }
                   7253:              epj[nlstate+1] +=epj[j];
1.126     brouard  7254:            }
                   7255: 
1.128     brouard  7256:            for(i=1, vepp=0.;i <=nlstate;i++)
                   7257:              for(j=1;j <=nlstate;j++)
                   7258:                vepp += vareij[i][j][(int)age];
                   7259:            fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                   7260:            for(j=1;j <=nlstate;j++){
                   7261:              fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                   7262:            }
                   7263:            fprintf(ficrest,"\n");
1.126     brouard  7264:          }
                   7265:        }
                   7266:        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   7267:        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   7268:        free_vector(epj,1,nlstate+1);
1.145     brouard  7269:       /*}*/
1.126     brouard  7270:     }
                   7271:     free_vector(weight,1,n);
1.145     brouard  7272:     free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126     brouard  7273:     free_imatrix(s,1,maxwav+1,1,n);
                   7274:     free_matrix(anint,1,maxwav,1,n); 
                   7275:     free_matrix(mint,1,maxwav,1,n);
                   7276:     free_ivector(cod,1,n);
                   7277:     free_ivector(tab,1,NCOVMAX);
                   7278:     fclose(ficresstdeij);
                   7279:     fclose(ficrescveij);
                   7280:     fclose(ficresvij);
                   7281:     fclose(ficrest);
                   7282:     fclose(ficpar);
                   7283:   
                   7284:     /*------- Variance of period (stable) prevalence------*/   
                   7285: 
                   7286:     strcpy(fileresvpl,"vpl");
                   7287:     strcat(fileresvpl,fileres);
                   7288:     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
                   7289:       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
                   7290:       exit(0);
                   7291:     }
                   7292:     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
                   7293: 
1.145     brouard  7294:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
                   7295:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                   7296:           
                   7297:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
                   7298:        fprintf(ficresvpl,"\n#****** ");
1.126     brouard  7299:        for(j=1;j<=cptcoveff;j++) 
                   7300:          fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   7301:        fprintf(ficresvpl,"******\n");
                   7302:       
                   7303:        varpl=matrix(1,nlstate,(int) bage, (int) fage);
                   7304:        oldm=oldms;savm=savms;
                   7305:        varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
                   7306:        free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145     brouard  7307:       /*}*/
1.126     brouard  7308:     }
                   7309: 
                   7310:     fclose(ficresvpl);
                   7311: 
                   7312:     /*---------- End : free ----------------*/
                   7313:     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   7314:     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   7315:   }  /* mle==-3 arrives here for freeing */
1.164     brouard  7316:  /* endfree:*/
1.141     brouard  7317:     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126     brouard  7318:     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
                   7319:     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   7320:     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   7321:     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   7322:     free_matrix(covar,0,NCOVMAX,1,n);
                   7323:     free_matrix(matcov,1,npar,1,npar);
                   7324:     /*free_vector(delti,1,npar);*/
                   7325:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
                   7326:     free_matrix(agev,1,maxwav,1,imx);
                   7327:     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
                   7328: 
1.145     brouard  7329:     free_ivector(ncodemax,1,NCOVMAX);
                   7330:     free_ivector(Tvar,1,NCOVMAX);
                   7331:     free_ivector(Tprod,1,NCOVMAX);
                   7332:     free_ivector(Tvaraff,1,NCOVMAX);
                   7333:     free_ivector(Tage,1,NCOVMAX);
1.126     brouard  7334: 
                   7335:     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
                   7336:     free_imatrix(codtab,1,100,1,10);
                   7337:   fflush(fichtm);
                   7338:   fflush(ficgp);
                   7339:   
                   7340: 
                   7341:   if((nberr >0) || (nbwarn>0)){
                   7342:     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
                   7343:     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
                   7344:   }else{
                   7345:     printf("End of Imach\n");
                   7346:     fprintf(ficlog,"End of Imach\n");
                   7347:   }
                   7348:   printf("See log file on %s\n",filelog);
                   7349:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
1.157     brouard  7350:   /*(void) gettimeofday(&end_time,&tzp);*/
                   7351:   rend_time = time(NULL);  
                   7352:   end_time = *localtime(&rend_time);
                   7353:   /* tml = *localtime(&end_time.tm_sec); */
                   7354:   strcpy(strtend,asctime(&end_time));
1.126     brouard  7355:   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
                   7356:   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
1.157     brouard  7357:   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126     brouard  7358: 
1.157     brouard  7359:   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
                   7360:   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
                   7361:   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126     brouard  7362:   /*  printf("Total time was %d uSec.\n", total_usecs);*/
                   7363: /*   if(fileappend(fichtm,optionfilehtm)){ */
                   7364:   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   7365:   fclose(fichtm);
                   7366:   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
                   7367:   fclose(fichtmcov);
                   7368:   fclose(ficgp);
                   7369:   fclose(ficlog);
                   7370:   /*------ End -----------*/
                   7371: 
                   7372: 
                   7373:    printf("Before Current directory %s!\n",pathcd);
1.184   ! brouard  7374: #ifdef WIN32
        !          7375:    if (_chdir(pathcd) != 0)
        !          7376:           printf("Can't move to directory %s!\n",path);
        !          7377:    if(_getcwd(pathcd,MAXLINE) > 0)
        !          7378: #else
1.126     brouard  7379:    if(chdir(pathcd) != 0)
1.184   ! brouard  7380:           printf("Can't move to directory %s!\n", path);
        !          7381:    if (getcwd(pathcd, MAXLINE) > 0)
        !          7382: #endif 
1.126     brouard  7383:     printf("Current directory %s!\n",pathcd);
                   7384:   /*strcat(plotcmd,CHARSEPARATOR);*/
                   7385:   sprintf(plotcmd,"gnuplot");
1.157     brouard  7386: #ifdef _WIN32
1.126     brouard  7387:   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
                   7388: #endif
                   7389:   if(!stat(plotcmd,&info)){
1.158     brouard  7390:     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126     brouard  7391:     if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158     brouard  7392:       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126     brouard  7393:     }else
                   7394:       strcpy(pplotcmd,plotcmd);
1.157     brouard  7395: #ifdef __unix
1.126     brouard  7396:     strcpy(plotcmd,GNUPLOTPROGRAM);
                   7397:     if(!stat(plotcmd,&info)){
1.158     brouard  7398:       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126     brouard  7399:     }else
                   7400:       strcpy(pplotcmd,plotcmd);
                   7401: #endif
                   7402:   }else
                   7403:     strcpy(pplotcmd,plotcmd);
                   7404:   
                   7405:   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158     brouard  7406:   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126     brouard  7407: 
                   7408:   if((outcmd=system(plotcmd)) != 0){
1.158     brouard  7409:     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154     brouard  7410:     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152     brouard  7411:     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150     brouard  7412:     if((outcmd=system(plotcmd)) != 0)
1.153     brouard  7413:       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126     brouard  7414:   }
1.158     brouard  7415:   printf(" Successful, please wait...");
1.126     brouard  7416:   while (z[0] != 'q') {
                   7417:     /* chdir(path); */
1.154     brouard  7418:     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126     brouard  7419:     scanf("%s",z);
                   7420: /*     if (z[0] == 'c') system("./imach"); */
                   7421:     if (z[0] == 'e') {
1.158     brouard  7422: #ifdef __APPLE__
1.152     brouard  7423:       sprintf(pplotcmd, "open %s", optionfilehtm);
1.157     brouard  7424: #elif __linux
                   7425:       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153     brouard  7426: #else
1.152     brouard  7427:       sprintf(pplotcmd, "%s", optionfilehtm);
1.153     brouard  7428: #endif
                   7429:       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
                   7430:       system(pplotcmd);
1.126     brouard  7431:     }
                   7432:     else if (z[0] == 'g') system(plotcmd);
                   7433:     else if (z[0] == 'q') exit(0);
                   7434:   }
                   7435:   end:
                   7436:   while (z[0] != 'q') {
                   7437:     printf("\nType  q for exiting: ");
                   7438:     scanf("%s",z);
                   7439:   }
                   7440: }

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