File:  [Local Repository] / imach / src / imach.c
Revision 1.153: download - view: text, annotated - select for diffs
Fri Jun 20 16:45:46 2014 UTC (9 years, 11 months ago) by brouard
Branches: MAIN
CVS tags: HEAD
Summary: If 3 live state, convergence to period prevalence on same graph
Author: Brouard

    1: /* $Id: imach.c,v 1.153 2014/06/20 16:45:46 brouard Exp $
    2:   $State: Exp $
    3:   $Log: imach.c,v $
    4:   Revision 1.153  2014/06/20 16:45:46  brouard
    5:   Summary: If 3 live state, convergence to period prevalence on same graph
    6:   Author: Brouard
    7: 
    8:   Revision 1.152  2014/06/18 17:54:09  brouard
    9:   Summary: open browser, use gnuplot on same dir than imach if not found in the path
   10: 
   11:   Revision 1.151  2014/06/18 16:43:30  brouard
   12:   *** empty log message ***
   13: 
   14:   Revision 1.150  2014/06/18 16:42:35  brouard
   15:   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   16:   Author: brouard
   17: 
   18:   Revision 1.149  2014/06/18 15:51:14  brouard
   19:   Summary: Some fixes in parameter files errors
   20:   Author: Nicolas Brouard
   21: 
   22:   Revision 1.148  2014/06/17 17:38:48  brouard
   23:   Summary: Nothing new
   24:   Author: Brouard
   25: 
   26:   Just a new packaging for OS/X version 0.98nS
   27: 
   28:   Revision 1.147  2014/06/16 10:33:11  brouard
   29:   *** empty log message ***
   30: 
   31:   Revision 1.146  2014/06/16 10:20:28  brouard
   32:   Summary: Merge
   33:   Author: Brouard
   34: 
   35:   Merge, before building revised version.
   36: 
   37:   Revision 1.145  2014/06/10 21:23:15  brouard
   38:   Summary: Debugging with valgrind
   39:   Author: Nicolas Brouard
   40: 
   41:   Lot of changes in order to output the results with some covariates
   42:   After the Edimburgh REVES conference 2014, it seems mandatory to
   43:   improve the code.
   44:   No more memory valgrind error but a lot has to be done in order to
   45:   continue the work of splitting the code into subroutines.
   46:   Also, decodemodel has been improved. Tricode is still not
   47:   optimal. nbcode should be improved. Documentation has been added in
   48:   the source code.
   49: 
   50:   Revision 1.143  2014/01/26 09:45:38  brouard
   51:   Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   52: 
   53:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   54:   (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   55: 
   56:   Revision 1.142  2014/01/26 03:57:36  brouard
   57:   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   58: 
   59:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   60: 
   61:   Revision 1.141  2014/01/26 02:42:01  brouard
   62:   * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   63: 
   64:   Revision 1.140  2011/09/02 10:37:54  brouard
   65:   Summary: times.h is ok with mingw32 now.
   66: 
   67:   Revision 1.139  2010/06/14 07:50:17  brouard
   68:   After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   69:   I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   70: 
   71:   Revision 1.138  2010/04/30 18:19:40  brouard
   72:   *** empty log message ***
   73: 
   74:   Revision 1.137  2010/04/29 18:11:38  brouard
   75:   (Module): Checking covariates for more complex models
   76:   than V1+V2. A lot of change to be done. Unstable.
   77: 
   78:   Revision 1.136  2010/04/26 20:30:53  brouard
   79:   (Module): merging some libgsl code. Fixing computation
   80:   of likelione (using inter/intrapolation if mle = 0) in order to
   81:   get same likelihood as if mle=1.
   82:   Some cleaning of code and comments added.
   83: 
   84:   Revision 1.135  2009/10/29 15:33:14  brouard
   85:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   86: 
   87:   Revision 1.134  2009/10/29 13:18:53  brouard
   88:   (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   89: 
   90:   Revision 1.133  2009/07/06 10:21:25  brouard
   91:   just nforces
   92: 
   93:   Revision 1.132  2009/07/06 08:22:05  brouard
   94:   Many tings
   95: 
   96:   Revision 1.131  2009/06/20 16:22:47  brouard
   97:   Some dimensions resccaled
   98: 
   99:   Revision 1.130  2009/05/26 06:44:34  brouard
  100:   (Module): Max Covariate is now set to 20 instead of 8. A
  101:   lot of cleaning with variables initialized to 0. Trying to make
  102:   V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
  103: 
  104:   Revision 1.129  2007/08/31 13:49:27  lievre
  105:   Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
  106: 
  107:   Revision 1.128  2006/06/30 13:02:05  brouard
  108:   (Module): Clarifications on computing e.j
  109: 
  110:   Revision 1.127  2006/04/28 18:11:50  brouard
  111:   (Module): Yes the sum of survivors was wrong since
  112:   imach-114 because nhstepm was no more computed in the age
  113:   loop. Now we define nhstepma in the age loop.
  114:   (Module): In order to speed up (in case of numerous covariates) we
  115:   compute health expectancies (without variances) in a first step
  116:   and then all the health expectancies with variances or standard
  117:   deviation (needs data from the Hessian matrices) which slows the
  118:   computation.
  119:   In the future we should be able to stop the program is only health
  120:   expectancies and graph are needed without standard deviations.
  121: 
  122:   Revision 1.126  2006/04/28 17:23:28  brouard
  123:   (Module): Yes the sum of survivors was wrong since
  124:   imach-114 because nhstepm was no more computed in the age
  125:   loop. Now we define nhstepma in the age loop.
  126:   Version 0.98h
  127: 
  128:   Revision 1.125  2006/04/04 15:20:31  lievre
  129:   Errors in calculation of health expectancies. Age was not initialized.
  130:   Forecasting file added.
  131: 
  132:   Revision 1.124  2006/03/22 17:13:53  lievre
  133:   Parameters are printed with %lf instead of %f (more numbers after the comma).
  134:   The log-likelihood is printed in the log file
  135: 
  136:   Revision 1.123  2006/03/20 10:52:43  brouard
  137:   * imach.c (Module): <title> changed, corresponds to .htm file
  138:   name. <head> headers where missing.
  139: 
  140:   * imach.c (Module): Weights can have a decimal point as for
  141:   English (a comma might work with a correct LC_NUMERIC environment,
  142:   otherwise the weight is truncated).
  143:   Modification of warning when the covariates values are not 0 or
  144:   1.
  145:   Version 0.98g
  146: 
  147:   Revision 1.122  2006/03/20 09:45:41  brouard
  148:   (Module): Weights can have a decimal point as for
  149:   English (a comma might work with a correct LC_NUMERIC environment,
  150:   otherwise the weight is truncated).
  151:   Modification of warning when the covariates values are not 0 or
  152:   1.
  153:   Version 0.98g
  154: 
  155:   Revision 1.121  2006/03/16 17:45:01  lievre
  156:   * imach.c (Module): Comments concerning covariates added
  157: 
  158:   * imach.c (Module): refinements in the computation of lli if
  159:   status=-2 in order to have more reliable computation if stepm is
  160:   not 1 month. Version 0.98f
  161: 
  162:   Revision 1.120  2006/03/16 15:10:38  lievre
  163:   (Module): refinements in the computation of lli if
  164:   status=-2 in order to have more reliable computation if stepm is
  165:   not 1 month. Version 0.98f
  166: 
  167:   Revision 1.119  2006/03/15 17:42:26  brouard
  168:   (Module): Bug if status = -2, the loglikelihood was
  169:   computed as likelihood omitting the logarithm. Version O.98e
  170: 
  171:   Revision 1.118  2006/03/14 18:20:07  brouard
  172:   (Module): varevsij Comments added explaining the second
  173:   table of variances if popbased=1 .
  174:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
  175:   (Module): Function pstamp added
  176:   (Module): Version 0.98d
  177: 
  178:   Revision 1.117  2006/03/14 17:16:22  brouard
  179:   (Module): varevsij Comments added explaining the second
  180:   table of variances if popbased=1 .
  181:   (Module): Covariances of eij, ekl added, graphs fixed, new html link.
  182:   (Module): Function pstamp added
  183:   (Module): Version 0.98d
  184: 
  185:   Revision 1.116  2006/03/06 10:29:27  brouard
  186:   (Module): Variance-covariance wrong links and
  187:   varian-covariance of ej. is needed (Saito).
  188: 
  189:   Revision 1.115  2006/02/27 12:17:45  brouard
  190:   (Module): One freematrix added in mlikeli! 0.98c
  191: 
  192:   Revision 1.114  2006/02/26 12:57:58  brouard
  193:   (Module): Some improvements in processing parameter
  194:   filename with strsep.
  195: 
  196:   Revision 1.113  2006/02/24 14:20:24  brouard
  197:   (Module): Memory leaks checks with valgrind and:
  198:   datafile was not closed, some imatrix were not freed and on matrix
  199:   allocation too.
  200: 
  201:   Revision 1.112  2006/01/30 09:55:26  brouard
  202:   (Module): Back to gnuplot.exe instead of wgnuplot.exe
  203: 
  204:   Revision 1.111  2006/01/25 20:38:18  brouard
  205:   (Module): Lots of cleaning and bugs added (Gompertz)
  206:   (Module): Comments can be added in data file. Missing date values
  207:   can be a simple dot '.'.
  208: 
  209:   Revision 1.110  2006/01/25 00:51:50  brouard
  210:   (Module): Lots of cleaning and bugs added (Gompertz)
  211: 
  212:   Revision 1.109  2006/01/24 19:37:15  brouard
  213:   (Module): Comments (lines starting with a #) are allowed in data.
  214: 
  215:   Revision 1.108  2006/01/19 18:05:42  lievre
  216:   Gnuplot problem appeared...
  217:   To be fixed
  218: 
  219:   Revision 1.107  2006/01/19 16:20:37  brouard
  220:   Test existence of gnuplot in imach path
  221: 
  222:   Revision 1.106  2006/01/19 13:24:36  brouard
  223:   Some cleaning and links added in html output
  224: 
  225:   Revision 1.105  2006/01/05 20:23:19  lievre
  226:   *** empty log message ***
  227: 
  228:   Revision 1.104  2005/09/30 16:11:43  lievre
  229:   (Module): sump fixed, loop imx fixed, and simplifications.
  230:   (Module): If the status is missing at the last wave but we know
  231:   that the person is alive, then we can code his/her status as -2
  232:   (instead of missing=-1 in earlier versions) and his/her
  233:   contributions to the likelihood is 1 - Prob of dying from last
  234:   health status (= 1-p13= p11+p12 in the easiest case of somebody in
  235:   the healthy state at last known wave). Version is 0.98
  236: 
  237:   Revision 1.103  2005/09/30 15:54:49  lievre
  238:   (Module): sump fixed, loop imx fixed, and simplifications.
  239: 
  240:   Revision 1.102  2004/09/15 17:31:30  brouard
  241:   Add the possibility to read data file including tab characters.
  242: 
  243:   Revision 1.101  2004/09/15 10:38:38  brouard
  244:   Fix on curr_time
  245: 
  246:   Revision 1.100  2004/07/12 18:29:06  brouard
  247:   Add version for Mac OS X. Just define UNIX in Makefile
  248: 
  249:   Revision 1.99  2004/06/05 08:57:40  brouard
  250:   *** empty log message ***
  251: 
  252:   Revision 1.98  2004/05/16 15:05:56  brouard
  253:   New version 0.97 . First attempt to estimate force of mortality
  254:   directly from the data i.e. without the need of knowing the health
  255:   state at each age, but using a Gompertz model: log u =a + b*age .
  256:   This is the basic analysis of mortality and should be done before any
  257:   other analysis, in order to test if the mortality estimated from the
  258:   cross-longitudinal survey is different from the mortality estimated
  259:   from other sources like vital statistic data.
  260: 
  261:   The same imach parameter file can be used but the option for mle should be -3.
  262: 
  263:   Agnès, who wrote this part of the code, tried to keep most of the
  264:   former routines in order to include the new code within the former code.
  265: 
  266:   The output is very simple: only an estimate of the intercept and of
  267:   the slope with 95% confident intervals.
  268: 
  269:   Current limitations:
  270:   A) Even if you enter covariates, i.e. with the
  271:   model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
  272:   B) There is no computation of Life Expectancy nor Life Table.
  273: 
  274:   Revision 1.97  2004/02/20 13:25:42  lievre
  275:   Version 0.96d. Population forecasting command line is (temporarily)
  276:   suppressed.
  277: 
  278:   Revision 1.96  2003/07/15 15:38:55  brouard
  279:   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
  280:   rewritten within the same printf. Workaround: many printfs.
  281: 
  282:   Revision 1.95  2003/07/08 07:54:34  brouard
  283:   * imach.c (Repository):
  284:   (Repository): Using imachwizard code to output a more meaningful covariance
  285:   matrix (cov(a12,c31) instead of numbers.
  286: 
  287:   Revision 1.94  2003/06/27 13:00:02  brouard
  288:   Just cleaning
  289: 
  290:   Revision 1.93  2003/06/25 16:33:55  brouard
  291:   (Module): On windows (cygwin) function asctime_r doesn't
  292:   exist so I changed back to asctime which exists.
  293:   (Module): Version 0.96b
  294: 
  295:   Revision 1.92  2003/06/25 16:30:45  brouard
  296:   (Module): On windows (cygwin) function asctime_r doesn't
  297:   exist so I changed back to asctime which exists.
  298: 
  299:   Revision 1.91  2003/06/25 15:30:29  brouard
  300:   * imach.c (Repository): Duplicated warning errors corrected.
  301:   (Repository): Elapsed time after each iteration is now output. It
  302:   helps to forecast when convergence will be reached. Elapsed time
  303:   is stamped in powell.  We created a new html file for the graphs
  304:   concerning matrix of covariance. It has extension -cov.htm.
  305: 
  306:   Revision 1.90  2003/06/24 12:34:15  brouard
  307:   (Module): Some bugs corrected for windows. Also, when
  308:   mle=-1 a template is output in file "or"mypar.txt with the design
  309:   of the covariance matrix to be input.
  310: 
  311:   Revision 1.89  2003/06/24 12:30:52  brouard
  312:   (Module): Some bugs corrected for windows. Also, when
  313:   mle=-1 a template is output in file "or"mypar.txt with the design
  314:   of the covariance matrix to be input.
  315: 
  316:   Revision 1.88  2003/06/23 17:54:56  brouard
  317:   * 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.
  318: 
  319:   Revision 1.87  2003/06/18 12:26:01  brouard
  320:   Version 0.96
  321: 
  322:   Revision 1.86  2003/06/17 20:04:08  brouard
  323:   (Module): Change position of html and gnuplot routines and added
  324:   routine fileappend.
  325: 
  326:   Revision 1.85  2003/06/17 13:12:43  brouard
  327:   * imach.c (Repository): Check when date of death was earlier that
  328:   current date of interview. It may happen when the death was just
  329:   prior to the death. In this case, dh was negative and likelihood
  330:   was wrong (infinity). We still send an "Error" but patch by
  331:   assuming that the date of death was just one stepm after the
  332:   interview.
  333:   (Repository): Because some people have very long ID (first column)
  334:   we changed int to long in num[] and we added a new lvector for
  335:   memory allocation. But we also truncated to 8 characters (left
  336:   truncation)
  337:   (Repository): No more line truncation errors.
  338: 
  339:   Revision 1.84  2003/06/13 21:44:43  brouard
  340:   * imach.c (Repository): Replace "freqsummary" at a correct
  341:   place. It differs from routine "prevalence" which may be called
  342:   many times. Probs is memory consuming and must be used with
  343:   parcimony.
  344:   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
  345: 
  346:   Revision 1.83  2003/06/10 13:39:11  lievre
  347:   *** empty log message ***
  348: 
  349:   Revision 1.82  2003/06/05 15:57:20  brouard
  350:   Add log in  imach.c and  fullversion number is now printed.
  351: 
  352: */
  353: /*
  354:    Interpolated Markov Chain
  355: 
  356:   Short summary of the programme:
  357:   
  358:   This program computes Healthy Life Expectancies from
  359:   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
  360:   first survey ("cross") where individuals from different ages are
  361:   interviewed on their health status or degree of disability (in the
  362:   case of a health survey which is our main interest) -2- at least a
  363:   second wave of interviews ("longitudinal") which measure each change
  364:   (if any) in individual health status.  Health expectancies are
  365:   computed from the time spent in each health state according to a
  366:   model. More health states you consider, more time is necessary to reach the
  367:   Maximum Likelihood of the parameters involved in the model.  The
  368:   simplest model is the multinomial logistic model where pij is the
  369:   probability to be observed in state j at the second wave
  370:   conditional to be observed in state i at the first wave. Therefore
  371:   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
  372:   'age' is age and 'sex' is a covariate. If you want to have a more
  373:   complex model than "constant and age", you should modify the program
  374:   where the markup *Covariates have to be included here again* invites
  375:   you to do it.  More covariates you add, slower the
  376:   convergence.
  377: 
  378:   The advantage of this computer programme, compared to a simple
  379:   multinomial logistic model, is clear when the delay between waves is not
  380:   identical for each individual. Also, if a individual missed an
  381:   intermediate interview, the information is lost, but taken into
  382:   account using an interpolation or extrapolation.  
  383: 
  384:   hPijx is the probability to be observed in state i at age x+h
  385:   conditional to the observed state i at age x. The delay 'h' can be
  386:   split into an exact number (nh*stepm) of unobserved intermediate
  387:   states. This elementary transition (by month, quarter,
  388:   semester or year) is modelled as a multinomial logistic.  The hPx
  389:   matrix is simply the matrix product of nh*stepm elementary matrices
  390:   and the contribution of each individual to the likelihood is simply
  391:   hPijx.
  392: 
  393:   Also this programme outputs the covariance matrix of the parameters but also
  394:   of the life expectancies. It also computes the period (stable) prevalence. 
  395:   
  396:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
  397:            Institut national d'études démographiques, Paris.
  398:   This software have been partly granted by Euro-REVES, a concerted action
  399:   from the European Union.
  400:   It is copyrighted identically to a GNU software product, ie programme and
  401:   software can be distributed freely for non commercial use. Latest version
  402:   can be accessed at http://euroreves.ined.fr/imach .
  403: 
  404:   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
  405:   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
  406:   
  407:   **********************************************************************/
  408: /*
  409:   main
  410:   read parameterfile
  411:   read datafile
  412:   concatwav
  413:   freqsummary
  414:   if (mle >= 1)
  415:     mlikeli
  416:   print results files
  417:   if mle==1 
  418:      computes hessian
  419:   read end of parameter file: agemin, agemax, bage, fage, estepm
  420:       begin-prev-date,...
  421:   open gnuplot file
  422:   open html file
  423:   period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
  424:    for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
  425:                                   | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
  426:     freexexit2 possible for memory heap.
  427: 
  428:   h Pij x                         | pij_nom  ficrestpij
  429:    # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
  430:        1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
  431:        1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
  432: 
  433:        1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
  434:        1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
  435:   variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
  436:    Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
  437:    Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
  438: 
  439:   forecasting if prevfcast==1 prevforecast call prevalence()
  440:   health expectancies
  441:   Variance-covariance of DFLE
  442:   prevalence()
  443:    movingaverage()
  444:   varevsij() 
  445:   if popbased==1 varevsij(,popbased)
  446:   total life expectancies
  447:   Variance of period (stable) prevalence
  448:  end
  449: */
  450: 
  451: 
  452: 
  453:  
  454: #include <math.h>
  455: #include <stdio.h>
  456: #include <stdlib.h>
  457: #include <string.h>
  458: #include <unistd.h>
  459: 
  460: #include <limits.h>
  461: #include <sys/types.h>
  462: #include <sys/stat.h>
  463: #include <errno.h>
  464: extern int errno;
  465: 
  466: #ifdef LINUX
  467: #include <time.h>
  468: #include "timeval.h"
  469: #else
  470: #include <sys/time.h>
  471: #endif
  472: 
  473: #ifdef GSL
  474: #include <gsl/gsl_errno.h>
  475: #include <gsl/gsl_multimin.h>
  476: #endif
  477: 
  478: /* #include <libintl.h> */
  479: /* #define _(String) gettext (String) */
  480: 
  481: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
  482: 
  483: #define GNUPLOTPROGRAM "gnuplot"
  484: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
  485: #define FILENAMELENGTH 132
  486: 
  487: #define	GLOCK_ERROR_NOPATH		-1	/* empty path */
  488: #define	GLOCK_ERROR_GETCWD		-2	/* cannot get cwd */
  489: 
  490: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
  491: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
  492: 
  493: #define NINTERVMAX 8
  494: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
  495: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
  496: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
  497: #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
  498: #define MAXN 20000
  499: #define YEARM 12. /**< Number of months per year */
  500: #define AGESUP 130
  501: #define AGEBASE 40
  502: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
  503: #ifdef UNIX
  504: #define DIRSEPARATOR '/'
  505: #define CHARSEPARATOR "/"
  506: #define ODIRSEPARATOR '\\'
  507: #else
  508: #define DIRSEPARATOR '\\'
  509: #define CHARSEPARATOR "\\"
  510: #define ODIRSEPARATOR '/'
  511: #endif
  512: 
  513: /* $Id: imach.c,v 1.153 2014/06/20 16:45:46 brouard Exp $ */
  514: /* $State: Exp $ */
  515: 
  516: char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
  517: char fullversion[]="$Revision: 1.153 $ $Date: 2014/06/20 16:45:46 $"; 
  518: char strstart[80];
  519: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
  520: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  521: int nvar=0, nforce=0; /* Number of variables, number of forces */
  522: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
  523: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
  524: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
  525: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
  526: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
  527: int cptcovprodnoage=0; /**< Number of covariate products without age */   
  528: int cptcoveff=0; /* Total number of covariates to vary for printing results */
  529: int cptcov=0; /* Working variable */
  530: int npar=NPARMAX;
  531: int nlstate=2; /* Number of live states */
  532: int ndeath=1; /* Number of dead states */
  533: int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
  534: int popbased=0;
  535: 
  536: int *wav; /* Number of waves for this individuual 0 is possible */
  537: int maxwav=0; /* Maxim number of waves */
  538: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
  539: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
  540: int gipmx=0, gsw=0; /* Global variables on the number of contributions 
  541: 		   to the likelihood and the sum of weights (done by funcone)*/
  542: int mle=1, weightopt=0;
  543: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  544: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  545: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
  546: 	   * wave mi and wave mi+1 is not an exact multiple of stepm. */
  547: double jmean=1; /* Mean space between 2 waves */
  548: double **matprod2(); /* test */
  549: double **oldm, **newm, **savm; /* Working pointers to matrices */
  550: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
  551: /*FILE *fic ; */ /* Used in readdata only */
  552: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  553: FILE *ficlog, *ficrespow;
  554: int globpr=0; /* Global variable for printing or not */
  555: double fretone; /* Only one call to likelihood */
  556: long ipmx=0; /* Number of contributions */
  557: double sw; /* Sum of weights */
  558: char filerespow[FILENAMELENGTH];
  559: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
  560: FILE *ficresilk;
  561: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
  562: FILE *ficresprobmorprev;
  563: FILE *fichtm, *fichtmcov; /* Html File */
  564: FILE *ficreseij;
  565: char filerese[FILENAMELENGTH];
  566: FILE *ficresstdeij;
  567: char fileresstde[FILENAMELENGTH];
  568: FILE *ficrescveij;
  569: char filerescve[FILENAMELENGTH];
  570: FILE  *ficresvij;
  571: char fileresv[FILENAMELENGTH];
  572: FILE  *ficresvpl;
  573: char fileresvpl[FILENAMELENGTH];
  574: char title[MAXLINE];
  575: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
  576: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  577: char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
  578: char command[FILENAMELENGTH];
  579: int  outcmd=0;
  580: 
  581: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
  582: 
  583: char filelog[FILENAMELENGTH]; /* Log file */
  584: char filerest[FILENAMELENGTH];
  585: char fileregp[FILENAMELENGTH];
  586: char popfile[FILENAMELENGTH];
  587: 
  588: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
  589: 
  590: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
  591: struct timezone tzp;
  592: extern int gettimeofday();
  593: struct tm tmg, tm, tmf, *gmtime(), *localtime();
  594: long time_value;
  595: extern long time();
  596: char strcurr[80], strfor[80];
  597: 
  598: char *endptr;
  599: long lval;
  600: double dval;
  601: 
  602: #define NR_END 1
  603: #define FREE_ARG char*
  604: #define FTOL 1.0e-10
  605: 
  606: #define NRANSI 
  607: #define ITMAX 200 
  608: 
  609: #define TOL 2.0e-4 
  610: 
  611: #define CGOLD 0.3819660 
  612: #define ZEPS 1.0e-10 
  613: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
  614: 
  615: #define GOLD 1.618034 
  616: #define GLIMIT 100.0 
  617: #define TINY 1.0e-20 
  618: 
  619: static double maxarg1,maxarg2;
  620: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
  621: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
  622:   
  623: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  624: #define rint(a) floor(a+0.5)
  625: 
  626: static double sqrarg;
  627: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  628: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
  629: int agegomp= AGEGOMP;
  630: 
  631: int imx; 
  632: int stepm=1;
  633: /* Stepm, step in month: minimum step interpolation*/
  634: 
  635: int estepm;
  636: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  637: 
  638: int m,nb;
  639: long *num;
  640: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
  641: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  642: double **pmmij, ***probs;
  643: double *ageexmed,*agecens;
  644: double dateintmean=0;
  645: 
  646: double *weight;
  647: int **s; /* Status */
  648: double *agedc;
  649: double  **covar; /**< covar[j,i], value of jth covariate for individual i,
  650: 		  * covar=matrix(0,NCOVMAX,1,n); 
  651: 		  * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
  652: double  idx; 
  653: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
  654: int *Ndum; /** Freq of modality (tricode */
  655: int **codtab; /**< codtab=imatrix(1,100,1,10); */
  656: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
  657: double *lsurv, *lpop, *tpop;
  658: 
  659: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
  660: double ftolhess; /**< Tolerance for computing hessian */
  661: 
  662: /**************** split *************************/
  663: static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
  664: {
  665:   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
  666:      the name of the file (name), its extension only (ext) and its first part of the name (finame)
  667:   */ 
  668:   char	*ss;				/* pointer */
  669:   int	l1, l2;				/* length counters */
  670: 
  671:   l1 = strlen(path );			/* length of path */
  672:   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
  673:   ss= strrchr( path, DIRSEPARATOR );		/* find last / */
  674:   if ( ss == NULL ) {			/* no directory, so determine current directory */
  675:     strcpy( name, path );		/* we got the fullname name because no directory */
  676:     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
  677:       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
  678:     /* get current working directory */
  679:     /*    extern  char* getcwd ( char *buf , int len);*/
  680:     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
  681:       return( GLOCK_ERROR_GETCWD );
  682:     }
  683:     /* got dirc from getcwd*/
  684:     printf(" DIRC = %s \n",dirc);
  685:   } else {				/* strip direcotry from path */
  686:     ss++;				/* after this, the filename */
  687:     l2 = strlen( ss );			/* length of filename */
  688:     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
  689:     strcpy( name, ss );		/* save file name */
  690:     strncpy( dirc, path, l1 - l2 );	/* now the directory */
  691:     dirc[l1-l2] = 0;			/* add zero */
  692:     printf(" DIRC2 = %s \n",dirc);
  693:   }
  694:   /* We add a separator at the end of dirc if not exists */
  695:   l1 = strlen( dirc );			/* length of directory */
  696:   if( dirc[l1-1] != DIRSEPARATOR ){
  697:     dirc[l1] =  DIRSEPARATOR;
  698:     dirc[l1+1] = 0; 
  699:     printf(" DIRC3 = %s \n",dirc);
  700:   }
  701:   ss = strrchr( name, '.' );		/* find last / */
  702:   if (ss >0){
  703:     ss++;
  704:     strcpy(ext,ss);			/* save extension */
  705:     l1= strlen( name);
  706:     l2= strlen(ss)+1;
  707:     strncpy( finame, name, l1-l2);
  708:     finame[l1-l2]= 0;
  709:   }
  710: 
  711:   return( 0 );				/* we're done */
  712: }
  713: 
  714: 
  715: /******************************************/
  716: 
  717: void replace_back_to_slash(char *s, char*t)
  718: {
  719:   int i;
  720:   int lg=0;
  721:   i=0;
  722:   lg=strlen(t);
  723:   for(i=0; i<= lg; i++) {
  724:     (s[i] = t[i]);
  725:     if (t[i]== '\\') s[i]='/';
  726:   }
  727: }
  728: 
  729: char *trimbb(char *out, char *in)
  730: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
  731:   char *s;
  732:   s=out;
  733:   while (*in != '\0'){
  734:     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
  735:       in++;
  736:     }
  737:     *out++ = *in++;
  738:   }
  739:   *out='\0';
  740:   return s;
  741: }
  742: 
  743: char *cutl(char *blocc, char *alocc, char *in, char occ)
  744: {
  745:   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
  746:      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
  747:      gives blocc="abcdef2ghi" and alocc="j".
  748:      If occ is not found blocc is null and alocc is equal to in. Returns blocc
  749:   */
  750:   char *s, *t, *bl;
  751:   t=in;s=in;
  752:   while ((*in != occ) && (*in != '\0')){
  753:     *alocc++ = *in++;
  754:   }
  755:   if( *in == occ){
  756:     *(alocc)='\0';
  757:     s=++in;
  758:   }
  759:  
  760:   if (s == t) {/* occ not found */
  761:     *(alocc-(in-s))='\0';
  762:     in=s;
  763:   }
  764:   while ( *in != '\0'){
  765:     *blocc++ = *in++;
  766:   }
  767: 
  768:   *blocc='\0';
  769:   return t;
  770: }
  771: char *cutv(char *blocc, char *alocc, char *in, char occ)
  772: {
  773:   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
  774:      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
  775:      gives blocc="abcdef2ghi" and alocc="j".
  776:      If occ is not found blocc is null and alocc is equal to in. Returns alocc
  777:   */
  778:   char *s, *t;
  779:   t=in;s=in;
  780:   while (*in != '\0'){
  781:     while( *in == occ){
  782:       *blocc++ = *in++;
  783:       s=in;
  784:     }
  785:     *blocc++ = *in++;
  786:   }
  787:   if (s == t) /* occ not found */
  788:     *(blocc-(in-s))='\0';
  789:   else
  790:     *(blocc-(in-s)-1)='\0';
  791:   in=s;
  792:   while ( *in != '\0'){
  793:     *alocc++ = *in++;
  794:   }
  795: 
  796:   *alocc='\0';
  797:   return s;
  798: }
  799: 
  800: int nbocc(char *s, char occ)
  801: {
  802:   int i,j=0;
  803:   int lg=20;
  804:   i=0;
  805:   lg=strlen(s);
  806:   for(i=0; i<= lg; i++) {
  807:   if  (s[i] == occ ) j++;
  808:   }
  809:   return j;
  810: }
  811: 
  812: /* void cutv(char *u,char *v, char*t, char occ) */
  813: /* { */
  814: /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
  815: /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
  816: /*      gives u="abcdef2ghi" and v="j" *\/ */
  817: /*   int i,lg,j,p=0; */
  818: /*   i=0; */
  819: /*   lg=strlen(t); */
  820: /*   for(j=0; j<=lg-1; j++) { */
  821: /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
  822: /*   } */
  823: 
  824: /*   for(j=0; j<p; j++) { */
  825: /*     (u[j] = t[j]); */
  826: /*   } */
  827: /*      u[p]='\0'; */
  828: 
  829: /*    for(j=0; j<= lg; j++) { */
  830: /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
  831: /*   } */
  832: /* } */
  833: 
  834: /********************** nrerror ********************/
  835: 
  836: void nrerror(char error_text[])
  837: {
  838:   fprintf(stderr,"ERREUR ...\n");
  839:   fprintf(stderr,"%s\n",error_text);
  840:   exit(EXIT_FAILURE);
  841: }
  842: /*********************** vector *******************/
  843: double *vector(int nl, int nh)
  844: {
  845:   double *v;
  846:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
  847:   if (!v) nrerror("allocation failure in vector");
  848:   return v-nl+NR_END;
  849: }
  850: 
  851: /************************ free vector ******************/
  852: void free_vector(double*v, int nl, int nh)
  853: {
  854:   free((FREE_ARG)(v+nl-NR_END));
  855: }
  856: 
  857: /************************ivector *******************************/
  858: int *ivector(long nl,long nh)
  859: {
  860:   int *v;
  861:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
  862:   if (!v) nrerror("allocation failure in ivector");
  863:   return v-nl+NR_END;
  864: }
  865: 
  866: /******************free ivector **************************/
  867: void free_ivector(int *v, long nl, long nh)
  868: {
  869:   free((FREE_ARG)(v+nl-NR_END));
  870: }
  871: 
  872: /************************lvector *******************************/
  873: long *lvector(long nl,long nh)
  874: {
  875:   long *v;
  876:   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
  877:   if (!v) nrerror("allocation failure in ivector");
  878:   return v-nl+NR_END;
  879: }
  880: 
  881: /******************free lvector **************************/
  882: void free_lvector(long *v, long nl, long nh)
  883: {
  884:   free((FREE_ARG)(v+nl-NR_END));
  885: }
  886: 
  887: /******************* imatrix *******************************/
  888: int **imatrix(long nrl, long nrh, long ncl, long nch) 
  889:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
  890: { 
  891:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
  892:   int **m; 
  893:   
  894:   /* allocate pointers to rows */ 
  895:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
  896:   if (!m) nrerror("allocation failure 1 in matrix()"); 
  897:   m += NR_END; 
  898:   m -= nrl; 
  899:   
  900:   
  901:   /* allocate rows and set pointers to them */ 
  902:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
  903:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
  904:   m[nrl] += NR_END; 
  905:   m[nrl] -= ncl; 
  906:   
  907:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
  908:   
  909:   /* return pointer to array of pointers to rows */ 
  910:   return m; 
  911: } 
  912: 
  913: /****************** free_imatrix *************************/
  914: void free_imatrix(m,nrl,nrh,ncl,nch)
  915:       int **m;
  916:       long nch,ncl,nrh,nrl; 
  917:      /* free an int matrix allocated by imatrix() */ 
  918: { 
  919:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
  920:   free((FREE_ARG) (m+nrl-NR_END)); 
  921: } 
  922: 
  923: /******************* matrix *******************************/
  924: double **matrix(long nrl, long nrh, long ncl, long nch)
  925: {
  926:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
  927:   double **m;
  928: 
  929:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
  930:   if (!m) nrerror("allocation failure 1 in matrix()");
  931:   m += NR_END;
  932:   m -= nrl;
  933: 
  934:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
  935:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
  936:   m[nrl] += NR_END;
  937:   m[nrl] -= ncl;
  938: 
  939:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
  940:   return m;
  941:   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
  942: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
  943: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
  944:    */
  945: }
  946: 
  947: /*************************free matrix ************************/
  948: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
  949: {
  950:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
  951:   free((FREE_ARG)(m+nrl-NR_END));
  952: }
  953: 
  954: /******************* ma3x *******************************/
  955: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
  956: {
  957:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
  958:   double ***m;
  959: 
  960:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
  961:   if (!m) nrerror("allocation failure 1 in matrix()");
  962:   m += NR_END;
  963:   m -= nrl;
  964: 
  965:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
  966:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
  967:   m[nrl] += NR_END;
  968:   m[nrl] -= ncl;
  969: 
  970:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
  971: 
  972:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
  973:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
  974:   m[nrl][ncl] += NR_END;
  975:   m[nrl][ncl] -= nll;
  976:   for (j=ncl+1; j<=nch; j++) 
  977:     m[nrl][j]=m[nrl][j-1]+nlay;
  978:   
  979:   for (i=nrl+1; i<=nrh; i++) {
  980:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
  981:     for (j=ncl+1; j<=nch; j++) 
  982:       m[i][j]=m[i][j-1]+nlay;
  983:   }
  984:   return m; 
  985:   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
  986:            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
  987:   */
  988: }
  989: 
  990: /*************************free ma3x ************************/
  991: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
  992: {
  993:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
  994:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
  995:   free((FREE_ARG)(m+nrl-NR_END));
  996: }
  997: 
  998: /*************** function subdirf ***********/
  999: char *subdirf(char fileres[])
 1000: {
 1001:   /* Caution optionfilefiname is hidden */
 1002:   strcpy(tmpout,optionfilefiname);
 1003:   strcat(tmpout,"/"); /* Add to the right */
 1004:   strcat(tmpout,fileres);
 1005:   return tmpout;
 1006: }
 1007: 
 1008: /*************** function subdirf2 ***********/
 1009: char *subdirf2(char fileres[], char *preop)
 1010: {
 1011:   
 1012:   /* Caution optionfilefiname is hidden */
 1013:   strcpy(tmpout,optionfilefiname);
 1014:   strcat(tmpout,"/");
 1015:   strcat(tmpout,preop);
 1016:   strcat(tmpout,fileres);
 1017:   return tmpout;
 1018: }
 1019: 
 1020: /*************** function subdirf3 ***********/
 1021: char *subdirf3(char fileres[], char *preop, char *preop2)
 1022: {
 1023:   
 1024:   /* Caution optionfilefiname is hidden */
 1025:   strcpy(tmpout,optionfilefiname);
 1026:   strcat(tmpout,"/");
 1027:   strcat(tmpout,preop);
 1028:   strcat(tmpout,preop2);
 1029:   strcat(tmpout,fileres);
 1030:   return tmpout;
 1031: }
 1032: 
 1033: /***************** f1dim *************************/
 1034: extern int ncom; 
 1035: extern double *pcom,*xicom;
 1036: extern double (*nrfunc)(double []); 
 1037:  
 1038: double f1dim(double x) 
 1039: { 
 1040:   int j; 
 1041:   double f;
 1042:   double *xt; 
 1043:  
 1044:   xt=vector(1,ncom); 
 1045:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 1046:   f=(*nrfunc)(xt); 
 1047:   free_vector(xt,1,ncom); 
 1048:   return f; 
 1049: } 
 1050: 
 1051: /*****************brent *************************/
 1052: double brent(double ax, double bx, double cx, double (*f)(double), double tol, 	double *xmin) 
 1053: { 
 1054:   int iter; 
 1055:   double a,b,d,etemp;
 1056:   double fu,fv,fw,fx;
 1057:   double ftemp;
 1058:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
 1059:   double e=0.0; 
 1060:  
 1061:   a=(ax < cx ? ax : cx); 
 1062:   b=(ax > cx ? ax : cx); 
 1063:   x=w=v=bx; 
 1064:   fw=fv=fx=(*f)(x); 
 1065:   for (iter=1;iter<=ITMAX;iter++) { 
 1066:     xm=0.5*(a+b); 
 1067:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 1068:     /*		if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 1069:     printf(".");fflush(stdout);
 1070:     fprintf(ficlog,".");fflush(ficlog);
 1071: #ifdef DEBUG
 1072:     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);
 1073:     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);
 1074:     /*		if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 1075: #endif
 1076:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 1077:       *xmin=x; 
 1078:       return fx; 
 1079:     } 
 1080:     ftemp=fu;
 1081:     if (fabs(e) > tol1) { 
 1082:       r=(x-w)*(fx-fv); 
 1083:       q=(x-v)*(fx-fw); 
 1084:       p=(x-v)*q-(x-w)*r; 
 1085:       q=2.0*(q-r); 
 1086:       if (q > 0.0) p = -p; 
 1087:       q=fabs(q); 
 1088:       etemp=e; 
 1089:       e=d; 
 1090:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 1091: 	d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 1092:       else { 
 1093: 	d=p/q; 
 1094: 	u=x+d; 
 1095: 	if (u-a < tol2 || b-u < tol2) 
 1096: 	  d=SIGN(tol1,xm-x); 
 1097:       } 
 1098:     } else { 
 1099:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 1100:     } 
 1101:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 1102:     fu=(*f)(u); 
 1103:     if (fu <= fx) { 
 1104:       if (u >= x) a=x; else b=x; 
 1105:       SHFT(v,w,x,u) 
 1106: 	SHFT(fv,fw,fx,fu) 
 1107: 	} else { 
 1108: 	  if (u < x) a=u; else b=u; 
 1109: 	  if (fu <= fw || w == x) { 
 1110: 	    v=w; 
 1111: 	    w=u; 
 1112: 	    fv=fw; 
 1113: 	    fw=fu; 
 1114: 	  } else if (fu <= fv || v == x || v == w) { 
 1115: 	    v=u; 
 1116: 	    fv=fu; 
 1117: 	  } 
 1118: 	} 
 1119:   } 
 1120:   nrerror("Too many iterations in brent"); 
 1121:   *xmin=x; 
 1122:   return fx; 
 1123: } 
 1124: 
 1125: /****************** mnbrak ***********************/
 1126: 
 1127: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 1128: 	    double (*func)(double)) 
 1129: { 
 1130:   double ulim,u,r,q, dum;
 1131:   double fu; 
 1132:  
 1133:   *fa=(*func)(*ax); 
 1134:   *fb=(*func)(*bx); 
 1135:   if (*fb > *fa) { 
 1136:     SHFT(dum,*ax,*bx,dum) 
 1137:       SHFT(dum,*fb,*fa,dum) 
 1138:       } 
 1139:   *cx=(*bx)+GOLD*(*bx-*ax); 
 1140:   *fc=(*func)(*cx); 
 1141:   while (*fb > *fc) { 
 1142:     r=(*bx-*ax)*(*fb-*fc); 
 1143:     q=(*bx-*cx)*(*fb-*fa); 
 1144:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 1145:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 1146:     ulim=(*bx)+GLIMIT*(*cx-*bx); 
 1147:     if ((*bx-u)*(u-*cx) > 0.0) { 
 1148:       fu=(*func)(u); 
 1149:     } else if ((*cx-u)*(u-ulim) > 0.0) { 
 1150:       fu=(*func)(u); 
 1151:       if (fu < *fc) { 
 1152: 	SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 1153: 	  SHFT(*fb,*fc,fu,(*func)(u)) 
 1154: 	  } 
 1155:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 1156:       u=ulim; 
 1157:       fu=(*func)(u); 
 1158:     } else { 
 1159:       u=(*cx)+GOLD*(*cx-*bx); 
 1160:       fu=(*func)(u); 
 1161:     } 
 1162:     SHFT(*ax,*bx,*cx,u) 
 1163:       SHFT(*fa,*fb,*fc,fu) 
 1164:       } 
 1165: } 
 1166: 
 1167: /*************** linmin ************************/
 1168: 
 1169: int ncom; 
 1170: double *pcom,*xicom;
 1171: double (*nrfunc)(double []); 
 1172:  
 1173: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 1174: { 
 1175:   double brent(double ax, double bx, double cx, 
 1176: 	       double (*f)(double), double tol, double *xmin); 
 1177:   double f1dim(double x); 
 1178:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 1179: 	      double *fc, double (*func)(double)); 
 1180:   int j; 
 1181:   double xx,xmin,bx,ax; 
 1182:   double fx,fb,fa;
 1183:  
 1184:   ncom=n; 
 1185:   pcom=vector(1,n); 
 1186:   xicom=vector(1,n); 
 1187:   nrfunc=func; 
 1188:   for (j=1;j<=n;j++) { 
 1189:     pcom[j]=p[j]; 
 1190:     xicom[j]=xi[j]; 
 1191:   } 
 1192:   ax=0.0; 
 1193:   xx=1.0; 
 1194:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 1195:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 1196: #ifdef DEBUG
 1197:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 1198:   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 1199: #endif
 1200:   for (j=1;j<=n;j++) { 
 1201:     xi[j] *= xmin; 
 1202:     p[j] += xi[j]; 
 1203:   } 
 1204:   free_vector(xicom,1,n); 
 1205:   free_vector(pcom,1,n); 
 1206: } 
 1207: 
 1208: char *asc_diff_time(long time_sec, char ascdiff[])
 1209: {
 1210:   long sec_left, days, hours, minutes;
 1211:   days = (time_sec) / (60*60*24);
 1212:   sec_left = (time_sec) % (60*60*24);
 1213:   hours = (sec_left) / (60*60) ;
 1214:   sec_left = (sec_left) %(60*60);
 1215:   minutes = (sec_left) /60;
 1216:   sec_left = (sec_left) % (60);
 1217:   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
 1218:   return ascdiff;
 1219: }
 1220: 
 1221: /*************** powell ************************/
 1222: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 1223: 	    double (*func)(double [])) 
 1224: { 
 1225:   void linmin(double p[], double xi[], int n, double *fret, 
 1226: 	      double (*func)(double [])); 
 1227:   int i,ibig,j; 
 1228:   double del,t,*pt,*ptt,*xit;
 1229:   double fp,fptt;
 1230:   double *xits;
 1231:   int niterf, itmp;
 1232: 
 1233:   pt=vector(1,n); 
 1234:   ptt=vector(1,n); 
 1235:   xit=vector(1,n); 
 1236:   xits=vector(1,n); 
 1237:   *fret=(*func)(p); 
 1238:   for (j=1;j<=n;j++) pt[j]=p[j]; 
 1239:   for (*iter=1;;++(*iter)) { 
 1240:     fp=(*fret); 
 1241:     ibig=0; 
 1242:     del=0.0; 
 1243:     last_time=curr_time;
 1244:     (void) gettimeofday(&curr_time,&tzp);
 1245:     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 1246:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
 1247: /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
 1248:    for (i=1;i<=n;i++) {
 1249:       printf(" %d %.12f",i, p[i]);
 1250:       fprintf(ficlog," %d %.12lf",i, p[i]);
 1251:       fprintf(ficrespow," %.12lf", p[i]);
 1252:     }
 1253:     printf("\n");
 1254:     fprintf(ficlog,"\n");
 1255:     fprintf(ficrespow,"\n");fflush(ficrespow);
 1256:     if(*iter <=3){
 1257:       tm = *localtime(&curr_time.tv_sec);
 1258:       strcpy(strcurr,asctime(&tm));
 1259: /*       asctime_r(&tm,strcurr); */
 1260:       forecast_time=curr_time; 
 1261:       itmp = strlen(strcurr);
 1262:       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 1263: 	strcurr[itmp-1]='\0';
 1264:       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 1265:       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 1266:       for(niterf=10;niterf<=30;niterf+=10){
 1267: 	forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
 1268: 	tmf = *localtime(&forecast_time.tv_sec);
 1269: /* 	asctime_r(&tmf,strfor); */
 1270: 	strcpy(strfor,asctime(&tmf));
 1271: 	itmp = strlen(strfor);
 1272: 	if(strfor[itmp-1]=='\n')
 1273: 	strfor[itmp-1]='\0';
 1274: 	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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 1275: 	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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 1276:       }
 1277:     }
 1278:     for (i=1;i<=n;i++) { 
 1279:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 1280:       fptt=(*fret); 
 1281: #ifdef DEBUG
 1282:       printf("fret=%lf \n",*fret);
 1283:       fprintf(ficlog,"fret=%lf \n",*fret);
 1284: #endif
 1285:       printf("%d",i);fflush(stdout);
 1286:       fprintf(ficlog,"%d",i);fflush(ficlog);
 1287:       linmin(p,xit,n,fret,func); 
 1288:       if (fabs(fptt-(*fret)) > del) { 
 1289: 	del=fabs(fptt-(*fret)); 
 1290: 	ibig=i; 
 1291:       } 
 1292: #ifdef DEBUG
 1293:       printf("%d %.12e",i,(*fret));
 1294:       fprintf(ficlog,"%d %.12e",i,(*fret));
 1295:       for (j=1;j<=n;j++) {
 1296: 	xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 1297: 	printf(" x(%d)=%.12e",j,xit[j]);
 1298: 	fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 1299:       }
 1300:       for(j=1;j<=n;j++) {
 1301: 	printf(" p=%.12e",p[j]);
 1302: 	fprintf(ficlog," p=%.12e",p[j]);
 1303:       }
 1304:       printf("\n");
 1305:       fprintf(ficlog,"\n");
 1306: #endif
 1307:     } 
 1308:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 1309: #ifdef DEBUG
 1310:       int k[2],l;
 1311:       k[0]=1;
 1312:       k[1]=-1;
 1313:       printf("Max: %.12e",(*func)(p));
 1314:       fprintf(ficlog,"Max: %.12e",(*func)(p));
 1315:       for (j=1;j<=n;j++) {
 1316: 	printf(" %.12e",p[j]);
 1317: 	fprintf(ficlog," %.12e",p[j]);
 1318:       }
 1319:       printf("\n");
 1320:       fprintf(ficlog,"\n");
 1321:       for(l=0;l<=1;l++) {
 1322: 	for (j=1;j<=n;j++) {
 1323: 	  ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 1324: 	  printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 1325: 	  fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 1326: 	}
 1327: 	printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 1328: 	fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 1329:       }
 1330: #endif
 1331: 
 1332: 
 1333:       free_vector(xit,1,n); 
 1334:       free_vector(xits,1,n); 
 1335:       free_vector(ptt,1,n); 
 1336:       free_vector(pt,1,n); 
 1337:       return; 
 1338:     } 
 1339:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 1340:     for (j=1;j<=n;j++) { 
 1341:       ptt[j]=2.0*p[j]-pt[j]; 
 1342:       xit[j]=p[j]-pt[j]; 
 1343:       pt[j]=p[j]; 
 1344:     } 
 1345:     fptt=(*func)(ptt); 
 1346:     if (fptt < fp) { 
 1347:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 1348:       if (t < 0.0) { 
 1349: 	linmin(p,xit,n,fret,func); 
 1350: 	for (j=1;j<=n;j++) { 
 1351: 	  xi[j][ibig]=xi[j][n]; 
 1352: 	  xi[j][n]=xit[j]; 
 1353: 	}
 1354: #ifdef DEBUG
 1355: 	printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 1356: 	fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 1357: 	for(j=1;j<=n;j++){
 1358: 	  printf(" %.12e",xit[j]);
 1359: 	  fprintf(ficlog," %.12e",xit[j]);
 1360: 	}
 1361: 	printf("\n");
 1362: 	fprintf(ficlog,"\n");
 1363: #endif
 1364:       }
 1365:     } 
 1366:   } 
 1367: } 
 1368: 
 1369: /**** Prevalence limit (stable or period prevalence)  ****************/
 1370: 
 1371: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 1372: {
 1373:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 1374:      matrix by transitions matrix until convergence is reached */
 1375: 
 1376:   int i, ii,j,k;
 1377:   double min, max, maxmin, maxmax,sumnew=0.;
 1378:   /* double **matprod2(); */ /* test */
 1379:   double **out, cov[NCOVMAX+1], **pmij();
 1380:   double **newm;
 1381:   double agefin, delaymax=50 ; /* Max number of years to converge */
 1382: 
 1383:   for (ii=1;ii<=nlstate+ndeath;ii++)
 1384:     for (j=1;j<=nlstate+ndeath;j++){
 1385:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 1386:     }
 1387: 
 1388:    cov[1]=1.;
 1389:  
 1390:  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 1391:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 1392:     newm=savm;
 1393:     /* Covariates have to be included here again */
 1394:     cov[2]=agefin;
 1395:     
 1396:     for (k=1; k<=cptcovn;k++) {
 1397:       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 1398:       /*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]]);*/
 1399:     }
 1400:     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
 1401:     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
 1402:     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
 1403:     
 1404:     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 1405:     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 1406:     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 1407:     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 1408:     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
 1409:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
 1410:     
 1411:     savm=oldm;
 1412:     oldm=newm;
 1413:     maxmax=0.;
 1414:     for(j=1;j<=nlstate;j++){
 1415:       min=1.;
 1416:       max=0.;
 1417:       for(i=1; i<=nlstate; i++) {
 1418: 	sumnew=0;
 1419: 	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 1420: 	prlim[i][j]= newm[i][j]/(1-sumnew);
 1421:         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
 1422: 	max=FMAX(max,prlim[i][j]);
 1423: 	min=FMIN(min,prlim[i][j]);
 1424:       }
 1425:       maxmin=max-min;
 1426:       maxmax=FMAX(maxmax,maxmin);
 1427:     }
 1428:     if(maxmax < ftolpl){
 1429:       return prlim;
 1430:     }
 1431:   }
 1432: }
 1433: 
 1434: /*************** transition probabilities ***************/ 
 1435: 
 1436: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 1437: {
 1438:   /* According to parameters values stored in x and the covariate's values stored in cov,
 1439:      computes the probability to be observed in state j being in state i by appying the
 1440:      model to the ncovmodel covariates (including constant and age).
 1441:      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
 1442:      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
 1443:      ncth covariate in the global vector x is given by the formula:
 1444:      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
 1445:      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
 1446:      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
 1447:      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
 1448:      Outputs ps[i][j] the probability to be observed in j being in j according to
 1449:      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
 1450:   */
 1451:   double s1, lnpijopii;
 1452:   /*double t34;*/
 1453:   int i,j,j1, nc, ii, jj;
 1454: 
 1455:     for(i=1; i<= nlstate; i++){
 1456:       for(j=1; j<i;j++){
 1457: 	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 1458: 	  /*lnpijopii += param[i][j][nc]*cov[nc];*/
 1459: 	  lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
 1460: /* 	 printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
 1461: 	}
 1462: 	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 1463: /* 	printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
 1464:       }
 1465:       for(j=i+1; j<=nlstate+ndeath;j++){
 1466: 	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 1467: 	  /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
 1468: 	  lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 1469: /* 	  printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
 1470: 	}
 1471: 	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 1472:       }
 1473:     }
 1474:     
 1475:     for(i=1; i<= nlstate; i++){
 1476:       s1=0;
 1477:       for(j=1; j<i; j++){
 1478: 	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 1479: 	/*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
 1480:       }
 1481:       for(j=i+1; j<=nlstate+ndeath; j++){
 1482: 	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 1483: 	/*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
 1484:       }
 1485:       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
 1486:       ps[i][i]=1./(s1+1.);
 1487:       /* Computing other pijs */
 1488:       for(j=1; j<i; j++)
 1489: 	ps[i][j]= exp(ps[i][j])*ps[i][i];
 1490:       for(j=i+1; j<=nlstate+ndeath; j++)
 1491: 	ps[i][j]= exp(ps[i][j])*ps[i][i];
 1492:       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 1493:     } /* end i */
 1494:     
 1495:     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 1496:       for(jj=1; jj<= nlstate+ndeath; jj++){
 1497: 	ps[ii][jj]=0;
 1498: 	ps[ii][ii]=1;
 1499:       }
 1500:     }
 1501:     
 1502:     
 1503:     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
 1504:     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
 1505:     /* 	printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
 1506:     /*   } */
 1507:     /*   printf("\n "); */
 1508:     /* } */
 1509:     /* printf("\n ");printf("%lf ",cov[2]);*/
 1510:     /*
 1511:       for(i=1; i<= npar; i++) printf("%f ",x[i]);
 1512:       goto end;*/
 1513:     return ps;
 1514: }
 1515: 
 1516: /**************** Product of 2 matrices ******************/
 1517: 
 1518: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
 1519: {
 1520:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 1521:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 1522:   /* in, b, out are matrice of pointers which should have been initialized 
 1523:      before: only the contents of out is modified. The function returns
 1524:      a pointer to pointers identical to out */
 1525:   int i, j, k;
 1526:   for(i=nrl; i<= nrh; i++)
 1527:     for(k=ncolol; k<=ncoloh; k++){
 1528:       out[i][k]=0.;
 1529:       for(j=ncl; j<=nch; j++)
 1530:   	out[i][k] +=in[i][j]*b[j][k];
 1531:     }
 1532:   return out;
 1533: }
 1534: 
 1535: 
 1536: /************* Higher Matrix Product ***************/
 1537: 
 1538: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 1539: {
 1540:   /* Computes the transition matrix starting at age 'age' over 
 1541:      'nhstepm*hstepm*stepm' months (i.e. until
 1542:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 1543:      nhstepm*hstepm matrices. 
 1544:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 1545:      (typically every 2 years instead of every month which is too big 
 1546:      for the memory).
 1547:      Model is determined by parameters x and covariates have to be 
 1548:      included manually here. 
 1549: 
 1550:      */
 1551: 
 1552:   int i, j, d, h, k;
 1553:   double **out, cov[NCOVMAX+1];
 1554:   double **newm;
 1555: 
 1556:   /* Hstepm could be zero and should return the unit matrix */
 1557:   for (i=1;i<=nlstate+ndeath;i++)
 1558:     for (j=1;j<=nlstate+ndeath;j++){
 1559:       oldm[i][j]=(i==j ? 1.0 : 0.0);
 1560:       po[i][j][0]=(i==j ? 1.0 : 0.0);
 1561:     }
 1562:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 1563:   for(h=1; h <=nhstepm; h++){
 1564:     for(d=1; d <=hstepm; d++){
 1565:       newm=savm;
 1566:       /* Covariates have to be included here again */
 1567:       cov[1]=1.;
 1568:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 1569:       for (k=1; k<=cptcovn;k++) 
 1570: 	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 1571:       for (k=1; k<=cptcovage;k++)
 1572: 	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 1573:       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 1574: 	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 1575: 
 1576: 
 1577:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 1578:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 1579:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 1580: 		   pmij(pmmij,cov,ncovmodel,x,nlstate));
 1581:       savm=oldm;
 1582:       oldm=newm;
 1583:     }
 1584:     for(i=1; i<=nlstate+ndeath; i++)
 1585:       for(j=1;j<=nlstate+ndeath;j++) {
 1586: 	po[i][j][h]=newm[i][j];
 1587: 	/*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 1588:       }
 1589:     /*printf("h=%d ",h);*/
 1590:   } /* end h */
 1591: /*     printf("\n H=%d \n",h); */
 1592:   return po;
 1593: }
 1594: 
 1595: 
 1596: /*************** log-likelihood *************/
 1597: double func( double *x)
 1598: {
 1599:   int i, ii, j, k, mi, d, kk;
 1600:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 1601:   double **out;
 1602:   double sw; /* Sum of weights */
 1603:   double lli; /* Individual log likelihood */
 1604:   int s1, s2;
 1605:   double bbh, survp;
 1606:   long ipmx;
 1607:   /*extern weight */
 1608:   /* We are differentiating ll according to initial status */
 1609:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 1610:   /*for(i=1;i<imx;i++) 
 1611:     printf(" %d\n",s[4][i]);
 1612:   */
 1613:   cov[1]=1.;
 1614: 
 1615:   for(k=1; k<=nlstate; k++) ll[k]=0.;
 1616: 
 1617:   if(mle==1){
 1618:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 1619:       /* Computes the values of the ncovmodel covariates of the model
 1620: 	 depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
 1621: 	 Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
 1622: 	 to be observed in j being in i according to the model.
 1623:        */
 1624:       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
 1625: 	cov[2+k]=covar[Tvar[k]][i];
 1626:       }
 1627:       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
 1628: 	 is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
 1629: 	 has been calculated etc */
 1630:       for(mi=1; mi<= wav[i]-1; mi++){
 1631: 	for (ii=1;ii<=nlstate+ndeath;ii++)
 1632: 	  for (j=1;j<=nlstate+ndeath;j++){
 1633: 	    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 1634: 	    savm[ii][j]=(ii==j ? 1.0 : 0.0);
 1635: 	  }
 1636: 	for(d=0; d<dh[mi][i]; d++){
 1637: 	  newm=savm;
 1638: 	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 1639: 	  for (kk=1; kk<=cptcovage;kk++) {
 1640: 	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
 1641: 	  }
 1642: 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 1643: 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 1644: 	  savm=oldm;
 1645: 	  oldm=newm;
 1646: 	} /* end mult */
 1647:       
 1648: 	/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 1649: 	/* But now since version 0.9 we anticipate for bias at large stepm.
 1650: 	 * If stepm is larger than one month (smallest stepm) and if the exact delay 
 1651: 	 * (in months) between two waves is not a multiple of stepm, we rounded to 
 1652: 	 * the nearest (and in case of equal distance, to the lowest) interval but now
 1653: 	 * we keep into memory the bias bh[mi][i] and also the previous matrix product
 1654: 	 * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 1655: 	 * probability in order to take into account the bias as a fraction of the way
 1656: 	 * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 1657: 	 * -stepm/2 to stepm/2 .
 1658: 	 * For stepm=1 the results are the same as for previous versions of Imach.
 1659: 	 * For stepm > 1 the results are less biased than in previous versions. 
 1660: 	 */
 1661: 	s1=s[mw[mi][i]][i];
 1662: 	s2=s[mw[mi+1][i]][i];
 1663: 	bbh=(double)bh[mi][i]/(double)stepm; 
 1664: 	/* bias bh is positive if real duration
 1665: 	 * is higher than the multiple of stepm and negative otherwise.
 1666: 	 */
 1667: 	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 1668: 	if( s2 > nlstate){ 
 1669: 	  /* i.e. if s2 is a death state and if the date of death is known 
 1670: 	     then the contribution to the likelihood is the probability to 
 1671: 	     die between last step unit time and current  step unit time, 
 1672: 	     which is also equal to probability to die before dh 
 1673: 	     minus probability to die before dh-stepm . 
 1674: 	     In version up to 0.92 likelihood was computed
 1675: 	as if date of death was unknown. Death was treated as any other
 1676: 	health state: the date of the interview describes the actual state
 1677: 	and not the date of a change in health state. The former idea was
 1678: 	to consider that at each interview the state was recorded
 1679: 	(healthy, disable or death) and IMaCh was corrected; but when we
 1680: 	introduced the exact date of death then we should have modified
 1681: 	the contribution of an exact death to the likelihood. This new
 1682: 	contribution is smaller and very dependent of the step unit
 1683: 	stepm. It is no more the probability to die between last interview
 1684: 	and month of death but the probability to survive from last
 1685: 	interview up to one month before death multiplied by the
 1686: 	probability to die within a month. Thanks to Chris
 1687: 	Jackson for correcting this bug.  Former versions increased
 1688: 	mortality artificially. The bad side is that we add another loop
 1689: 	which slows down the processing. The difference can be up to 10%
 1690: 	lower mortality.
 1691: 	  */
 1692: 	  lli=log(out[s1][s2] - savm[s1][s2]);
 1693: 
 1694: 
 1695: 	} else if  (s2==-2) {
 1696: 	  for (j=1,survp=0. ; j<=nlstate; j++) 
 1697: 	    survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 1698: 	  /*survp += out[s1][j]; */
 1699: 	  lli= log(survp);
 1700: 	}
 1701: 	
 1702:  	else if  (s2==-4) { 
 1703: 	  for (j=3,survp=0. ; j<=nlstate; j++)  
 1704: 	    survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 1705:  	  lli= log(survp); 
 1706:  	} 
 1707: 
 1708:  	else if  (s2==-5) { 
 1709:  	  for (j=1,survp=0. ; j<=2; j++)  
 1710: 	    survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 1711:  	  lli= log(survp); 
 1712:  	} 
 1713: 	
 1714: 	else{
 1715: 	  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 1716: 	  /*  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 */
 1717: 	} 
 1718: 	/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 1719: 	/*if(lli ==000.0)*/
 1720: 	/*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); */
 1721:   	ipmx +=1;
 1722: 	sw += weight[i];
 1723: 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 1724:       } /* end of wave */
 1725:     } /* end of individual */
 1726:   }  else if(mle==2){
 1727:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 1728:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 1729:       for(mi=1; mi<= wav[i]-1; mi++){
 1730: 	for (ii=1;ii<=nlstate+ndeath;ii++)
 1731: 	  for (j=1;j<=nlstate+ndeath;j++){
 1732: 	    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 1733: 	    savm[ii][j]=(ii==j ? 1.0 : 0.0);
 1734: 	  }
 1735: 	for(d=0; d<=dh[mi][i]; d++){
 1736: 	  newm=savm;
 1737: 	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 1738: 	  for (kk=1; kk<=cptcovage;kk++) {
 1739: 	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 1740: 	  }
 1741: 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 1742: 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 1743: 	  savm=oldm;
 1744: 	  oldm=newm;
 1745: 	} /* end mult */
 1746:       
 1747: 	s1=s[mw[mi][i]][i];
 1748: 	s2=s[mw[mi+1][i]][i];
 1749: 	bbh=(double)bh[mi][i]/(double)stepm; 
 1750: 	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 */
 1751: 	ipmx +=1;
 1752: 	sw += weight[i];
 1753: 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 1754:       } /* end of wave */
 1755:     } /* end of individual */
 1756:   }  else if(mle==3){  /* exponential inter-extrapolation */
 1757:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 1758:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 1759:       for(mi=1; mi<= wav[i]-1; mi++){
 1760: 	for (ii=1;ii<=nlstate+ndeath;ii++)
 1761: 	  for (j=1;j<=nlstate+ndeath;j++){
 1762: 	    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 1763: 	    savm[ii][j]=(ii==j ? 1.0 : 0.0);
 1764: 	  }
 1765: 	for(d=0; d<dh[mi][i]; d++){
 1766: 	  newm=savm;
 1767: 	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 1768: 	  for (kk=1; kk<=cptcovage;kk++) {
 1769: 	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 1770: 	  }
 1771: 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 1772: 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 1773: 	  savm=oldm;
 1774: 	  oldm=newm;
 1775: 	} /* end mult */
 1776:       
 1777: 	s1=s[mw[mi][i]][i];
 1778: 	s2=s[mw[mi+1][i]][i];
 1779: 	bbh=(double)bh[mi][i]/(double)stepm; 
 1780: 	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 */
 1781: 	ipmx +=1;
 1782: 	sw += weight[i];
 1783: 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 1784:       } /* end of wave */
 1785:     } /* end of individual */
 1786:   }else if (mle==4){  /* ml=4 no inter-extrapolation */
 1787:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 1788:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 1789:       for(mi=1; mi<= wav[i]-1; mi++){
 1790: 	for (ii=1;ii<=nlstate+ndeath;ii++)
 1791: 	  for (j=1;j<=nlstate+ndeath;j++){
 1792: 	    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 1793: 	    savm[ii][j]=(ii==j ? 1.0 : 0.0);
 1794: 	  }
 1795: 	for(d=0; d<dh[mi][i]; d++){
 1796: 	  newm=savm;
 1797: 	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 1798: 	  for (kk=1; kk<=cptcovage;kk++) {
 1799: 	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 1800: 	  }
 1801: 	
 1802: 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 1803: 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 1804: 	  savm=oldm;
 1805: 	  oldm=newm;
 1806: 	} /* end mult */
 1807:       
 1808: 	s1=s[mw[mi][i]][i];
 1809: 	s2=s[mw[mi+1][i]][i];
 1810: 	if( s2 > nlstate){ 
 1811: 	  lli=log(out[s1][s2] - savm[s1][s2]);
 1812: 	}else{
 1813: 	  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 1814: 	}
 1815: 	ipmx +=1;
 1816: 	sw += weight[i];
 1817: 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 1818: /* 	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]); */
 1819:       } /* end of wave */
 1820:     } /* end of individual */
 1821:   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 1822:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 1823:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 1824:       for(mi=1; mi<= wav[i]-1; mi++){
 1825: 	for (ii=1;ii<=nlstate+ndeath;ii++)
 1826: 	  for (j=1;j<=nlstate+ndeath;j++){
 1827: 	    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 1828: 	    savm[ii][j]=(ii==j ? 1.0 : 0.0);
 1829: 	  }
 1830: 	for(d=0; d<dh[mi][i]; d++){
 1831: 	  newm=savm;
 1832: 	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 1833: 	  for (kk=1; kk<=cptcovage;kk++) {
 1834: 	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 1835: 	  }
 1836: 	
 1837: 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 1838: 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 1839: 	  savm=oldm;
 1840: 	  oldm=newm;
 1841: 	} /* end mult */
 1842:       
 1843: 	s1=s[mw[mi][i]][i];
 1844: 	s2=s[mw[mi+1][i]][i];
 1845: 	lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 1846: 	ipmx +=1;
 1847: 	sw += weight[i];
 1848: 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 1849: 	/*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]);*/
 1850:       } /* end of wave */
 1851:     } /* end of individual */
 1852:   } /* End of if */
 1853:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 1854:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 1855:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 1856:   return -l;
 1857: }
 1858: 
 1859: /*************** log-likelihood *************/
 1860: double funcone( double *x)
 1861: {
 1862:   /* Same as likeli but slower because of a lot of printf and if */
 1863:   int i, ii, j, k, mi, d, kk;
 1864:   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 1865:   double **out;
 1866:   double lli; /* Individual log likelihood */
 1867:   double llt;
 1868:   int s1, s2;
 1869:   double bbh, survp;
 1870:   /*extern weight */
 1871:   /* We are differentiating ll according to initial status */
 1872:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 1873:   /*for(i=1;i<imx;i++) 
 1874:     printf(" %d\n",s[4][i]);
 1875:   */
 1876:   cov[1]=1.;
 1877: 
 1878:   for(k=1; k<=nlstate; k++) ll[k]=0.;
 1879: 
 1880:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 1881:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 1882:     for(mi=1; mi<= wav[i]-1; mi++){
 1883:       for (ii=1;ii<=nlstate+ndeath;ii++)
 1884: 	for (j=1;j<=nlstate+ndeath;j++){
 1885: 	  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 1886: 	  savm[ii][j]=(ii==j ? 1.0 : 0.0);
 1887: 	}
 1888:       for(d=0; d<dh[mi][i]; d++){
 1889: 	newm=savm;
 1890: 	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 1891: 	for (kk=1; kk<=cptcovage;kk++) {
 1892: 	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 1893: 	}
 1894: 	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 1895: 	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 1896: 		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 1897: 	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 1898: 	/* 	     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
 1899: 	savm=oldm;
 1900: 	oldm=newm;
 1901:       } /* end mult */
 1902:       
 1903:       s1=s[mw[mi][i]][i];
 1904:       s2=s[mw[mi+1][i]][i];
 1905:       bbh=(double)bh[mi][i]/(double)stepm; 
 1906:       /* bias is positive if real duration
 1907:        * is higher than the multiple of stepm and negative otherwise.
 1908:        */
 1909:       if( s2 > nlstate && (mle <5) ){  /* Jackson */
 1910: 	lli=log(out[s1][s2] - savm[s1][s2]);
 1911:       } else if  (s2==-2) {
 1912: 	for (j=1,survp=0. ; j<=nlstate; j++) 
 1913: 	  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 1914: 	lli= log(survp);
 1915:       }else if (mle==1){
 1916: 	lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 1917:       } else if(mle==2){
 1918: 	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 */
 1919:       } else if(mle==3){  /* exponential inter-extrapolation */
 1920: 	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 */
 1921:       } else if (mle==4){  /* mle=4 no inter-extrapolation */
 1922: 	lli=log(out[s1][s2]); /* Original formula */
 1923:       } else{  /* mle=0 back to 1 */
 1924: 	lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 1925: 	/*lli=log(out[s1][s2]); */ /* Original formula */
 1926:       } /* End of if */
 1927:       ipmx +=1;
 1928:       sw += weight[i];
 1929:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 1930:       /*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]); */
 1931:       if(globpr){
 1932: 	fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 1933:  %11.6f %11.6f %11.6f ", \
 1934: 		num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 1935: 		2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 1936: 	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 1937: 	  llt +=ll[k]*gipmx/gsw;
 1938: 	  fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
 1939: 	}
 1940: 	fprintf(ficresilk," %10.6f\n", -llt);
 1941:       }
 1942:     } /* end of wave */
 1943:   } /* end of individual */
 1944:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 1945:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 1946:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 1947:   if(globpr==0){ /* First time we count the contributions and weights */
 1948:     gipmx=ipmx;
 1949:     gsw=sw;
 1950:   }
 1951:   return -l;
 1952: }
 1953: 
 1954: 
 1955: /*************** function likelione ***********/
 1956: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 1957: {
 1958:   /* This routine should help understanding what is done with 
 1959:      the selection of individuals/waves and
 1960:      to check the exact contribution to the likelihood.
 1961:      Plotting could be done.
 1962:    */
 1963:   int k;
 1964: 
 1965:   if(*globpri !=0){ /* Just counts and sums, no printings */
 1966:     strcpy(fileresilk,"ilk"); 
 1967:     strcat(fileresilk,fileres);
 1968:     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 1969:       printf("Problem with resultfile: %s\n", fileresilk);
 1970:       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 1971:     }
 1972:     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");
 1973:     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
 1974:     /* 	i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 1975:     for(k=1; k<=nlstate; k++) 
 1976:       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 1977:     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 1978:   }
 1979: 
 1980:   *fretone=(*funcone)(p);
 1981:   if(*globpri !=0){
 1982:     fclose(ficresilk);
 1983:     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 1984:     fflush(fichtm); 
 1985:   } 
 1986:   return;
 1987: }
 1988: 
 1989: 
 1990: /*********** Maximum Likelihood Estimation ***************/
 1991: 
 1992: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 1993: {
 1994:   int i,j, iter;
 1995:   double **xi;
 1996:   double fret;
 1997:   double fretone; /* Only one call to likelihood */
 1998:   /*  char filerespow[FILENAMELENGTH];*/
 1999:   xi=matrix(1,npar,1,npar);
 2000:   for (i=1;i<=npar;i++)
 2001:     for (j=1;j<=npar;j++)
 2002:       xi[i][j]=(i==j ? 1.0 : 0.0);
 2003:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
 2004:   strcpy(filerespow,"pow"); 
 2005:   strcat(filerespow,fileres);
 2006:   if((ficrespow=fopen(filerespow,"w"))==NULL) {
 2007:     printf("Problem with resultfile: %s\n", filerespow);
 2008:     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 2009:   }
 2010:   fprintf(ficrespow,"# Powell\n# iter -2*LL");
 2011:   for (i=1;i<=nlstate;i++)
 2012:     for(j=1;j<=nlstate+ndeath;j++)
 2013:       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 2014:   fprintf(ficrespow,"\n");
 2015: 
 2016:   powell(p,xi,npar,ftol,&iter,&fret,func);
 2017: 
 2018:   free_matrix(xi,1,npar,1,npar);
 2019:   fclose(ficrespow);
 2020:   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 2021:   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 2022:   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 2023: 
 2024: }
 2025: 
 2026: /**** Computes Hessian and covariance matrix ***/
 2027: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 2028: {
 2029:   double  **a,**y,*x,pd;
 2030:   double **hess;
 2031:   int i, j,jk;
 2032:   int *indx;
 2033: 
 2034:   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
 2035:   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 2036:   void lubksb(double **a, int npar, int *indx, double b[]) ;
 2037:   void ludcmp(double **a, int npar, int *indx, double *d) ;
 2038:   double gompertz(double p[]);
 2039:   hess=matrix(1,npar,1,npar);
 2040: 
 2041:   printf("\nCalculation of the hessian matrix. Wait...\n");
 2042:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 2043:   for (i=1;i<=npar;i++){
 2044:     printf("%d",i);fflush(stdout);
 2045:     fprintf(ficlog,"%d",i);fflush(ficlog);
 2046:    
 2047:      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
 2048:     
 2049:     /*  printf(" %f ",p[i]);
 2050: 	printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
 2051:   }
 2052:   
 2053:   for (i=1;i<=npar;i++) {
 2054:     for (j=1;j<=npar;j++)  {
 2055:       if (j>i) { 
 2056: 	printf(".%d%d",i,j);fflush(stdout);
 2057: 	fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 2058: 	hess[i][j]=hessij(p,delti,i,j,func,npar);
 2059: 	
 2060: 	hess[j][i]=hess[i][j];    
 2061: 	/*printf(" %lf ",hess[i][j]);*/
 2062:       }
 2063:     }
 2064:   }
 2065:   printf("\n");
 2066:   fprintf(ficlog,"\n");
 2067: 
 2068:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 2069:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 2070:   
 2071:   a=matrix(1,npar,1,npar);
 2072:   y=matrix(1,npar,1,npar);
 2073:   x=vector(1,npar);
 2074:   indx=ivector(1,npar);
 2075:   for (i=1;i<=npar;i++)
 2076:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 2077:   ludcmp(a,npar,indx,&pd);
 2078: 
 2079:   for (j=1;j<=npar;j++) {
 2080:     for (i=1;i<=npar;i++) x[i]=0;
 2081:     x[j]=1;
 2082:     lubksb(a,npar,indx,x);
 2083:     for (i=1;i<=npar;i++){ 
 2084:       matcov[i][j]=x[i];
 2085:     }
 2086:   }
 2087: 
 2088:   printf("\n#Hessian matrix#\n");
 2089:   fprintf(ficlog,"\n#Hessian matrix#\n");
 2090:   for (i=1;i<=npar;i++) { 
 2091:     for (j=1;j<=npar;j++) { 
 2092:       printf("%.3e ",hess[i][j]);
 2093:       fprintf(ficlog,"%.3e ",hess[i][j]);
 2094:     }
 2095:     printf("\n");
 2096:     fprintf(ficlog,"\n");
 2097:   }
 2098: 
 2099:   /* Recompute Inverse */
 2100:   for (i=1;i<=npar;i++)
 2101:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 2102:   ludcmp(a,npar,indx,&pd);
 2103: 
 2104:   /*  printf("\n#Hessian matrix recomputed#\n");
 2105: 
 2106:   for (j=1;j<=npar;j++) {
 2107:     for (i=1;i<=npar;i++) x[i]=0;
 2108:     x[j]=1;
 2109:     lubksb(a,npar,indx,x);
 2110:     for (i=1;i<=npar;i++){ 
 2111:       y[i][j]=x[i];
 2112:       printf("%.3e ",y[i][j]);
 2113:       fprintf(ficlog,"%.3e ",y[i][j]);
 2114:     }
 2115:     printf("\n");
 2116:     fprintf(ficlog,"\n");
 2117:   }
 2118:   */
 2119: 
 2120:   free_matrix(a,1,npar,1,npar);
 2121:   free_matrix(y,1,npar,1,npar);
 2122:   free_vector(x,1,npar);
 2123:   free_ivector(indx,1,npar);
 2124:   free_matrix(hess,1,npar,1,npar);
 2125: 
 2126: 
 2127: }
 2128: 
 2129: /*************** hessian matrix ****************/
 2130: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 2131: {
 2132:   int i;
 2133:   int l=1, lmax=20;
 2134:   double k1,k2;
 2135:   double p2[MAXPARM+1]; /* identical to x */
 2136:   double res;
 2137:   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 2138:   double fx;
 2139:   int k=0,kmax=10;
 2140:   double l1;
 2141: 
 2142:   fx=func(x);
 2143:   for (i=1;i<=npar;i++) p2[i]=x[i];
 2144:   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
 2145:     l1=pow(10,l);
 2146:     delts=delt;
 2147:     for(k=1 ; k <kmax; k=k+1){
 2148:       delt = delta*(l1*k);
 2149:       p2[theta]=x[theta] +delt;
 2150:       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
 2151:       p2[theta]=x[theta]-delt;
 2152:       k2=func(p2)-fx;
 2153:       /*res= (k1-2.0*fx+k2)/delt/delt; */
 2154:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 2155:       
 2156: #ifdef DEBUGHESS
 2157:       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);
 2158:       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);
 2159: #endif
 2160:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 2161:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 2162: 	k=kmax;
 2163:       }
 2164:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 2165: 	k=kmax; l=lmax*10.;
 2166:       }
 2167:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 2168: 	delts=delt;
 2169:       }
 2170:     }
 2171:   }
 2172:   delti[theta]=delts;
 2173:   return res; 
 2174:   
 2175: }
 2176: 
 2177: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 2178: {
 2179:   int i;
 2180:   int l=1, l1, lmax=20;
 2181:   double k1,k2,k3,k4,res,fx;
 2182:   double p2[MAXPARM+1];
 2183:   int k;
 2184: 
 2185:   fx=func(x);
 2186:   for (k=1; k<=2; k++) {
 2187:     for (i=1;i<=npar;i++) p2[i]=x[i];
 2188:     p2[thetai]=x[thetai]+delti[thetai]/k;
 2189:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 2190:     k1=func(p2)-fx;
 2191:   
 2192:     p2[thetai]=x[thetai]+delti[thetai]/k;
 2193:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 2194:     k2=func(p2)-fx;
 2195:   
 2196:     p2[thetai]=x[thetai]-delti[thetai]/k;
 2197:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 2198:     k3=func(p2)-fx;
 2199:   
 2200:     p2[thetai]=x[thetai]-delti[thetai]/k;
 2201:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 2202:     k4=func(p2)-fx;
 2203:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 2204: #ifdef DEBUG
 2205:     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);
 2206:     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);
 2207: #endif
 2208:   }
 2209:   return res;
 2210: }
 2211: 
 2212: /************** Inverse of matrix **************/
 2213: void ludcmp(double **a, int n, int *indx, double *d) 
 2214: { 
 2215:   int i,imax,j,k; 
 2216:   double big,dum,sum,temp; 
 2217:   double *vv; 
 2218:  
 2219:   vv=vector(1,n); 
 2220:   *d=1.0; 
 2221:   for (i=1;i<=n;i++) { 
 2222:     big=0.0; 
 2223:     for (j=1;j<=n;j++) 
 2224:       if ((temp=fabs(a[i][j])) > big) big=temp; 
 2225:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 2226:     vv[i]=1.0/big; 
 2227:   } 
 2228:   for (j=1;j<=n;j++) { 
 2229:     for (i=1;i<j;i++) { 
 2230:       sum=a[i][j]; 
 2231:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 2232:       a[i][j]=sum; 
 2233:     } 
 2234:     big=0.0; 
 2235:     for (i=j;i<=n;i++) { 
 2236:       sum=a[i][j]; 
 2237:       for (k=1;k<j;k++) 
 2238: 	sum -= a[i][k]*a[k][j]; 
 2239:       a[i][j]=sum; 
 2240:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
 2241: 	big=dum; 
 2242: 	imax=i; 
 2243:       } 
 2244:     } 
 2245:     if (j != imax) { 
 2246:       for (k=1;k<=n;k++) { 
 2247: 	dum=a[imax][k]; 
 2248: 	a[imax][k]=a[j][k]; 
 2249: 	a[j][k]=dum; 
 2250:       } 
 2251:       *d = -(*d); 
 2252:       vv[imax]=vv[j]; 
 2253:     } 
 2254:     indx[j]=imax; 
 2255:     if (a[j][j] == 0.0) a[j][j]=TINY; 
 2256:     if (j != n) { 
 2257:       dum=1.0/(a[j][j]); 
 2258:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 2259:     } 
 2260:   } 
 2261:   free_vector(vv,1,n);  /* Doesn't work */
 2262: ;
 2263: } 
 2264: 
 2265: void lubksb(double **a, int n, int *indx, double b[]) 
 2266: { 
 2267:   int i,ii=0,ip,j; 
 2268:   double sum; 
 2269:  
 2270:   for (i=1;i<=n;i++) { 
 2271:     ip=indx[i]; 
 2272:     sum=b[ip]; 
 2273:     b[ip]=b[i]; 
 2274:     if (ii) 
 2275:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 2276:     else if (sum) ii=i; 
 2277:     b[i]=sum; 
 2278:   } 
 2279:   for (i=n;i>=1;i--) { 
 2280:     sum=b[i]; 
 2281:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 2282:     b[i]=sum/a[i][i]; 
 2283:   } 
 2284: } 
 2285: 
 2286: void pstamp(FILE *fichier)
 2287: {
 2288:   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
 2289: }
 2290: 
 2291: /************ Frequencies ********************/
 2292: 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[])
 2293: {  /* Some frequencies */
 2294:   
 2295:   int i, m, jk, k1,i1, j1, bool, z1,j;
 2296:   int first;
 2297:   double ***freq; /* Frequencies */
 2298:   double *pp, **prop;
 2299:   double pos,posprop, k2, dateintsum=0,k2cpt=0;
 2300:   char fileresp[FILENAMELENGTH];
 2301:   
 2302:   pp=vector(1,nlstate);
 2303:   prop=matrix(1,nlstate,iagemin,iagemax+3);
 2304:   strcpy(fileresp,"p");
 2305:   strcat(fileresp,fileres);
 2306:   if((ficresp=fopen(fileresp,"w"))==NULL) {
 2307:     printf("Problem with prevalence resultfile: %s\n", fileresp);
 2308:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 2309:     exit(0);
 2310:   }
 2311:   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 2312:   j1=0;
 2313:   
 2314:   j=cptcoveff;
 2315:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 2316: 
 2317:   first=1;
 2318: 
 2319:   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
 2320:   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
 2321:   /*    j1++;
 2322: */
 2323:   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
 2324:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 2325: 	scanf("%d", i);*/
 2326:       for (i=-5; i<=nlstate+ndeath; i++)  
 2327: 	for (jk=-5; jk<=nlstate+ndeath; jk++)  
 2328: 	  for(m=iagemin; m <= iagemax+3; m++)
 2329: 	    freq[i][jk][m]=0;
 2330:       
 2331:       for (i=1; i<=nlstate; i++)  
 2332: 	for(m=iagemin; m <= iagemax+3; m++)
 2333: 	  prop[i][m]=0;
 2334:       
 2335:       dateintsum=0;
 2336:       k2cpt=0;
 2337:       for (i=1; i<=imx; i++) {
 2338: 	bool=1;
 2339: 	if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
 2340: 	  for (z1=1; z1<=cptcoveff; z1++)       
 2341:             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
 2342:                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
 2343:               bool=0;
 2344:               /* 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", 
 2345:                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
 2346:                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
 2347:               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
 2348:             } 
 2349: 	}
 2350:  
 2351: 	if (bool==1){
 2352: 	  for(m=firstpass; m<=lastpass; m++){
 2353: 	    k2=anint[m][i]+(mint[m][i]/12.);
 2354: 	    /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 2355: 	      if(agev[m][i]==0) agev[m][i]=iagemax+1;
 2356: 	      if(agev[m][i]==1) agev[m][i]=iagemax+2;
 2357: 	      if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 2358: 	      if (m<lastpass) {
 2359: 		freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 2360: 		freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 2361: 	      }
 2362: 	      
 2363: 	      if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 2364: 		dateintsum=dateintsum+k2;
 2365: 		k2cpt++;
 2366: 	      }
 2367: 	      /*}*/
 2368: 	  }
 2369: 	}
 2370:       } /* end i */
 2371:        
 2372:       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 2373:       pstamp(ficresp);
 2374:       if  (cptcovn>0) {
 2375: 	fprintf(ficresp, "\n#********** Variable "); 
 2376: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 2377: 	fprintf(ficresp, "**********\n#");
 2378: 	fprintf(ficlog, "\n#********** Variable "); 
 2379: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 2380: 	fprintf(ficlog, "**********\n#");
 2381:       }
 2382:       for(i=1; i<=nlstate;i++) 
 2383: 	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 2384:       fprintf(ficresp, "\n");
 2385:       
 2386:       for(i=iagemin; i <= iagemax+3; i++){
 2387: 	if(i==iagemax+3){
 2388: 	  fprintf(ficlog,"Total");
 2389: 	}else{
 2390: 	  if(first==1){
 2391: 	    first=0;
 2392: 	    printf("See log file for details...\n");
 2393: 	  }
 2394: 	  fprintf(ficlog,"Age %d", i);
 2395: 	}
 2396: 	for(jk=1; jk <=nlstate ; jk++){
 2397: 	  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 2398: 	    pp[jk] += freq[jk][m][i]; 
 2399: 	}
 2400: 	for(jk=1; jk <=nlstate ; jk++){
 2401: 	  for(m=-1, pos=0; m <=0 ; m++)
 2402: 	    pos += freq[jk][m][i];
 2403: 	  if(pp[jk]>=1.e-10){
 2404: 	    if(first==1){
 2405: 	      printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 2406: 	    }
 2407: 	    fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 2408: 	  }else{
 2409: 	    if(first==1)
 2410: 	      printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 2411: 	    fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 2412: 	  }
 2413: 	}
 2414: 
 2415: 	for(jk=1; jk <=nlstate ; jk++){
 2416: 	  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 2417: 	    pp[jk] += freq[jk][m][i];
 2418: 	}	
 2419: 	for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 2420: 	  pos += pp[jk];
 2421: 	  posprop += prop[jk][i];
 2422: 	}
 2423: 	for(jk=1; jk <=nlstate ; jk++){
 2424: 	  if(pos>=1.e-5){
 2425: 	    if(first==1)
 2426: 	      printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 2427: 	    fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 2428: 	  }else{
 2429: 	    if(first==1)
 2430: 	      printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 2431: 	    fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 2432: 	  }
 2433: 	  if( i <= iagemax){
 2434: 	    if(pos>=1.e-5){
 2435: 	      fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 2436: 	      /*probs[i][jk][j1]= pp[jk]/pos;*/
 2437: 	      /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 2438: 	    }
 2439: 	    else
 2440: 	      fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 2441: 	  }
 2442: 	}
 2443: 	
 2444: 	for(jk=-1; jk <=nlstate+ndeath; jk++)
 2445: 	  for(m=-1; m <=nlstate+ndeath; m++)
 2446: 	    if(freq[jk][m][i] !=0 ) {
 2447: 	    if(first==1)
 2448: 	      printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 2449: 	      fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 2450: 	    }
 2451: 	if(i <= iagemax)
 2452: 	  fprintf(ficresp,"\n");
 2453: 	if(first==1)
 2454: 	  printf("Others in log...\n");
 2455: 	fprintf(ficlog,"\n");
 2456:       }
 2457:       /*}*/
 2458:   }
 2459:   dateintmean=dateintsum/k2cpt; 
 2460:  
 2461:   fclose(ficresp);
 2462:   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 2463:   free_vector(pp,1,nlstate);
 2464:   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 2465:   /* End of Freq */
 2466: }
 2467: 
 2468: /************ Prevalence ********************/
 2469: 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)
 2470: {  
 2471:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 2472:      in each health status at the date of interview (if between dateprev1 and dateprev2).
 2473:      We still use firstpass and lastpass as another selection.
 2474:   */
 2475:  
 2476:   int i, m, jk, k1, i1, j1, bool, z1,j;
 2477:   double ***freq; /* Frequencies */
 2478:   double *pp, **prop;
 2479:   double pos,posprop; 
 2480:   double  y2; /* in fractional years */
 2481:   int iagemin, iagemax;
 2482:   int first; /** to stop verbosity which is redirected to log file */
 2483: 
 2484:   iagemin= (int) agemin;
 2485:   iagemax= (int) agemax;
 2486:   /*pp=vector(1,nlstate);*/
 2487:   prop=matrix(1,nlstate,iagemin,iagemax+3); 
 2488:   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 2489:   j1=0;
 2490:   
 2491:   /*j=cptcoveff;*/
 2492:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 2493:   
 2494:   first=1;
 2495:   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
 2496:     /*for(i1=1; i1<=ncodemax[k1];i1++){
 2497:       j1++;*/
 2498:       
 2499:       for (i=1; i<=nlstate; i++)  
 2500: 	for(m=iagemin; m <= iagemax+3; m++)
 2501: 	  prop[i][m]=0.0;
 2502:      
 2503:       for (i=1; i<=imx; i++) { /* Each individual */
 2504: 	bool=1;
 2505: 	if  (cptcovn>0) {
 2506: 	  for (z1=1; z1<=cptcoveff; z1++) 
 2507: 	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 2508: 	      bool=0;
 2509: 	} 
 2510: 	if (bool==1) { 
 2511: 	  for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 2512: 	    y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 2513: 	    if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 2514: 	      if(agev[m][i]==0) agev[m][i]=iagemax+1;
 2515: 	      if(agev[m][i]==1) agev[m][i]=iagemax+2;
 2516: 	      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); 
 2517:  	      if (s[m][i]>0 && s[m][i]<=nlstate) { 
 2518: 		/*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]]);*/
 2519:  		prop[s[m][i]][(int)agev[m][i]] += weight[i];
 2520:  		prop[s[m][i]][iagemax+3] += weight[i]; 
 2521:  	      } 
 2522: 	    }
 2523: 	  } /* end selection of waves */
 2524: 	}
 2525:       }
 2526:       for(i=iagemin; i <= iagemax+3; i++){  
 2527:  	for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 2528:  	  posprop += prop[jk][i]; 
 2529:  	} 
 2530: 	
 2531:  	for(jk=1; jk <=nlstate ; jk++){	    
 2532:  	  if( i <=  iagemax){ 
 2533:  	    if(posprop>=1.e-5){ 
 2534:  	      probs[i][jk][j1]= prop[jk][i]/posprop;
 2535:  	    } else{
 2536: 	      if(first==1){
 2537: 		first=0;
 2538: 		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]);
 2539: 	      }
 2540: 	    }
 2541:  	  } 
 2542:  	}/* end jk */ 
 2543:       }/* end i */ 
 2544:     /*} *//* end i1 */
 2545:   } /* end j1 */
 2546:   
 2547:   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 2548:   /*free_vector(pp,1,nlstate);*/
 2549:   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 2550: }  /* End of prevalence */
 2551: 
 2552: /************* Waves Concatenation ***************/
 2553: 
 2554: 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)
 2555: {
 2556:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 2557:      Death is a valid wave (if date is known).
 2558:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 2559:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 2560:      and mw[mi+1][i]. dh depends on stepm.
 2561:      */
 2562: 
 2563:   int i, mi, m;
 2564:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 2565:      double sum=0., jmean=0.;*/
 2566:   int first;
 2567:   int j, k=0,jk, ju, jl;
 2568:   double sum=0.;
 2569:   first=0;
 2570:   jmin=1e+5;
 2571:   jmax=-1;
 2572:   jmean=0.;
 2573:   for(i=1; i<=imx; i++){
 2574:     mi=0;
 2575:     m=firstpass;
 2576:     while(s[m][i] <= nlstate){
 2577:       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 2578: 	mw[++mi][i]=m;
 2579:       if(m >=lastpass)
 2580: 	break;
 2581:       else
 2582: 	m++;
 2583:     }/* end while */
 2584:     if (s[m][i] > nlstate){
 2585:       mi++;	/* Death is another wave */
 2586:       /* if(mi==0)  never been interviewed correctly before death */
 2587: 	 /* Only death is a correct wave */
 2588:       mw[mi][i]=m;
 2589:     }
 2590: 
 2591:     wav[i]=mi;
 2592:     if(mi==0){
 2593:       nbwarn++;
 2594:       if(first==0){
 2595: 	printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 2596: 	first=1;
 2597:       }
 2598:       if(first==1){
 2599: 	fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
 2600:       }
 2601:     } /* end mi==0 */
 2602:   } /* End individuals */
 2603: 
 2604:   for(i=1; i<=imx; i++){
 2605:     for(mi=1; mi<wav[i];mi++){
 2606:       if (stepm <=0)
 2607: 	dh[mi][i]=1;
 2608:       else{
 2609: 	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 2610: 	  if (agedc[i] < 2*AGESUP) {
 2611: 	    j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 2612: 	    if(j==0) j=1;  /* Survives at least one month after exam */
 2613: 	    else if(j<0){
 2614: 	      nberr++;
 2615: 	      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]);
 2616: 	      j=1; /* Temporary Dangerous patch */
 2617: 	      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);
 2618: 	      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]);
 2619: 	      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);
 2620: 	    }
 2621: 	    k=k+1;
 2622: 	    if (j >= jmax){
 2623: 	      jmax=j;
 2624: 	      ijmax=i;
 2625: 	    }
 2626: 	    if (j <= jmin){
 2627: 	      jmin=j;
 2628: 	      ijmin=i;
 2629: 	    }
 2630: 	    sum=sum+j;
 2631: 	    /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 2632: 	    /*	  printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 2633: 	  }
 2634: 	}
 2635: 	else{
 2636: 	  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 2637: /* 	  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]); */
 2638: 
 2639: 	  k=k+1;
 2640: 	  if (j >= jmax) {
 2641: 	    jmax=j;
 2642: 	    ijmax=i;
 2643: 	  }
 2644: 	  else if (j <= jmin){
 2645: 	    jmin=j;
 2646: 	    ijmin=i;
 2647: 	  }
 2648: 	  /*	    if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 2649: 	  /*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]);*/
 2650: 	  if(j<0){
 2651: 	    nberr++;
 2652: 	    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]);
 2653: 	    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]);
 2654: 	  }
 2655: 	  sum=sum+j;
 2656: 	}
 2657: 	jk= j/stepm;
 2658: 	jl= j -jk*stepm;
 2659: 	ju= j -(jk+1)*stepm;
 2660: 	if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 2661: 	  if(jl==0){
 2662: 	    dh[mi][i]=jk;
 2663: 	    bh[mi][i]=0;
 2664: 	  }else{ /* We want a negative bias in order to only have interpolation ie
 2665: 		  * to avoid the price of an extra matrix product in likelihood */
 2666: 	    dh[mi][i]=jk+1;
 2667: 	    bh[mi][i]=ju;
 2668: 	  }
 2669: 	}else{
 2670: 	  if(jl <= -ju){
 2671: 	    dh[mi][i]=jk;
 2672: 	    bh[mi][i]=jl;	/* bias is positive if real duration
 2673: 				 * is higher than the multiple of stepm and negative otherwise.
 2674: 				 */
 2675: 	  }
 2676: 	  else{
 2677: 	    dh[mi][i]=jk+1;
 2678: 	    bh[mi][i]=ju;
 2679: 	  }
 2680: 	  if(dh[mi][i]==0){
 2681: 	    dh[mi][i]=1; /* At least one step */
 2682: 	    bh[mi][i]=ju; /* At least one step */
 2683: 	    /*  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);*/
 2684: 	  }
 2685: 	} /* end if mle */
 2686:       }
 2687:     } /* end wave */
 2688:   }
 2689:   jmean=sum/k;
 2690:   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);
 2691:   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);
 2692:  }
 2693: 
 2694: /*********** Tricode ****************************/
 2695: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
 2696: {
 2697:   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
 2698:   /*	  Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
 2699:   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
 2700:    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
 2701:   /* nbcode[Tvar[j]][1]= 
 2702:   */
 2703: 
 2704:   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
 2705:   int modmaxcovj=0; /* Modality max of covariates j */
 2706:   int cptcode=0; /* Modality max of covariates j */
 2707:   int modmincovj=0; /* Modality min of covariates j */
 2708: 
 2709: 
 2710:   cptcoveff=0; 
 2711:  
 2712:   for (k=-1; k < maxncov; k++) Ndum[k]=0;
 2713:   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
 2714: 
 2715:   /* Loop on covariates without age and products */
 2716:   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
 2717:     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
 2718: 			       modality of this covariate Vj*/ 
 2719:       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
 2720: 				    * If product of Vn*Vm, still boolean *:
 2721: 				    * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
 2722: 				    * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
 2723:       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
 2724: 				      modality of the nth covariate of individual i. */
 2725:       if (ij > modmaxcovj)
 2726:         modmaxcovj=ij; 
 2727:       else if (ij < modmincovj) 
 2728: 	modmincovj=ij; 
 2729:       if ((ij < -1) && (ij > NCOVMAX)){
 2730: 	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
 2731: 	exit(1);
 2732:       }else
 2733:       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
 2734:       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
 2735:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 2736:       /* getting the maximum value of the modality of the covariate
 2737: 	 (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
 2738: 	 female is 1, then modmaxcovj=1.*/
 2739:     }
 2740:     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
 2741:     cptcode=modmaxcovj;
 2742:     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
 2743:    /*for (i=0; i<=cptcode; i++) {*/
 2744:     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
 2745:       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
 2746:       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
 2747: 	ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
 2748:       }
 2749:       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
 2750: 	 historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
 2751:     } /* Ndum[-1] number of undefined modalities */
 2752: 
 2753:     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
 2754:     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
 2755:     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
 2756:        modmincovj=3; modmaxcovj = 7;
 2757:        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
 2758:        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
 2759:        variables V1_1 and V1_2.
 2760:        nbcode[Tvar[j]][ij]=k;
 2761:        nbcode[Tvar[j]][1]=0;
 2762:        nbcode[Tvar[j]][2]=1;
 2763:        nbcode[Tvar[j]][3]=2;
 2764:     */
 2765:     ij=1; /* ij is similar to i but can jumps over null modalities */
 2766:     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
 2767:       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
 2768: 	/*recode from 0 */
 2769: 	if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
 2770: 	  nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
 2771: 				     k is a modality. If we have model=V1+V1*sex 
 2772: 				     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
 2773: 	  ij++;
 2774: 	}
 2775: 	if (ij > ncodemax[j]) break; 
 2776:       }  /* end of loop on */
 2777:     } /* end of loop on modality */ 
 2778:   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
 2779:   
 2780:  for (k=-1; k< maxncov; k++) Ndum[k]=0; 
 2781:   
 2782:   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
 2783:    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
 2784:    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
 2785:    Ndum[ij]++; 
 2786:  } 
 2787: 
 2788:  ij=1;
 2789:  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
 2790:    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
 2791:    if((Ndum[i]!=0) && (i<=ncovcol)){
 2792:      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
 2793:      Tvaraff[ij]=i; /*For printing (unclear) */
 2794:      ij++;
 2795:    }else
 2796:        Tvaraff[ij]=0;
 2797:  }
 2798:  ij--;
 2799:  cptcoveff=ij; /*Number of total covariates*/
 2800: 
 2801: }
 2802: 
 2803: 
 2804: /*********** Health Expectancies ****************/
 2805: 
 2806: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
 2807: 
 2808: {
 2809:   /* Health expectancies, no variances */
 2810:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
 2811:   int nhstepma, nstepma; /* Decreasing with age */
 2812:   double age, agelim, hf;
 2813:   double ***p3mat;
 2814:   double eip;
 2815: 
 2816:   pstamp(ficreseij);
 2817:   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
 2818:   fprintf(ficreseij,"# Age");
 2819:   for(i=1; i<=nlstate;i++){
 2820:     for(j=1; j<=nlstate;j++){
 2821:       fprintf(ficreseij," e%1d%1d ",i,j);
 2822:     }
 2823:     fprintf(ficreseij," e%1d. ",i);
 2824:   }
 2825:   fprintf(ficreseij,"\n");
 2826: 
 2827:   
 2828:   if(estepm < stepm){
 2829:     printf ("Problem %d lower than %d\n",estepm, stepm);
 2830:   }
 2831:   else  hstepm=estepm;   
 2832:   /* We compute the life expectancy from trapezoids spaced every estepm months
 2833:    * This is mainly to measure the difference between two models: for example
 2834:    * if stepm=24 months pijx are given only every 2 years and by summing them
 2835:    * we are calculating an estimate of the Life Expectancy assuming a linear 
 2836:    * progression in between and thus overestimating or underestimating according
 2837:    * to the curvature of the survival function. If, for the same date, we 
 2838:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
 2839:    * to compare the new estimate of Life expectancy with the same linear 
 2840:    * hypothesis. A more precise result, taking into account a more precise
 2841:    * curvature will be obtained if estepm is as small as stepm. */
 2842: 
 2843:   /* For example we decided to compute the life expectancy with the smallest unit */
 2844:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 2845:      nhstepm is the number of hstepm from age to agelim 
 2846:      nstepm is the number of stepm from age to agelin. 
 2847:      Look at hpijx to understand the reason of that which relies in memory size
 2848:      and note for a fixed period like estepm months */
 2849:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 2850:      survival function given by stepm (the optimization length). Unfortunately it
 2851:      means that if the survival funtion is printed only each two years of age and if
 2852:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 2853:      results. So we changed our mind and took the option of the best precision.
 2854:   */
 2855:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 2856: 
 2857:   agelim=AGESUP;
 2858:   /* If stepm=6 months */
 2859:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
 2860:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 2861:     
 2862: /* nhstepm age range expressed in number of stepm */
 2863:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 2864:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 2865:   /* if (stepm >= YEARM) hstepm=1;*/
 2866:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 2867:   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2868: 
 2869:   for (age=bage; age<=fage; age ++){ 
 2870:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 2871:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 2872:     /* if (stepm >= YEARM) hstepm=1;*/
 2873:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
 2874: 
 2875:     /* If stepm=6 months */
 2876:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
 2877:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
 2878:     
 2879:     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 2880:     
 2881:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 2882:     
 2883:     printf("%d|",(int)age);fflush(stdout);
 2884:     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 2885:     
 2886:     /* Computing expectancies */
 2887:     for(i=1; i<=nlstate;i++)
 2888:       for(j=1; j<=nlstate;j++)
 2889: 	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 2890: 	  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 2891: 	  
 2892: 	  /* 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]);*/
 2893: 
 2894: 	}
 2895: 
 2896:     fprintf(ficreseij,"%3.0f",age );
 2897:     for(i=1; i<=nlstate;i++){
 2898:       eip=0;
 2899:       for(j=1; j<=nlstate;j++){
 2900: 	eip +=eij[i][j][(int)age];
 2901: 	fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
 2902:       }
 2903:       fprintf(ficreseij,"%9.4f", eip );
 2904:     }
 2905:     fprintf(ficreseij,"\n");
 2906:     
 2907:   }
 2908:   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2909:   printf("\n");
 2910:   fprintf(ficlog,"\n");
 2911:   
 2912: }
 2913: 
 2914: 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[] )
 2915: 
 2916: {
 2917:   /* Covariances of health expectancies eij and of total life expectancies according
 2918:    to initial status i, ei. .
 2919:   */
 2920:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
 2921:   int nhstepma, nstepma; /* Decreasing with age */
 2922:   double age, agelim, hf;
 2923:   double ***p3matp, ***p3matm, ***varhe;
 2924:   double **dnewm,**doldm;
 2925:   double *xp, *xm;
 2926:   double **gp, **gm;
 2927:   double ***gradg, ***trgradg;
 2928:   int theta;
 2929: 
 2930:   double eip, vip;
 2931: 
 2932:   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 2933:   xp=vector(1,npar);
 2934:   xm=vector(1,npar);
 2935:   dnewm=matrix(1,nlstate*nlstate,1,npar);
 2936:   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 2937:   
 2938:   pstamp(ficresstdeij);
 2939:   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
 2940:   fprintf(ficresstdeij,"# Age");
 2941:   for(i=1; i<=nlstate;i++){
 2942:     for(j=1; j<=nlstate;j++)
 2943:       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
 2944:     fprintf(ficresstdeij," e%1d. ",i);
 2945:   }
 2946:   fprintf(ficresstdeij,"\n");
 2947: 
 2948:   pstamp(ficrescveij);
 2949:   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
 2950:   fprintf(ficrescveij,"# Age");
 2951:   for(i=1; i<=nlstate;i++)
 2952:     for(j=1; j<=nlstate;j++){
 2953:       cptj= (j-1)*nlstate+i;
 2954:       for(i2=1; i2<=nlstate;i2++)
 2955: 	for(j2=1; j2<=nlstate;j2++){
 2956: 	  cptj2= (j2-1)*nlstate+i2;
 2957: 	  if(cptj2 <= cptj)
 2958: 	    fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
 2959: 	}
 2960:     }
 2961:   fprintf(ficrescveij,"\n");
 2962:   
 2963:   if(estepm < stepm){
 2964:     printf ("Problem %d lower than %d\n",estepm, stepm);
 2965:   }
 2966:   else  hstepm=estepm;   
 2967:   /* We compute the life expectancy from trapezoids spaced every estepm months
 2968:    * This is mainly to measure the difference between two models: for example
 2969:    * if stepm=24 months pijx are given only every 2 years and by summing them
 2970:    * we are calculating an estimate of the Life Expectancy assuming a linear 
 2971:    * progression in between and thus overestimating or underestimating according
 2972:    * to the curvature of the survival function. If, for the same date, we 
 2973:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
 2974:    * to compare the new estimate of Life expectancy with the same linear 
 2975:    * hypothesis. A more precise result, taking into account a more precise
 2976:    * curvature will be obtained if estepm is as small as stepm. */
 2977: 
 2978:   /* For example we decided to compute the life expectancy with the smallest unit */
 2979:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 2980:      nhstepm is the number of hstepm from age to agelim 
 2981:      nstepm is the number of stepm from age to agelin. 
 2982:      Look at hpijx to understand the reason of that which relies in memory size
 2983:      and note for a fixed period like estepm months */
 2984:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 2985:      survival function given by stepm (the optimization length). Unfortunately it
 2986:      means that if the survival funtion is printed only each two years of age and if
 2987:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 2988:      results. So we changed our mind and took the option of the best precision.
 2989:   */
 2990:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 2991: 
 2992:   /* If stepm=6 months */
 2993:   /* nhstepm age range expressed in number of stepm */
 2994:   agelim=AGESUP;
 2995:   nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
 2996:   /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 2997:   /* if (stepm >= YEARM) hstepm=1;*/
 2998:   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 2999:   
 3000:   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3001:   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3002:   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 3003:   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 3004:   gp=matrix(0,nhstepm,1,nlstate*nlstate);
 3005:   gm=matrix(0,nhstepm,1,nlstate*nlstate);
 3006: 
 3007:   for (age=bage; age<=fage; age ++){ 
 3008:     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 3009:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 3010:     /* if (stepm >= YEARM) hstepm=1;*/
 3011:     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
 3012: 
 3013:     /* If stepm=6 months */
 3014:     /* Computed by stepm unit matrices, product of hstepma matrices, stored
 3015:        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
 3016:     
 3017:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 3018: 
 3019:     /* Computing  Variances of health expectancies */
 3020:     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
 3021:        decrease memory allocation */
 3022:     for(theta=1; theta <=npar; theta++){
 3023:       for(i=1; i<=npar; i++){ 
 3024: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 3025: 	xm[i] = x[i] - (i==theta ?delti[theta]:0);
 3026:       }
 3027:       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
 3028:       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
 3029:   
 3030:       for(j=1; j<= nlstate; j++){
 3031: 	for(i=1; i<=nlstate; i++){
 3032: 	  for(h=0; h<=nhstepm-1; h++){
 3033: 	    gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
 3034: 	    gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
 3035: 	  }
 3036: 	}
 3037:       }
 3038:      
 3039:       for(ij=1; ij<= nlstate*nlstate; ij++)
 3040: 	for(h=0; h<=nhstepm-1; h++){
 3041: 	  gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 3042: 	}
 3043:     }/* End theta */
 3044:     
 3045:     
 3046:     for(h=0; h<=nhstepm-1; h++)
 3047:       for(j=1; j<=nlstate*nlstate;j++)
 3048: 	for(theta=1; theta <=npar; theta++)
 3049: 	  trgradg[h][j][theta]=gradg[h][theta][j];
 3050:     
 3051: 
 3052:      for(ij=1;ij<=nlstate*nlstate;ij++)
 3053:       for(ji=1;ji<=nlstate*nlstate;ji++)
 3054: 	varhe[ij][ji][(int)age] =0.;
 3055: 
 3056:      printf("%d|",(int)age);fflush(stdout);
 3057:      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 3058:      for(h=0;h<=nhstepm-1;h++){
 3059:       for(k=0;k<=nhstepm-1;k++){
 3060: 	matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 3061: 	matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
 3062: 	for(ij=1;ij<=nlstate*nlstate;ij++)
 3063: 	  for(ji=1;ji<=nlstate*nlstate;ji++)
 3064: 	    varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
 3065:       }
 3066:     }
 3067: 
 3068:     /* Computing expectancies */
 3069:     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 3070:     for(i=1; i<=nlstate;i++)
 3071:       for(j=1; j<=nlstate;j++)
 3072: 	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 3073: 	  eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
 3074: 	  
 3075: 	  /* 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]);*/
 3076: 
 3077: 	}
 3078: 
 3079:     fprintf(ficresstdeij,"%3.0f",age );
 3080:     for(i=1; i<=nlstate;i++){
 3081:       eip=0.;
 3082:       vip=0.;
 3083:       for(j=1; j<=nlstate;j++){
 3084: 	eip += eij[i][j][(int)age];
 3085: 	for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
 3086: 	  vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
 3087: 	fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
 3088:       }
 3089:       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
 3090:     }
 3091:     fprintf(ficresstdeij,"\n");
 3092: 
 3093:     fprintf(ficrescveij,"%3.0f",age );
 3094:     for(i=1; i<=nlstate;i++)
 3095:       for(j=1; j<=nlstate;j++){
 3096: 	cptj= (j-1)*nlstate+i;
 3097: 	for(i2=1; i2<=nlstate;i2++)
 3098: 	  for(j2=1; j2<=nlstate;j2++){
 3099: 	    cptj2= (j2-1)*nlstate+i2;
 3100: 	    if(cptj2 <= cptj)
 3101: 	      fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
 3102: 	  }
 3103:       }
 3104:     fprintf(ficrescveij,"\n");
 3105:    
 3106:   }
 3107:   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 3108:   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 3109:   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
 3110:   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
 3111:   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3112:   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3113:   printf("\n");
 3114:   fprintf(ficlog,"\n");
 3115: 
 3116:   free_vector(xm,1,npar);
 3117:   free_vector(xp,1,npar);
 3118:   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 3119:   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 3120:   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 3121: }
 3122: 
 3123: /************ Variance ******************/
 3124: 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[])
 3125: {
 3126:   /* Variance of health expectancies */
 3127:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 3128:   /* double **newm;*/
 3129:   double **dnewm,**doldm;
 3130:   double **dnewmp,**doldmp;
 3131:   int i, j, nhstepm, hstepm, h, nstepm ;
 3132:   int k, cptcode;
 3133:   double *xp;
 3134:   double **gp, **gm;  /* for var eij */
 3135:   double ***gradg, ***trgradg; /*for var eij */
 3136:   double **gradgp, **trgradgp; /* for var p point j */
 3137:   double *gpp, *gmp; /* for var p point j */
 3138:   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 3139:   double ***p3mat;
 3140:   double age,agelim, hf;
 3141:   double ***mobaverage;
 3142:   int theta;
 3143:   char digit[4];
 3144:   char digitp[25];
 3145: 
 3146:   char fileresprobmorprev[FILENAMELENGTH];
 3147: 
 3148:   if(popbased==1){
 3149:     if(mobilav!=0)
 3150:       strcpy(digitp,"-populbased-mobilav-");
 3151:     else strcpy(digitp,"-populbased-nomobil-");
 3152:   }
 3153:   else 
 3154:     strcpy(digitp,"-stablbased-");
 3155: 
 3156:   if (mobilav!=0) {
 3157:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 3158:     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 3159:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 3160:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
 3161:     }
 3162:   }
 3163: 
 3164:   strcpy(fileresprobmorprev,"prmorprev"); 
 3165:   sprintf(digit,"%-d",ij);
 3166:   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 3167:   strcat(fileresprobmorprev,digit); /* Tvar to be done */
 3168:   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 3169:   strcat(fileresprobmorprev,fileres);
 3170:   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
 3171:     printf("Problem with resultfile: %s\n", fileresprobmorprev);
 3172:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 3173:   }
 3174:   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 3175:  
 3176:   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 3177:   pstamp(ficresprobmorprev);
 3178:   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);
 3179:   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 3180:   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 3181:     fprintf(ficresprobmorprev," p.%-d SE",j);
 3182:     for(i=1; i<=nlstate;i++)
 3183:       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 3184:   }  
 3185:   fprintf(ficresprobmorprev,"\n");
 3186:   fprintf(ficgp,"\n# Routine varevsij");
 3187:   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
 3188:   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");
 3189:   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 3190: /*   } */
 3191:   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 3192:   pstamp(ficresvij);
 3193:   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
 3194:   if(popbased==1)
 3195:     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);
 3196:   else
 3197:     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
 3198:   fprintf(ficresvij,"# Age");
 3199:   for(i=1; i<=nlstate;i++)
 3200:     for(j=1; j<=nlstate;j++)
 3201:       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
 3202:   fprintf(ficresvij,"\n");
 3203: 
 3204:   xp=vector(1,npar);
 3205:   dnewm=matrix(1,nlstate,1,npar);
 3206:   doldm=matrix(1,nlstate,1,nlstate);
 3207:   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 3208:   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 3209: 
 3210:   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 3211:   gpp=vector(nlstate+1,nlstate+ndeath);
 3212:   gmp=vector(nlstate+1,nlstate+ndeath);
 3213:   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 3214:   
 3215:   if(estepm < stepm){
 3216:     printf ("Problem %d lower than %d\n",estepm, stepm);
 3217:   }
 3218:   else  hstepm=estepm;   
 3219:   /* For example we decided to compute the life expectancy with the smallest unit */
 3220:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 3221:      nhstepm is the number of hstepm from age to agelim 
 3222:      nstepm is the number of stepm from age to agelin. 
 3223:      Look at function hpijx to understand why (it is linked to memory size questions) */
 3224:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 3225:      survival function given by stepm (the optimization length). Unfortunately it
 3226:      means that if the survival funtion is printed every two years of age and if
 3227:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 3228:      results. So we changed our mind and took the option of the best precision.
 3229:   */
 3230:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 3231:   agelim = AGESUP;
 3232:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 3233:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 3234:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 3235:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3236:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 3237:     gp=matrix(0,nhstepm,1,nlstate);
 3238:     gm=matrix(0,nhstepm,1,nlstate);
 3239: 
 3240: 
 3241:     for(theta=1; theta <=npar; theta++){
 3242:       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 3243: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 3244:       }
 3245:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 3246:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 3247: 
 3248:       if (popbased==1) {
 3249: 	if(mobilav ==0){
 3250: 	  for(i=1; i<=nlstate;i++)
 3251: 	    prlim[i][i]=probs[(int)age][i][ij];
 3252: 	}else{ /* mobilav */ 
 3253: 	  for(i=1; i<=nlstate;i++)
 3254: 	    prlim[i][i]=mobaverage[(int)age][i][ij];
 3255: 	}
 3256:       }
 3257:   
 3258:       for(j=1; j<= nlstate; j++){
 3259: 	for(h=0; h<=nhstepm; h++){
 3260: 	  for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 3261: 	    gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 3262: 	}
 3263:       }
 3264:       /* This for computing probability of death (h=1 means
 3265:          computed over hstepm matrices product = hstepm*stepm months) 
 3266:          as a weighted average of prlim.
 3267:       */
 3268:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
 3269: 	for(i=1,gpp[j]=0.; i<= nlstate; i++)
 3270: 	  gpp[j] += prlim[i][i]*p3mat[i][j][1];
 3271:       }    
 3272:       /* end probability of death */
 3273: 
 3274:       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 3275: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 3276:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 3277:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 3278:  
 3279:       if (popbased==1) {
 3280: 	if(mobilav ==0){
 3281: 	  for(i=1; i<=nlstate;i++)
 3282: 	    prlim[i][i]=probs[(int)age][i][ij];
 3283: 	}else{ /* mobilav */ 
 3284: 	  for(i=1; i<=nlstate;i++)
 3285: 	    prlim[i][i]=mobaverage[(int)age][i][ij];
 3286: 	}
 3287:       }
 3288: 
 3289:       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
 3290: 	for(h=0; h<=nhstepm; h++){
 3291: 	  for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 3292: 	    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 3293: 	}
 3294:       }
 3295:       /* This for computing probability of death (h=1 means
 3296:          computed over hstepm matrices product = hstepm*stepm months) 
 3297:          as a weighted average of prlim.
 3298:       */
 3299:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
 3300: 	for(i=1,gmp[j]=0.; i<= nlstate; i++)
 3301:          gmp[j] += prlim[i][i]*p3mat[i][j][1];
 3302:       }    
 3303:       /* end probability of death */
 3304: 
 3305:       for(j=1; j<= nlstate; j++) /* vareij */
 3306: 	for(h=0; h<=nhstepm; h++){
 3307: 	  gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 3308: 	}
 3309: 
 3310:       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 3311: 	gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 3312:       }
 3313: 
 3314:     } /* End theta */
 3315: 
 3316:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 3317: 
 3318:     for(h=0; h<=nhstepm; h++) /* veij */
 3319:       for(j=1; j<=nlstate;j++)
 3320: 	for(theta=1; theta <=npar; theta++)
 3321: 	  trgradg[h][j][theta]=gradg[h][theta][j];
 3322: 
 3323:     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 3324:       for(theta=1; theta <=npar; theta++)
 3325: 	trgradgp[j][theta]=gradgp[theta][j];
 3326:   
 3327: 
 3328:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 3329:     for(i=1;i<=nlstate;i++)
 3330:       for(j=1;j<=nlstate;j++)
 3331: 	vareij[i][j][(int)age] =0.;
 3332: 
 3333:     for(h=0;h<=nhstepm;h++){
 3334:       for(k=0;k<=nhstepm;k++){
 3335: 	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 3336: 	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 3337: 	for(i=1;i<=nlstate;i++)
 3338: 	  for(j=1;j<=nlstate;j++)
 3339: 	    vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 3340:       }
 3341:     }
 3342:   
 3343:     /* pptj */
 3344:     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 3345:     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
 3346:     for(j=nlstate+1;j<=nlstate+ndeath;j++)
 3347:       for(i=nlstate+1;i<=nlstate+ndeath;i++)
 3348: 	varppt[j][i]=doldmp[j][i];
 3349:     /* end ppptj */
 3350:     /*  x centered again */
 3351:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 3352:     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
 3353:  
 3354:     if (popbased==1) {
 3355:       if(mobilav ==0){
 3356: 	for(i=1; i<=nlstate;i++)
 3357: 	  prlim[i][i]=probs[(int)age][i][ij];
 3358:       }else{ /* mobilav */ 
 3359: 	for(i=1; i<=nlstate;i++)
 3360: 	  prlim[i][i]=mobaverage[(int)age][i][ij];
 3361:       }
 3362:     }
 3363:              
 3364:     /* This for computing probability of death (h=1 means
 3365:        computed over hstepm (estepm) matrices product = hstepm*stepm months) 
 3366:        as a weighted average of prlim.
 3367:     */
 3368:     for(j=nlstate+1;j<=nlstate+ndeath;j++){
 3369:       for(i=1,gmp[j]=0.;i<= nlstate; i++) 
 3370: 	gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
 3371:     }    
 3372:     /* end probability of death */
 3373: 
 3374:     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
 3375:     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 3376:       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
 3377:       for(i=1; i<=nlstate;i++){
 3378: 	fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
 3379:       }
 3380:     } 
 3381:     fprintf(ficresprobmorprev,"\n");
 3382: 
 3383:     fprintf(ficresvij,"%.0f ",age );
 3384:     for(i=1; i<=nlstate;i++)
 3385:       for(j=1; j<=nlstate;j++){
 3386: 	fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 3387:       }
 3388:     fprintf(ficresvij,"\n");
 3389:     free_matrix(gp,0,nhstepm,1,nlstate);
 3390:     free_matrix(gm,0,nhstepm,1,nlstate);
 3391:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 3392:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
 3393:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3394:   } /* End age */
 3395:   free_vector(gpp,nlstate+1,nlstate+ndeath);
 3396:   free_vector(gmp,nlstate+1,nlstate+ndeath);
 3397:   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
 3398:   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 3399:   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
 3400:   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
 3401:   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 3402: /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 3403: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 3404: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
 3405:   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
 3406:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
 3407:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
 3408:   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
 3409:   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);
 3410:   /*  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);
 3411: */
 3412: /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
 3413:   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
 3414: 
 3415:   free_vector(xp,1,npar);
 3416:   free_matrix(doldm,1,nlstate,1,nlstate);
 3417:   free_matrix(dnewm,1,nlstate,1,npar);
 3418:   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 3419:   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 3420:   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 3421:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 3422:   fclose(ficresprobmorprev);
 3423:   fflush(ficgp);
 3424:   fflush(fichtm); 
 3425: }  /* end varevsij */
 3426: 
 3427: /************ Variance of prevlim ******************/
 3428: 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[])
 3429: {
 3430:   /* Variance of prevalence limit */
 3431:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 3432:   double **newm;
 3433:   double **dnewm,**doldm;
 3434:   int i, j, nhstepm, hstepm;
 3435:   int k, cptcode;
 3436:   double *xp;
 3437:   double *gp, *gm;
 3438:   double **gradg, **trgradg;
 3439:   double age,agelim;
 3440:   int theta;
 3441:   
 3442:   pstamp(ficresvpl);
 3443:   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
 3444:   fprintf(ficresvpl,"# Age");
 3445:   for(i=1; i<=nlstate;i++)
 3446:       fprintf(ficresvpl," %1d-%1d",i,i);
 3447:   fprintf(ficresvpl,"\n");
 3448: 
 3449:   xp=vector(1,npar);
 3450:   dnewm=matrix(1,nlstate,1,npar);
 3451:   doldm=matrix(1,nlstate,1,nlstate);
 3452:   
 3453:   hstepm=1*YEARM; /* Every year of age */
 3454:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 3455:   agelim = AGESUP;
 3456:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 3457:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 3458:     if (stepm >= YEARM) hstepm=1;
 3459:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 3460:     gradg=matrix(1,npar,1,nlstate);
 3461:     gp=vector(1,nlstate);
 3462:     gm=vector(1,nlstate);
 3463: 
 3464:     for(theta=1; theta <=npar; theta++){
 3465:       for(i=1; i<=npar; i++){ /* Computes gradient */
 3466: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 3467:       }
 3468:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 3469:       for(i=1;i<=nlstate;i++)
 3470: 	gp[i] = prlim[i][i];
 3471:     
 3472:       for(i=1; i<=npar; i++) /* Computes gradient */
 3473: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 3474:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 3475:       for(i=1;i<=nlstate;i++)
 3476: 	gm[i] = prlim[i][i];
 3477: 
 3478:       for(i=1;i<=nlstate;i++)
 3479: 	gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 3480:     } /* End theta */
 3481: 
 3482:     trgradg =matrix(1,nlstate,1,npar);
 3483: 
 3484:     for(j=1; j<=nlstate;j++)
 3485:       for(theta=1; theta <=npar; theta++)
 3486: 	trgradg[j][theta]=gradg[theta][j];
 3487: 
 3488:     for(i=1;i<=nlstate;i++)
 3489:       varpl[i][(int)age] =0.;
 3490:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 3491:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 3492:     for(i=1;i<=nlstate;i++)
 3493:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 3494: 
 3495:     fprintf(ficresvpl,"%.0f ",age );
 3496:     for(i=1; i<=nlstate;i++)
 3497:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 3498:     fprintf(ficresvpl,"\n");
 3499:     free_vector(gp,1,nlstate);
 3500:     free_vector(gm,1,nlstate);
 3501:     free_matrix(gradg,1,npar,1,nlstate);
 3502:     free_matrix(trgradg,1,nlstate,1,npar);
 3503:   } /* End age */
 3504: 
 3505:   free_vector(xp,1,npar);
 3506:   free_matrix(doldm,1,nlstate,1,npar);
 3507:   free_matrix(dnewm,1,nlstate,1,nlstate);
 3508: 
 3509: }
 3510: 
 3511: /************ Variance of one-step probabilities  ******************/
 3512: 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[])
 3513: {
 3514:   int i, j=0,  i1, k1, l1, t, tj;
 3515:   int k2, l2, j1,  z1;
 3516:   int k=0,l, cptcode;
 3517:   int first=1, first1, first2;
 3518:   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 3519:   double **dnewm,**doldm;
 3520:   double *xp;
 3521:   double *gp, *gm;
 3522:   double **gradg, **trgradg;
 3523:   double **mu;
 3524:   double age,agelim, cov[NCOVMAX+1];
 3525:   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 3526:   int theta;
 3527:   char fileresprob[FILENAMELENGTH];
 3528:   char fileresprobcov[FILENAMELENGTH];
 3529:   char fileresprobcor[FILENAMELENGTH];
 3530:   double ***varpij;
 3531: 
 3532:   strcpy(fileresprob,"prob"); 
 3533:   strcat(fileresprob,fileres);
 3534:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 3535:     printf("Problem with resultfile: %s\n", fileresprob);
 3536:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 3537:   }
 3538:   strcpy(fileresprobcov,"probcov"); 
 3539:   strcat(fileresprobcov,fileres);
 3540:   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 3541:     printf("Problem with resultfile: %s\n", fileresprobcov);
 3542:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 3543:   }
 3544:   strcpy(fileresprobcor,"probcor"); 
 3545:   strcat(fileresprobcor,fileres);
 3546:   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 3547:     printf("Problem with resultfile: %s\n", fileresprobcor);
 3548:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
 3549:   }
 3550:   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 3551:   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 3552:   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 3553:   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 3554:   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 3555:   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 3556:   pstamp(ficresprob);
 3557:   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 3558:   fprintf(ficresprob,"# Age");
 3559:   pstamp(ficresprobcov);
 3560:   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 3561:   fprintf(ficresprobcov,"# Age");
 3562:   pstamp(ficresprobcor);
 3563:   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 3564:   fprintf(ficresprobcor,"# Age");
 3565: 
 3566: 
 3567:   for(i=1; i<=nlstate;i++)
 3568:     for(j=1; j<=(nlstate+ndeath);j++){
 3569:       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 3570:       fprintf(ficresprobcov," p%1d-%1d ",i,j);
 3571:       fprintf(ficresprobcor," p%1d-%1d ",i,j);
 3572:     }  
 3573:  /* fprintf(ficresprob,"\n");
 3574:   fprintf(ficresprobcov,"\n");
 3575:   fprintf(ficresprobcor,"\n");
 3576:  */
 3577:   xp=vector(1,npar);
 3578:   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 3579:   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 3580:   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
 3581:   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
 3582:   first=1;
 3583:   fprintf(ficgp,"\n# Routine varprob");
 3584:   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 3585:   fprintf(fichtm,"\n");
 3586: 
 3587:   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
 3588:   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
 3589:   file %s<br>\n",optionfilehtmcov);
 3590:   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
 3591: and drawn. It helps understanding how is the covariance between two incidences.\
 3592:  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
 3593:   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. \
 3594: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
 3595: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
 3596: standard deviations wide on each axis. <br>\
 3597:  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
 3598:  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
 3599: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
 3600: 
 3601:   cov[1]=1;
 3602:   /* tj=cptcoveff; */
 3603:   tj = (int) pow(2,cptcoveff);
 3604:   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 3605:   j1=0;
 3606:   for(j1=1; j1<=tj;j1++){
 3607:     /*for(i1=1; i1<=ncodemax[t];i1++){ */
 3608:     /*j1++;*/
 3609:       if  (cptcovn>0) {
 3610: 	fprintf(ficresprob, "\n#********** Variable "); 
 3611: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 3612: 	fprintf(ficresprob, "**********\n#\n");
 3613: 	fprintf(ficresprobcov, "\n#********** Variable "); 
 3614: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 3615: 	fprintf(ficresprobcov, "**********\n#\n");
 3616: 	
 3617: 	fprintf(ficgp, "\n#********** Variable "); 
 3618: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 3619: 	fprintf(ficgp, "**********\n#\n");
 3620: 	
 3621: 	
 3622: 	fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 3623: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 3624: 	fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 3625: 	
 3626: 	fprintf(ficresprobcor, "\n#********** Variable ");    
 3627: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 3628: 	fprintf(ficresprobcor, "**********\n#");    
 3629:       }
 3630:       
 3631:       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 3632:       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 3633:       gp=vector(1,(nlstate)*(nlstate+ndeath));
 3634:       gm=vector(1,(nlstate)*(nlstate+ndeath));
 3635:       for (age=bage; age<=fage; age ++){ 
 3636: 	cov[2]=age;
 3637: 	for (k=1; k<=cptcovn;k++) {
 3638: 	  cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
 3639: 							 * 1  1 1 1 1
 3640: 							 * 2  2 1 1 1
 3641: 							 * 3  1 2 1 1
 3642: 							 */
 3643: 	  /* nbcode[1][1]=0 nbcode[1][2]=1;*/
 3644: 	}
 3645: 	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 3646: 	for (k=1; k<=cptcovprod;k++)
 3647: 	  cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 3648: 	
 3649:     
 3650: 	for(theta=1; theta <=npar; theta++){
 3651: 	  for(i=1; i<=npar; i++)
 3652: 	    xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
 3653: 	  
 3654: 	  pmij(pmmij,cov,ncovmodel,xp,nlstate);
 3655: 	  
 3656: 	  k=0;
 3657: 	  for(i=1; i<= (nlstate); i++){
 3658: 	    for(j=1; j<=(nlstate+ndeath);j++){
 3659: 	      k=k+1;
 3660: 	      gp[k]=pmmij[i][j];
 3661: 	    }
 3662: 	  }
 3663: 	  
 3664: 	  for(i=1; i<=npar; i++)
 3665: 	    xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
 3666:     
 3667: 	  pmij(pmmij,cov,ncovmodel,xp,nlstate);
 3668: 	  k=0;
 3669: 	  for(i=1; i<=(nlstate); i++){
 3670: 	    for(j=1; j<=(nlstate+ndeath);j++){
 3671: 	      k=k+1;
 3672: 	      gm[k]=pmmij[i][j];
 3673: 	    }
 3674: 	  }
 3675:      
 3676: 	  for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
 3677: 	    gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
 3678: 	}
 3679: 
 3680: 	for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 3681: 	  for(theta=1; theta <=npar; theta++)
 3682: 	    trgradg[j][theta]=gradg[theta][j];
 3683: 	
 3684: 	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 3685: 	matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
 3686: 
 3687: 	pmij(pmmij,cov,ncovmodel,x,nlstate);
 3688: 	
 3689: 	k=0;
 3690: 	for(i=1; i<=(nlstate); i++){
 3691: 	  for(j=1; j<=(nlstate+ndeath);j++){
 3692: 	    k=k+1;
 3693: 	    mu[k][(int) age]=pmmij[i][j];
 3694: 	  }
 3695: 	}
 3696:      	for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
 3697: 	  for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
 3698: 	    varpij[i][j][(int)age] = doldm[i][j];
 3699: 
 3700: 	/*printf("\n%d ",(int)age);
 3701: 	  for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 3702: 	  printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 3703: 	  fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 3704: 	  }*/
 3705: 
 3706: 	fprintf(ficresprob,"\n%d ",(int)age);
 3707: 	fprintf(ficresprobcov,"\n%d ",(int)age);
 3708: 	fprintf(ficresprobcor,"\n%d ",(int)age);
 3709: 
 3710: 	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
 3711: 	  fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
 3712: 	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 3713: 	  fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 3714: 	  fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
 3715: 	}
 3716: 	i=0;
 3717: 	for (k=1; k<=(nlstate);k++){
 3718:  	  for (l=1; l<=(nlstate+ndeath);l++){ 
 3719:  	    i++;
 3720: 	    fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
 3721: 	    fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
 3722: 	    for (j=1; j<=i;j++){
 3723: 	      /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
 3724: 	      fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
 3725: 	      fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
 3726: 	    }
 3727: 	  }
 3728: 	}/* end of loop for state */
 3729:       } /* end of loop for age */
 3730:       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 3731:       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
 3732:       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 3733:       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 3734:       
 3735:       /* Confidence intervalle of pij  */
 3736:       /*
 3737: 	fprintf(ficgp,"\nunset parametric;unset label");
 3738: 	fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
 3739: 	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 3740: 	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);
 3741: 	fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
 3742: 	fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
 3743: 	fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
 3744:       */
 3745: 
 3746:       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
 3747:       first1=1;first2=2;
 3748:       for (k2=1; k2<=(nlstate);k2++){
 3749: 	for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 3750: 	  if(l2==k2) continue;
 3751: 	  j=(k2-1)*(nlstate+ndeath)+l2;
 3752: 	  for (k1=1; k1<=(nlstate);k1++){
 3753: 	    for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 3754: 	      if(l1==k1) continue;
 3755: 	      i=(k1-1)*(nlstate+ndeath)+l1;
 3756: 	      if(i<=j) continue;
 3757: 	      for (age=bage; age<=fage; age ++){ 
 3758: 		if ((int)age %5==0){
 3759: 		  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
 3760: 		  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
 3761: 		  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
 3762: 		  mu1=mu[i][(int) age]/stepm*YEARM ;
 3763: 		  mu2=mu[j][(int) age]/stepm*YEARM;
 3764: 		  c12=cv12/sqrt(v1*v2);
 3765: 		  /* Computing eigen value of matrix of covariance */
 3766: 		  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 3767: 		  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 3768: 		  if ((lc2 <0) || (lc1 <0) ){
 3769: 		    if(first2==1){
 3770: 		      first1=0;
 3771: 		    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);
 3772: 		    }
 3773: 		    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);
 3774: 		    /* lc1=fabs(lc1); */ /* If we want to have them positive */
 3775: 		    /* lc2=fabs(lc2); */
 3776: 		  }
 3777: 
 3778: 		  /* Eigen vectors */
 3779: 		  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 3780: 		  /*v21=sqrt(1.-v11*v11); *//* error */
 3781: 		  v21=(lc1-v1)/cv12*v11;
 3782: 		  v12=-v21;
 3783: 		  v22=v11;
 3784: 		  tnalp=v21/v11;
 3785: 		  if(first1==1){
 3786: 		    first1=0;
 3787: 		    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);
 3788: 		  }
 3789: 		  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);
 3790: 		  /*printf(fignu*/
 3791: 		  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
 3792: 		  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
 3793: 		  if(first==1){
 3794: 		    first=0;
 3795:  		    fprintf(ficgp,"\nset parametric;unset label");
 3796: 		    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);
 3797: 		    fprintf(ficgp,"\nset ter png small size 320, 240");
 3798: 		    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
 3799:  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
 3800: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
 3801: 			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
 3802: 			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 3803: 		    fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 3804: 		    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
 3805: 		    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 3806: 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 3807: 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 3808: 		    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",\
 3809: 			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 3810: 			    mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
 3811: 		  }else{
 3812: 		    first=0;
 3813: 		    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
 3814: 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 3815: 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 3816: 		    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",\
 3817: 			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 3818: 			    mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
 3819: 		  }/* if first */
 3820: 		} /* age mod 5 */
 3821: 	      } /* end loop age */
 3822: 	      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 3823: 	      first=1;
 3824: 	    } /*l12 */
 3825: 	  } /* k12 */
 3826: 	} /*l1 */
 3827:       }/* k1 */
 3828:       /* } /* loop covariates */
 3829:   }
 3830:   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
 3831:   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
 3832:   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 3833:   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
 3834:   free_vector(xp,1,npar);
 3835:   fclose(ficresprob);
 3836:   fclose(ficresprobcov);
 3837:   fclose(ficresprobcor);
 3838:   fflush(ficgp);
 3839:   fflush(fichtmcov);
 3840: }
 3841: 
 3842: 
 3843: /******************* Printing html file ***********/
 3844: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 3845: 		  int lastpass, int stepm, int weightopt, char model[],\
 3846: 		  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
 3847: 		  int popforecast, int estepm ,\
 3848: 		  double jprev1, double mprev1,double anprev1, \
 3849: 		  double jprev2, double mprev2,double anprev2){
 3850:   int jj1, k1, i1, cpt;
 3851: 
 3852:    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
 3853:    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
 3854: </ul>");
 3855:    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
 3856:  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
 3857: 	   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
 3858:    fprintf(fichtm,"\
 3859:  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
 3860: 	   stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
 3861:    fprintf(fichtm,"\
 3862:  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
 3863: 	   subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
 3864:    fprintf(fichtm,"\
 3865:  - (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): \
 3866:    <a href=\"%s\">%s</a> <br>\n",
 3867: 	   estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
 3868:    fprintf(fichtm,"\
 3869:  - Population projections by age and states: \
 3870:    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
 3871: 
 3872: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
 3873: 
 3874:  m=pow(2,cptcoveff);
 3875:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 3876: 
 3877:  jj1=0;
 3878:  for(k1=1; k1<=m;k1++){
 3879:    for(i1=1; i1<=ncodemax[k1];i1++){
 3880:      jj1++;
 3881:      if (cptcovn > 0) {
 3882:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 3883:        for (cpt=1; cpt<=cptcoveff;cpt++) 
 3884: 	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 3885:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 3886:      }
 3887:      /* Pij */
 3888:      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> \
 3889: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
 3890:      /* Quasi-incidences */
 3891:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
 3892:  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> \
 3893: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
 3894:        /* Period (stable) prevalence in each health state */
 3895:        for(cpt=1; cpt<nlstate;cpt++){
 3896: 	 fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
 3897: <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
 3898:        }
 3899:      for(cpt=1; cpt<=nlstate;cpt++) {
 3900:         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
 3901: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
 3902:      }
 3903:    } /* end i1 */
 3904:  }/* End k1 */
 3905:  fprintf(fichtm,"</ul>");
 3906: 
 3907: 
 3908:  fprintf(fichtm,"\
 3909: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
 3910:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
 3911: 
 3912:  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 3913: 	 subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
 3914:  fprintf(fichtm,"\
 3915:  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 3916: 	 subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
 3917: 
 3918:  fprintf(fichtm,"\
 3919:  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 3920: 	 subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
 3921:  fprintf(fichtm,"\
 3922:  - 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): \
 3923:    <a href=\"%s\">%s</a> <br>\n</li>",
 3924: 	   estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
 3925:  fprintf(fichtm,"\
 3926:  - (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): \
 3927:    <a href=\"%s\">%s</a> <br>\n</li>",
 3928: 	   estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
 3929:  fprintf(fichtm,"\
 3930:  - 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",
 3931: 	 estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
 3932:  fprintf(fichtm,"\
 3933:  - 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",
 3934: 	 estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
 3935:  fprintf(fichtm,"\
 3936:  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
 3937: 	 subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
 3938: 
 3939: /*  if(popforecast==1) fprintf(fichtm,"\n */
 3940: /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
 3941: /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
 3942: /* 	<br>",fileres,fileres,fileres,fileres); */
 3943: /*  else  */
 3944: /*    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); */
 3945:  fflush(fichtm);
 3946:  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 3947: 
 3948:  m=pow(2,cptcoveff);
 3949:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 3950: 
 3951:  jj1=0;
 3952:  for(k1=1; k1<=m;k1++){
 3953:    for(i1=1; i1<=ncodemax[k1];i1++){
 3954:      jj1++;
 3955:      if (cptcovn > 0) {
 3956:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 3957:        for (cpt=1; cpt<=cptcoveff;cpt++) 
 3958: 	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 3959:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 3960:      }
 3961:      for(cpt=1; cpt<=nlstate;cpt++) {
 3962:        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
 3963: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
 3964: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
 3965:      }
 3966:      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 3967: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
 3968: true period expectancies (those weighted with period prevalences are also\
 3969:  drawn in addition to the population based expectancies computed using\
 3970:  observed and cahotic prevalences: %s%d.png<br>\
 3971: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
 3972:    } /* end i1 */
 3973:  }/* End k1 */
 3974:  fprintf(fichtm,"</ul>");
 3975:  fflush(fichtm);
 3976: }
 3977: 
 3978: /******************* Gnuplot file **************/
 3979: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 3980: 
 3981:   char dirfileres[132],optfileres[132];
 3982:   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
 3983:   int ng=0;
 3984: /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 3985: /*     printf("Problem with file %s",optionfilegnuplot); */
 3986: /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
 3987: /*   } */
 3988: 
 3989:   /*#ifdef windows */
 3990:   fprintf(ficgp,"cd \"%s\" \n",pathc);
 3991:     /*#endif */
 3992:   m=pow(2,cptcoveff);
 3993: 
 3994:   strcpy(dirfileres,optionfilefiname);
 3995:   strcpy(optfileres,"vpl");
 3996:  /* 1eme*/
 3997:   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
 3998:   for (cpt=1; cpt<= nlstate ; cpt ++) {
 3999:     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
 4000:      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
 4001:      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
 4002:      fprintf(ficgp,"set xlabel \"Age\" \n\
 4003: set ylabel \"Probability\" \n\
 4004: set ter png small size 320, 240\n\
 4005: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
 4006: 
 4007:      for (i=1; i<= nlstate ; i ++) {
 4008:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 4009:        else        fprintf(ficgp," \%%*lf (\%%*lf)");
 4010:      }
 4011:      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);
 4012:      for (i=1; i<= nlstate ; i ++) {
 4013:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 4014:        else fprintf(ficgp," \%%*lf (\%%*lf)");
 4015:      } 
 4016:      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
 4017:      for (i=1; i<= nlstate ; i ++) {
 4018:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 4019:        else fprintf(ficgp," \%%*lf (\%%*lf)");
 4020:      }  
 4021:      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
 4022:    }
 4023:   }
 4024:   /*2 eme*/
 4025:   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
 4026:   for (k1=1; k1<= m ; k1 ++) { 
 4027:     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
 4028:     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
 4029:     
 4030:     for (i=1; i<= nlstate+1 ; i ++) {
 4031:       k=2*i;
 4032:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
 4033:       for (j=1; j<= nlstate+1 ; j ++) {
 4034: 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 4035: 	else fprintf(ficgp," \%%*lf (\%%*lf)");
 4036:       }   
 4037:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
 4038:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
 4039:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
 4040:       for (j=1; j<= nlstate+1 ; j ++) {
 4041: 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 4042: 	else fprintf(ficgp," \%%*lf (\%%*lf)");
 4043:       }   
 4044:       fprintf(ficgp,"\" t\"\" w l lt 0,");
 4045:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
 4046:       for (j=1; j<= nlstate+1 ; j ++) {
 4047: 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 4048: 	else fprintf(ficgp," \%%*lf (\%%*lf)");
 4049:       }   
 4050:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
 4051:       else fprintf(ficgp,"\" t\"\" w l lt 0,");
 4052:     }
 4053:   }
 4054:   
 4055:   /*3eme*/
 4056:   
 4057:   for (k1=1; k1<= m ; k1 ++) { 
 4058:     for (cpt=1; cpt<= nlstate ; cpt ++) {
 4059:       /*       k=2+nlstate*(2*cpt-2); */
 4060:       k=2+(nlstate+1)*(cpt-1);
 4061:       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
 4062:       fprintf(ficgp,"set ter png small size 320, 240\n\
 4063: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
 4064:       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 4065: 	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 4066: 	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 4067: 	fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 4068: 	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 4069: 	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 4070: 	
 4071:       */
 4072:       for (i=1; i< nlstate ; i ++) {
 4073: 	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);
 4074: 	/*	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);*/
 4075: 	
 4076:       } 
 4077:       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
 4078:     }
 4079:   }
 4080:   
 4081:   /* CV preval stable (period) */
 4082:   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
 4083:     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
 4084:       k=3;
 4085:       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
 4086:       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
 4087:       l=(nlstate+ndeath)*(cpt-1)+1;
 4088:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 4089: set ter png small size 320, 240\n\
 4090: unset log y\n\
 4091: plot [%.f:%.f]  ", ageminpar, agemaxpar);
 4092:       for (i=1; i<= nlstate ; i ++){
 4093: 	if(i==1)
 4094: 	  fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
 4095: 	else
 4096: 	  fprintf(ficgp,", '' ");
 4097: 	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l,k+l);
 4098: 	for (j=1; j<= (nlstate-1) ; j ++)
 4099: 	  fprintf(ficgp,"+$%d",k+l+j);
 4100: 	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
 4101:       } /* nlstate */
 4102:       fprintf(ficgp,"\n");
 4103:     } /* end cpt state*/ 
 4104:   } /* end covariate */  
 4105:   
 4106:   /* proba elementaires */
 4107:   for(i=1,jk=1; i <=nlstate; i++){
 4108:     for(k=1; k <=(nlstate+ndeath); k++){
 4109:       if (k != i) {
 4110: 	for(j=1; j <=ncovmodel; j++){
 4111: 	  fprintf(ficgp,"p%d=%f ",jk,p[jk]);
 4112: 	  jk++; 
 4113: 	  fprintf(ficgp,"\n");
 4114: 	}
 4115:       }
 4116:     }
 4117:    }
 4118:   /*goto avoid;*/
 4119:    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
 4120:      for(jk=1; jk <=m; jk++) {
 4121:        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
 4122:        if (ng==2)
 4123: 	 fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
 4124:        else
 4125: 	 fprintf(ficgp,"\nset title \"Probability\"\n");
 4126:        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 4127:        i=1;
 4128:        for(k2=1; k2<=nlstate; k2++) {
 4129: 	 k3=i;
 4130: 	 for(k=1; k<=(nlstate+ndeath); k++) {
 4131: 	   if (k != k2){
 4132: 	     if(ng==2)
 4133: 	       fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
 4134: 	     else
 4135: 	       fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
 4136: 	     ij=1;/* To be checked else nbcode[0][0] wrong */
 4137: 	     for(j=3; j <=ncovmodel; j++) {
 4138: 	       /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
 4139: 	       /* 	 /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
 4140: 	       /* 	 ij++; */
 4141: 	       /* } */
 4142: 	       /* else */
 4143: 		 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 4144: 	     }
 4145: 	     fprintf(ficgp,")/(1");
 4146: 	     
 4147: 	     for(k1=1; k1 <=nlstate; k1++){   
 4148: 	       fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
 4149: 	       ij=1;
 4150: 	       for(j=3; j <=ncovmodel; j++){
 4151: 		 /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
 4152: 		 /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
 4153: 		 /*   ij++; */
 4154: 		 /* } */
 4155: 		 /* else */
 4156: 		   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 4157: 	       }
 4158: 	       fprintf(ficgp,")");
 4159: 	     }
 4160: 	     fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 4161: 	     if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 4162: 	     i=i+ncovmodel;
 4163: 	   }
 4164: 	 } /* end k */
 4165:        } /* end k2 */
 4166:      } /* end jk */
 4167:    } /* end ng */
 4168:  avoid:
 4169:    fflush(ficgp); 
 4170: }  /* end gnuplot */
 4171: 
 4172: 
 4173: /*************** Moving average **************/
 4174: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
 4175: 
 4176:   int i, cpt, cptcod;
 4177:   int modcovmax =1;
 4178:   int mobilavrange, mob;
 4179:   double age;
 4180: 
 4181:   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
 4182: 			   a covariate has 2 modalities */
 4183:   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
 4184: 
 4185:   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
 4186:     if(mobilav==1) mobilavrange=5; /* default */
 4187:     else mobilavrange=mobilav;
 4188:     for (age=bage; age<=fage; age++)
 4189:       for (i=1; i<=nlstate;i++)
 4190: 	for (cptcod=1;cptcod<=modcovmax;cptcod++)
 4191: 	  mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
 4192:     /* We keep the original values on the extreme ages bage, fage and for 
 4193:        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
 4194:        we use a 5 terms etc. until the borders are no more concerned. 
 4195:     */ 
 4196:     for (mob=3;mob <=mobilavrange;mob=mob+2){
 4197:       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
 4198: 	for (i=1; i<=nlstate;i++){
 4199: 	  for (cptcod=1;cptcod<=modcovmax;cptcod++){
 4200: 	    mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
 4201: 	      for (cpt=1;cpt<=(mob-1)/2;cpt++){
 4202: 		mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
 4203: 		mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
 4204: 	      }
 4205: 	    mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
 4206: 	  }
 4207: 	}
 4208:       }/* end age */
 4209:     }/* end mob */
 4210:   }else return -1;
 4211:   return 0;
 4212: }/* End movingaverage */
 4213: 
 4214: 
 4215: /************** Forecasting ******************/
 4216: 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){
 4217:   /* proj1, year, month, day of starting projection 
 4218:      agemin, agemax range of age
 4219:      dateprev1 dateprev2 range of dates during which prevalence is computed
 4220:      anproj2 year of en of projection (same day and month as proj1).
 4221:   */
 4222:   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
 4223:   int *popage;
 4224:   double agec; /* generic age */
 4225:   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 4226:   double *popeffectif,*popcount;
 4227:   double ***p3mat;
 4228:   double ***mobaverage;
 4229:   char fileresf[FILENAMELENGTH];
 4230: 
 4231:   agelim=AGESUP;
 4232:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
 4233:  
 4234:   strcpy(fileresf,"f"); 
 4235:   strcat(fileresf,fileres);
 4236:   if((ficresf=fopen(fileresf,"w"))==NULL) {
 4237:     printf("Problem with forecast resultfile: %s\n", fileresf);
 4238:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
 4239:   }
 4240:   printf("Computing forecasting: result on file '%s' \n", fileresf);
 4241:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
 4242: 
 4243:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 4244: 
 4245:   if (mobilav!=0) {
 4246:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4247:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
 4248:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 4249:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
 4250:     }
 4251:   }
 4252: 
 4253:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 4254:   if (stepm<=12) stepsize=1;
 4255:   if(estepm < stepm){
 4256:     printf ("Problem %d lower than %d\n",estepm, stepm);
 4257:   }
 4258:   else  hstepm=estepm;   
 4259: 
 4260:   hstepm=hstepm/stepm; 
 4261:   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
 4262:                                fractional in yp1 */
 4263:   anprojmean=yp;
 4264:   yp2=modf((yp1*12),&yp);
 4265:   mprojmean=yp;
 4266:   yp1=modf((yp2*30.5),&yp);
 4267:   jprojmean=yp;
 4268:   if(jprojmean==0) jprojmean=1;
 4269:   if(mprojmean==0) jprojmean=1;
 4270: 
 4271:   i1=cptcoveff;
 4272:   if (cptcovn < 1){i1=1;}
 4273:   
 4274:   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
 4275:   
 4276:   fprintf(ficresf,"#****** Routine prevforecast **\n");
 4277: 
 4278: /* 	      if (h==(int)(YEARM*yearp)){ */
 4279:   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
 4280:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 4281:       k=k+1;
 4282:       fprintf(ficresf,"\n#******");
 4283:       for(j=1;j<=cptcoveff;j++) {
 4284: 	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]]);
 4285:       }
 4286:       fprintf(ficresf,"******\n");
 4287:       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
 4288:       for(j=1; j<=nlstate+ndeath;j++){ 
 4289: 	for(i=1; i<=nlstate;i++) 	      
 4290:           fprintf(ficresf," p%d%d",i,j);
 4291: 	fprintf(ficresf," p.%d",j);
 4292:       }
 4293:       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
 4294: 	fprintf(ficresf,"\n");
 4295: 	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
 4296: 
 4297:      	for (agec=fage; agec>=(ageminpar-1); agec--){ 
 4298: 	  nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
 4299: 	  nhstepm = nhstepm/hstepm; 
 4300: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 4301: 	  oldm=oldms;savm=savms;
 4302: 	  hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
 4303: 	
 4304: 	  for (h=0; h<=nhstepm; h++){
 4305: 	    if (h*hstepm/YEARM*stepm ==yearp) {
 4306:               fprintf(ficresf,"\n");
 4307:               for(j=1;j<=cptcoveff;j++) 
 4308:                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 4309: 	      fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
 4310: 	    } 
 4311: 	    for(j=1; j<=nlstate+ndeath;j++) {
 4312: 	      ppij=0.;
 4313: 	      for(i=1; i<=nlstate;i++) {
 4314: 		if (mobilav==1) 
 4315: 		  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
 4316: 		else {
 4317: 		  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
 4318: 		}
 4319: 		if (h*hstepm/YEARM*stepm== yearp) {
 4320: 		  fprintf(ficresf," %.3f", p3mat[i][j][h]);
 4321: 		}
 4322: 	      } /* end i */
 4323: 	      if (h*hstepm/YEARM*stepm==yearp) {
 4324: 		fprintf(ficresf," %.3f", ppij);
 4325: 	      }
 4326: 	    }/* end j */
 4327: 	  } /* end h */
 4328: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 4329: 	} /* end agec */
 4330:       } /* end yearp */
 4331:     } /* end cptcod */
 4332:   } /* end  cptcov */
 4333:        
 4334:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4335: 
 4336:   fclose(ficresf);
 4337: }
 4338: 
 4339: /************** Forecasting *****not tested NB*************/
 4340: 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){
 4341:   
 4342:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
 4343:   int *popage;
 4344:   double calagedatem, agelim, kk1, kk2;
 4345:   double *popeffectif,*popcount;
 4346:   double ***p3mat,***tabpop,***tabpopprev;
 4347:   double ***mobaverage;
 4348:   char filerespop[FILENAMELENGTH];
 4349: 
 4350:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4351:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4352:   agelim=AGESUP;
 4353:   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
 4354:   
 4355:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
 4356:   
 4357:   
 4358:   strcpy(filerespop,"pop"); 
 4359:   strcat(filerespop,fileres);
 4360:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
 4361:     printf("Problem with forecast resultfile: %s\n", filerespop);
 4362:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
 4363:   }
 4364:   printf("Computing forecasting: result on file '%s' \n", filerespop);
 4365:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
 4366: 
 4367:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 4368: 
 4369:   if (mobilav!=0) {
 4370:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4371:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
 4372:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 4373:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
 4374:     }
 4375:   }
 4376: 
 4377:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 4378:   if (stepm<=12) stepsize=1;
 4379:   
 4380:   agelim=AGESUP;
 4381:   
 4382:   hstepm=1;
 4383:   hstepm=hstepm/stepm; 
 4384:   
 4385:   if (popforecast==1) {
 4386:     if((ficpop=fopen(popfile,"r"))==NULL) {
 4387:       printf("Problem with population file : %s\n",popfile);exit(0);
 4388:       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
 4389:     } 
 4390:     popage=ivector(0,AGESUP);
 4391:     popeffectif=vector(0,AGESUP);
 4392:     popcount=vector(0,AGESUP);
 4393:     
 4394:     i=1;   
 4395:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
 4396:    
 4397:     imx=i;
 4398:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
 4399:   }
 4400: 
 4401:   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
 4402:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 4403:       k=k+1;
 4404:       fprintf(ficrespop,"\n#******");
 4405:       for(j=1;j<=cptcoveff;j++) {
 4406: 	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 4407:       }
 4408:       fprintf(ficrespop,"******\n");
 4409:       fprintf(ficrespop,"# Age");
 4410:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
 4411:       if (popforecast==1)  fprintf(ficrespop," [Population]");
 4412:       
 4413:       for (cpt=0; cpt<=0;cpt++) { 
 4414: 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 4415: 	
 4416:      	for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
 4417: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 4418: 	  nhstepm = nhstepm/hstepm; 
 4419: 	  
 4420: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 4421: 	  oldm=oldms;savm=savms;
 4422: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 4423: 	
 4424: 	  for (h=0; h<=nhstepm; h++){
 4425: 	    if (h==(int) (calagedatem+YEARM*cpt)) {
 4426: 	      fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 4427: 	    } 
 4428: 	    for(j=1; j<=nlstate+ndeath;j++) {
 4429: 	      kk1=0.;kk2=0;
 4430: 	      for(i=1; i<=nlstate;i++) {	      
 4431: 		if (mobilav==1) 
 4432: 		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 4433: 		else {
 4434: 		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 4435: 		}
 4436: 	      }
 4437: 	      if (h==(int)(calagedatem+12*cpt)){
 4438: 		tabpop[(int)(agedeb)][j][cptcod]=kk1;
 4439: 		  /*fprintf(ficrespop," %.3f", kk1);
 4440: 		    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
 4441: 	      }
 4442: 	    }
 4443: 	    for(i=1; i<=nlstate;i++){
 4444: 	      kk1=0.;
 4445: 		for(j=1; j<=nlstate;j++){
 4446: 		  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
 4447: 		}
 4448: 		  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
 4449: 	    }
 4450: 
 4451: 	    if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
 4452: 	      fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
 4453: 	  }
 4454: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 4455: 	}
 4456:       }
 4457:  
 4458:   /******/
 4459: 
 4460:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
 4461: 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 4462: 	for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
 4463: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 4464: 	  nhstepm = nhstepm/hstepm; 
 4465: 	  
 4466: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 4467: 	  oldm=oldms;savm=savms;
 4468: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 4469: 	  for (h=0; h<=nhstepm; h++){
 4470: 	    if (h==(int) (calagedatem+YEARM*cpt)) {
 4471: 	      fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 4472: 	    } 
 4473: 	    for(j=1; j<=nlstate+ndeath;j++) {
 4474: 	      kk1=0.;kk2=0;
 4475: 	      for(i=1; i<=nlstate;i++) {	      
 4476: 		kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	
 4477: 	      }
 4478: 	      if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);	
 4479: 	    }
 4480: 	  }
 4481: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 4482: 	}
 4483:       }
 4484:    } 
 4485:   }
 4486:  
 4487:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4488: 
 4489:   if (popforecast==1) {
 4490:     free_ivector(popage,0,AGESUP);
 4491:     free_vector(popeffectif,0,AGESUP);
 4492:     free_vector(popcount,0,AGESUP);
 4493:   }
 4494:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4495:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 4496:   fclose(ficrespop);
 4497: } /* End of popforecast */
 4498: 
 4499: int fileappend(FILE *fichier, char *optionfich)
 4500: {
 4501:   if((fichier=fopen(optionfich,"a"))==NULL) {
 4502:     printf("Problem with file: %s\n", optionfich);
 4503:     fprintf(ficlog,"Problem with file: %s\n", optionfich);
 4504:     return (0);
 4505:   }
 4506:   fflush(fichier);
 4507:   return (1);
 4508: }
 4509: 
 4510: 
 4511: /**************** function prwizard **********************/
 4512: void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
 4513: {
 4514: 
 4515:   /* Wizard to print covariance matrix template */
 4516: 
 4517:   char ca[32], cb[32], cc[32];
 4518:   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
 4519:   int numlinepar;
 4520: 
 4521:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 4522:   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 4523:   for(i=1; i <=nlstate; i++){
 4524:     jj=0;
 4525:     for(j=1; j <=nlstate+ndeath; j++){
 4526:       if(j==i) continue;
 4527:       jj++;
 4528:       /*ca[0]= k+'a'-1;ca[1]='\0';*/
 4529:       printf("%1d%1d",i,j);
 4530:       fprintf(ficparo,"%1d%1d",i,j);
 4531:       for(k=1; k<=ncovmodel;k++){
 4532: 	/* 	  printf(" %lf",param[i][j][k]); */
 4533: 	/* 	  fprintf(ficparo," %lf",param[i][j][k]); */
 4534: 	printf(" 0.");
 4535: 	fprintf(ficparo," 0.");
 4536:       }
 4537:       printf("\n");
 4538:       fprintf(ficparo,"\n");
 4539:     }
 4540:   }
 4541:   printf("# Scales (for hessian or gradient estimation)\n");
 4542:   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
 4543:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
 4544:   for(i=1; i <=nlstate; i++){
 4545:     jj=0;
 4546:     for(j=1; j <=nlstate+ndeath; j++){
 4547:       if(j==i) continue;
 4548:       jj++;
 4549:       fprintf(ficparo,"%1d%1d",i,j);
 4550:       printf("%1d%1d",i,j);
 4551:       fflush(stdout);
 4552:       for(k=1; k<=ncovmodel;k++){
 4553: 	/* 	printf(" %le",delti3[i][j][k]); */
 4554: 	/* 	fprintf(ficparo," %le",delti3[i][j][k]); */
 4555: 	printf(" 0.");
 4556: 	fprintf(ficparo," 0.");
 4557:       }
 4558:       numlinepar++;
 4559:       printf("\n");
 4560:       fprintf(ficparo,"\n");
 4561:     }
 4562:   }
 4563:   printf("# Covariance matrix\n");
 4564: /* # 121 Var(a12)\n\ */
 4565: /* # 122 Cov(b12,a12) Var(b12)\n\ */
 4566: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
 4567: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
 4568: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
 4569: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
 4570: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
 4571: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
 4572:   fflush(stdout);
 4573:   fprintf(ficparo,"# Covariance matrix\n");
 4574:   /* # 121 Var(a12)\n\ */
 4575:   /* # 122 Cov(b12,a12) Var(b12)\n\ */
 4576:   /* #   ...\n\ */
 4577:   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
 4578:   
 4579:   for(itimes=1;itimes<=2;itimes++){
 4580:     jj=0;
 4581:     for(i=1; i <=nlstate; i++){
 4582:       for(j=1; j <=nlstate+ndeath; j++){
 4583: 	if(j==i) continue;
 4584: 	for(k=1; k<=ncovmodel;k++){
 4585: 	  jj++;
 4586: 	  ca[0]= k+'a'-1;ca[1]='\0';
 4587: 	  if(itimes==1){
 4588: 	    printf("#%1d%1d%d",i,j,k);
 4589: 	    fprintf(ficparo,"#%1d%1d%d",i,j,k);
 4590: 	  }else{
 4591: 	    printf("%1d%1d%d",i,j,k);
 4592: 	    fprintf(ficparo,"%1d%1d%d",i,j,k);
 4593: 	    /* 	printf(" %.5le",matcov[i][j]); */
 4594: 	  }
 4595: 	  ll=0;
 4596: 	  for(li=1;li <=nlstate; li++){
 4597: 	    for(lj=1;lj <=nlstate+ndeath; lj++){
 4598: 	      if(lj==li) continue;
 4599: 	      for(lk=1;lk<=ncovmodel;lk++){
 4600: 		ll++;
 4601: 		if(ll<=jj){
 4602: 		  cb[0]= lk +'a'-1;cb[1]='\0';
 4603: 		  if(ll<jj){
 4604: 		    if(itimes==1){
 4605: 		      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
 4606: 		      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
 4607: 		    }else{
 4608: 		      printf(" 0.");
 4609: 		      fprintf(ficparo," 0.");
 4610: 		    }
 4611: 		  }else{
 4612: 		    if(itimes==1){
 4613: 		      printf(" Var(%s%1d%1d)",ca,i,j);
 4614: 		      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
 4615: 		    }else{
 4616: 		      printf(" 0.");
 4617: 		      fprintf(ficparo," 0.");
 4618: 		    }
 4619: 		  }
 4620: 		}
 4621: 	      } /* end lk */
 4622: 	    } /* end lj */
 4623: 	  } /* end li */
 4624: 	  printf("\n");
 4625: 	  fprintf(ficparo,"\n");
 4626: 	  numlinepar++;
 4627: 	} /* end k*/
 4628:       } /*end j */
 4629:     } /* end i */
 4630:   } /* end itimes */
 4631: 
 4632: } /* end of prwizard */
 4633: /******************* Gompertz Likelihood ******************************/
 4634: double gompertz(double x[])
 4635: { 
 4636:   double A,B,L=0.0,sump=0.,num=0.;
 4637:   int i,n=0; /* n is the size of the sample */
 4638: 
 4639:   for (i=0;i<=imx-1 ; i++) {
 4640:     sump=sump+weight[i];
 4641:     /*    sump=sump+1;*/
 4642:     num=num+1;
 4643:   }
 4644:  
 4645:  
 4646:   /* for (i=0; i<=imx; i++) 
 4647:      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]);*/
 4648: 
 4649:   for (i=1;i<=imx ; i++)
 4650:     {
 4651:       if (cens[i] == 1 && wav[i]>1)
 4652: 	A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
 4653:       
 4654:       if (cens[i] == 0 && wav[i]>1)
 4655: 	A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
 4656: 	     +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
 4657:       
 4658:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
 4659:       if (wav[i] > 1 ) { /* ??? */
 4660: 	L=L+A*weight[i];
 4661: 	/* 	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]);*/
 4662:       }
 4663:     }
 4664: 
 4665:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
 4666:  
 4667:   return -2*L*num/sump;
 4668: }
 4669: 
 4670: #ifdef GSL
 4671: /******************* Gompertz_f Likelihood ******************************/
 4672: double gompertz_f(const gsl_vector *v, void *params)
 4673: { 
 4674:   double A,B,LL=0.0,sump=0.,num=0.;
 4675:   double *x= (double *) v->data;
 4676:   int i,n=0; /* n is the size of the sample */
 4677: 
 4678:   for (i=0;i<=imx-1 ; i++) {
 4679:     sump=sump+weight[i];
 4680:     /*    sump=sump+1;*/
 4681:     num=num+1;
 4682:   }
 4683:  
 4684:  
 4685:   /* for (i=0; i<=imx; i++) 
 4686:      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]);*/
 4687:   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
 4688:   for (i=1;i<=imx ; i++)
 4689:     {
 4690:       if (cens[i] == 1 && wav[i]>1)
 4691: 	A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
 4692:       
 4693:       if (cens[i] == 0 && wav[i]>1)
 4694: 	A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
 4695: 	     +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
 4696:       
 4697:       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
 4698:       if (wav[i] > 1 ) { /* ??? */
 4699: 	LL=LL+A*weight[i];
 4700: 	/* 	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]);*/
 4701:       }
 4702:     }
 4703: 
 4704:  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
 4705:   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
 4706:  
 4707:   return -2*LL*num/sump;
 4708: }
 4709: #endif
 4710: 
 4711: /******************* Printing html file ***********/
 4712: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
 4713: 		  int lastpass, int stepm, int weightopt, char model[],\
 4714: 		  int imx,  double p[],double **matcov,double agemortsup){
 4715:   int i,k;
 4716: 
 4717:   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
 4718:   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
 4719:   for (i=1;i<=2;i++) 
 4720:     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]));
 4721:   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
 4722:   fprintf(fichtm,"</ul>");
 4723: 
 4724: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
 4725: 
 4726:  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>");
 4727: 
 4728:  for (k=agegomp;k<(agemortsup-2);k++) 
 4729:    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]);
 4730: 
 4731:  
 4732:   fflush(fichtm);
 4733: }
 4734: 
 4735: /******************* Gnuplot file **************/
 4736: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 4737: 
 4738:   char dirfileres[132],optfileres[132];
 4739:   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
 4740:   int ng;
 4741: 
 4742: 
 4743:   /*#ifdef windows */
 4744:   fprintf(ficgp,"cd \"%s\" \n",pathc);
 4745:     /*#endif */
 4746: 
 4747: 
 4748:   strcpy(dirfileres,optionfilefiname);
 4749:   strcpy(optfileres,"vpl");
 4750:   fprintf(ficgp,"set out \"graphmort.png\"\n "); 
 4751:   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
 4752:   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
 4753:   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
 4754:   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
 4755: 
 4756: } 
 4757: 
 4758: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
 4759: {
 4760: 
 4761:   /*-------- data file ----------*/
 4762:   FILE *fic;
 4763:   char dummy[]="                         ";
 4764:   int i, j, n;
 4765:   int linei, month, year,iout;
 4766:   char line[MAXLINE], linetmp[MAXLINE];
 4767:   char stra[80], strb[80];
 4768:   char *stratrunc;
 4769:   int lstra;
 4770: 
 4771: 
 4772:   if((fic=fopen(datafile,"r"))==NULL)    {
 4773:     printf("Problem while opening datafile: %s\n", datafile);return 1;
 4774:     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
 4775:   }
 4776: 
 4777:   i=1;
 4778:   linei=0;
 4779:   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
 4780:     linei=linei+1;
 4781:     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
 4782:       if(line[j] == '\t')
 4783: 	line[j] = ' ';
 4784:     }
 4785:     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
 4786:       ;
 4787:     };
 4788:     line[j+1]=0;  /* Trims blanks at end of line */
 4789:     if(line[0]=='#'){
 4790:       fprintf(ficlog,"Comment line\n%s\n",line);
 4791:       printf("Comment line\n%s\n",line);
 4792:       continue;
 4793:     }
 4794:     trimbb(linetmp,line); /* Trims multiple blanks in line */
 4795:     for (j=0; line[j]!='\0';j++){
 4796:       line[j]=linetmp[j];
 4797:     }
 4798:   
 4799: 
 4800:     for (j=maxwav;j>=1;j--){
 4801:       cutv(stra, strb, line, ' '); 
 4802:       if(strb[0]=='.') { /* Missing status */
 4803: 	lval=-1;
 4804:       }else{
 4805: 	errno=0;
 4806: 	lval=strtol(strb,&endptr,10); 
 4807:       /*	if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
 4808: 	if( strb[0]=='\0' || (*endptr != '\0')){
 4809: 	  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);
 4810: 	  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);
 4811: 	  return 1;
 4812: 	}
 4813:       }
 4814:       s[j][i]=lval;
 4815:       
 4816:       strcpy(line,stra);
 4817:       cutv(stra, strb,line,' ');
 4818:       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
 4819:       }
 4820:       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
 4821: 	month=99;
 4822: 	year=9999;
 4823:       }else{
 4824: 	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);
 4825: 	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);
 4826: 	return 1;
 4827:       }
 4828:       anint[j][i]= (double) year; 
 4829:       mint[j][i]= (double)month; 
 4830:       strcpy(line,stra);
 4831:     } /* ENd Waves */
 4832:     
 4833:     cutv(stra, strb,line,' '); 
 4834:     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
 4835:     }
 4836:     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
 4837:       month=99;
 4838:       year=9999;
 4839:     }else{
 4840:       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);
 4841: 	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);
 4842: 	return 1;
 4843:     }
 4844:     andc[i]=(double) year; 
 4845:     moisdc[i]=(double) month; 
 4846:     strcpy(line,stra);
 4847:     
 4848:     cutv(stra, strb,line,' '); 
 4849:     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
 4850:     }
 4851:     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
 4852:       month=99;
 4853:       year=9999;
 4854:     }else{
 4855:       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);
 4856:       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);
 4857: 	return 1;
 4858:     }
 4859:     if (year==9999) {
 4860:       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);
 4861:       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);
 4862: 	return 1;
 4863: 
 4864:     }
 4865:     annais[i]=(double)(year);
 4866:     moisnais[i]=(double)(month); 
 4867:     strcpy(line,stra);
 4868:     
 4869:     cutv(stra, strb,line,' '); 
 4870:     errno=0;
 4871:     dval=strtod(strb,&endptr); 
 4872:     if( strb[0]=='\0' || (*endptr != '\0')){
 4873:       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
 4874:       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);
 4875:       fflush(ficlog);
 4876:       return 1;
 4877:     }
 4878:     weight[i]=dval; 
 4879:     strcpy(line,stra);
 4880:     
 4881:     for (j=ncovcol;j>=1;j--){
 4882:       cutv(stra, strb,line,' '); 
 4883:       if(strb[0]=='.') { /* Missing status */
 4884: 	lval=-1;
 4885:       }else{
 4886: 	errno=0;
 4887: 	lval=strtol(strb,&endptr,10); 
 4888: 	if( strb[0]=='\0' || (*endptr != '\0')){
 4889: 	  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);
 4890: 	  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);
 4891: 	  return 1;
 4892: 	}
 4893:       }
 4894:       if(lval <-1 || lval >1){
 4895: 	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
 4896:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
 4897:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
 4898:  For example, for multinomial values like 1, 2 and 3,\n \
 4899:  build V1=0 V2=0 for the reference value (1),\n \
 4900:         V1=1 V2=0 for (2) \n \
 4901:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
 4902:  output of IMaCh is often meaningless.\n \
 4903:  Exiting.\n",lval,linei, i,line,j);
 4904: 	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
 4905:  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
 4906:  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
 4907:  For example, for multinomial values like 1, 2 and 3,\n \
 4908:  build V1=0 V2=0 for the reference value (1),\n \
 4909:         V1=1 V2=0 for (2) \n \
 4910:  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
 4911:  output of IMaCh is often meaningless.\n \
 4912:  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
 4913: 	return 1;
 4914:       }
 4915:       covar[j][i]=(double)(lval);
 4916:       strcpy(line,stra);
 4917:     }  
 4918:     lstra=strlen(stra);
 4919:      
 4920:     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
 4921:       stratrunc = &(stra[lstra-9]);
 4922:       num[i]=atol(stratrunc);
 4923:     }
 4924:     else
 4925:       num[i]=atol(stra);
 4926:     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
 4927:       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;}*/
 4928:     
 4929:     i=i+1;
 4930:   } /* End loop reading  data */
 4931: 
 4932:   *imax=i-1; /* Number of individuals */
 4933:   fclose(fic);
 4934:  
 4935:   return (0);
 4936:   endread:
 4937:     printf("Exiting readdata: ");
 4938:     fclose(fic);
 4939:     return (1);
 4940: 
 4941: 
 4942: 
 4943: }
 4944: void removespace(char *str) {
 4945:   char *p1 = str, *p2 = str;
 4946:   do
 4947:     while (*p2 == ' ')
 4948:       p2++;
 4949:   while (*p1++ = *p2++);
 4950: }
 4951: 
 4952: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
 4953:    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
 4954:    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
 4955:    * - cptcovn or number of covariates k of the models excluding age*products =6
 4956:    * - cptcovage number of covariates with age*products =2
 4957:    * - cptcovs number of simple covariates
 4958:    * - 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
 4959:    *     which is a new column after the 9 (ncovcol) variables. 
 4960:    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
 4961:    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
 4962:    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
 4963:    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
 4964:  */
 4965: {
 4966:   int i, j, k, ks;
 4967:   int i1, j1, k1, k2;
 4968:   char modelsav[80];
 4969:   char stra[80], strb[80], strc[80], strd[80],stre[80];
 4970: 
 4971:   /*removespace(model);*/
 4972:   if (strlen(model) >1){ /* If there is at least 1 covariate */
 4973:     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
 4974:     j=nbocc(model,'+'); /**< j=Number of '+' */
 4975:     j1=nbocc(model,'*'); /**< j1=Number of '*' */
 4976:     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
 4977:     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
 4978:                   /* including age products which are counted in cptcovage.
 4979: 		  /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
 4980:     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
 4981:     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
 4982:     strcpy(modelsav,model); 
 4983:     if (strstr(model,"AGE") !=0){
 4984:       printf("Error. AGE must be in lower case 'age' model=%s ",model);
 4985:       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
 4986:       return 1;
 4987:     }
 4988:     if (strstr(model,"v") !=0){
 4989:       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
 4990:       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
 4991:       return 1;
 4992:     }
 4993:     
 4994:     /*   Design
 4995:      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
 4996:      *  <          ncovcol=8                >
 4997:      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
 4998:      *   k=  1    2      3       4     5       6      7        8
 4999:      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
 5000:      *  covar[k,i], value of kth covariate if not including age for individual i:
 5001:      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
 5002:      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
 5003:      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
 5004:      *  Tage[++cptcovage]=k
 5005:      *       if products, new covar are created after ncovcol with k1
 5006:      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
 5007:      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
 5008:      *  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
 5009:      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
 5010:      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
 5011:      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
 5012:      *  <          ncovcol=8                >
 5013:      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
 5014:      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
 5015:      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
 5016:      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
 5017:      * p Tprod[1]@2={                         6, 5}
 5018:      *p Tvard[1][1]@4= {7, 8, 5, 6}
 5019:      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
 5020:      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 5021:      *How to reorganize?
 5022:      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
 5023:      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
 5024:      *       {2,   1,     4,      8,    5,      6,     3,       7}
 5025:      * Struct []
 5026:      */
 5027: 
 5028:     /* This loop fills the array Tvar from the string 'model'.*/
 5029:     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
 5030:     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
 5031:     /* 	k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
 5032:     /* 	k=3 V4 Tvar[k=3]= 4 (from V4) */
 5033:     /* 	k=2 V1 Tvar[k=2]= 1 (from V1) */
 5034:     /* 	k=1 Tvar[1]=2 (from V2) */
 5035:     /* 	k=5 Tvar[5] */
 5036:     /* for (k=1; k<=cptcovn;k++) { */
 5037:     /* 	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
 5038:     /* 	} */
 5039:     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
 5040:     /*
 5041:      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
 5042:     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
 5043:         Tvar[k]=0;
 5044:     cptcovage=0;
 5045:     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
 5046:       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
 5047: 				     modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
 5048:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
 5049:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
 5050:       /*scanf("%d",i);*/
 5051:       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
 5052: 	cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
 5053: 	if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
 5054: 	  /* covar is not filled and then is empty */
 5055: 	  cptcovprod--;
 5056: 	  cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
 5057: 	  Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
 5058: 	  cptcovage++; /* Sums the number of covariates which include age as a product */
 5059: 	  Tage[cptcovage]=k;  /* Tage[1] = 4 */
 5060: 	  /*printf("stre=%s ", stre);*/
 5061: 	} else if (strcmp(strd,"age")==0) { /* or age*Vn */
 5062: 	  cptcovprod--;
 5063: 	  cutl(stre,strb,strc,'V');
 5064: 	  Tvar[k]=atoi(stre);
 5065: 	  cptcovage++;
 5066: 	  Tage[cptcovage]=k;
 5067: 	} else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
 5068: 	  /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
 5069: 	  cptcovn++;
 5070: 	  cptcovprodnoage++;k1++;
 5071: 	  cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
 5072: 	  Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
 5073: 				  because this model-covariate is a construction we invent a new column
 5074: 				  ncovcol + k1
 5075: 				  If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
 5076: 				  Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
 5077: 	  cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
 5078: 	  Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
 5079: 	  Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
 5080: 	  Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
 5081: 	  k2=k2+2;
 5082: 	  Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
 5083: 	  Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
 5084: 	  for (i=1; i<=lastobs;i++){
 5085: 	    /* Computes the new covariate which is a product of
 5086: 	       covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
 5087: 	    covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
 5088: 	  }
 5089: 	} /* End age is not in the model */
 5090:       } /* End if model includes a product */
 5091:       else { /* no more sum */
 5092: 	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
 5093:        /*  scanf("%d",i);*/
 5094: 	cutl(strd,strc,strb,'V');
 5095: 	ks++; /**< Number of simple covariates */
 5096: 	cptcovn++;
 5097: 	Tvar[k]=atoi(strd);
 5098:       }
 5099:       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
 5100:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
 5101: 	scanf("%d",i);*/
 5102:     } /* end of loop + */
 5103:   } /* end model */
 5104:   
 5105:   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
 5106:     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
 5107: 
 5108:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
 5109:   printf("cptcovprod=%d ", cptcovprod);
 5110:   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
 5111: 
 5112:   scanf("%d ",i);*/
 5113: 
 5114: 
 5115:   return (0); /* with covar[new additional covariate if product] and Tage if age */ 
 5116:   endread:
 5117:     printf("Exiting decodemodel: ");
 5118:     return (1);
 5119: }
 5120: 
 5121: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 5122: {
 5123:   int i, m;
 5124: 
 5125:   for (i=1; i<=imx; i++) {
 5126:     for(m=2; (m<= maxwav); m++) {
 5127:       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
 5128: 	anint[m][i]=9999;
 5129: 	s[m][i]=-1;
 5130:       }
 5131:       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
 5132: 	*nberr++;
 5133: 	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\n",(int)moisdc[i],(int)andc[i],num[i],i);
 5134: 	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\n",(int)moisdc[i],(int)andc[i],num[i],i);
 5135: 	s[m][i]=-1;
 5136:       }
 5137:       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
 5138: 	*nberr++;
 5139: 	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]); 
 5140: 	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]); 
 5141: 	s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
 5142:       }
 5143:     }
 5144:   }
 5145: 
 5146:   for (i=1; i<=imx; i++)  {
 5147:     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
 5148:     for(m=firstpass; (m<= lastpass); m++){
 5149:       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
 5150: 	if (s[m][i] >= nlstate+1) {
 5151: 	  if(agedc[i]>0)
 5152: 	    if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
 5153: 	      agev[m][i]=agedc[i];
 5154: 	  /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
 5155: 	    else {
 5156: 	      if ((int)andc[i]!=9999){
 5157: 		nbwarn++;
 5158: 		printf("Warning negative age at death: %ld line:%d\n",num[i],i);
 5159: 		fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
 5160: 		agev[m][i]=-1;
 5161: 	      }
 5162: 	    }
 5163: 	}
 5164: 	else if(s[m][i] !=9){ /* Standard case, age in fractional
 5165: 				 years but with the precision of a month */
 5166: 	  agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
 5167: 	  if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
 5168: 	    agev[m][i]=1;
 5169: 	  else if(agev[m][i] < *agemin){ 
 5170: 	    *agemin=agev[m][i];
 5171: 	    printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
 5172: 	  }
 5173: 	  else if(agev[m][i] >*agemax){
 5174: 	    *agemax=agev[m][i];
 5175: 	    printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
 5176: 	  }
 5177: 	  /*agev[m][i]=anint[m][i]-annais[i];*/
 5178: 	  /*	 agev[m][i] = age[i]+2*m;*/
 5179: 	}
 5180: 	else { /* =9 */
 5181: 	  agev[m][i]=1;
 5182: 	  s[m][i]=-1;
 5183: 	}
 5184:       }
 5185:       else /*= 0 Unknown */
 5186: 	agev[m][i]=1;
 5187:     }
 5188:     
 5189:   }
 5190:   for (i=1; i<=imx; i++)  {
 5191:     for(m=firstpass; (m<=lastpass); m++){
 5192:       if (s[m][i] > (nlstate+ndeath)) {
 5193: 	*nberr++;
 5194: 	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);	
 5195: 	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);	
 5196: 	return 1;
 5197:       }
 5198:     }
 5199:   }
 5200: 
 5201:   /*for (i=1; i<=imx; i++){
 5202:   for (m=firstpass; (m<lastpass); m++){
 5203:      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
 5204: }
 5205: 
 5206: }*/
 5207: 
 5208: 
 5209:   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
 5210:   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
 5211: 
 5212:   return (0);
 5213:   endread:
 5214:     printf("Exiting calandcheckages: ");
 5215:     return (1);
 5216: }
 5217: 
 5218: 
 5219: /***********************************************/
 5220: /**************** Main Program *****************/
 5221: /***********************************************/
 5222: 
 5223: int main(int argc, char *argv[])
 5224: {
 5225: #ifdef GSL
 5226:   const gsl_multimin_fminimizer_type *T;
 5227:   size_t iteri = 0, it;
 5228:   int rval = GSL_CONTINUE;
 5229:   int status = GSL_SUCCESS;
 5230:   double ssval;
 5231: #endif
 5232:   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
 5233:   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
 5234:   int linei, month, year,iout;
 5235:   int jj, ll, li, lj, lk, imk;
 5236:   int numlinepar=0; /* Current linenumber of parameter file */
 5237:   int itimes;
 5238:   int NDIM=2;
 5239:   int vpopbased=0;
 5240: 
 5241:   char ca[32], cb[32], cc[32];
 5242:   /*  FILE *fichtm; *//* Html File */
 5243:   /* FILE *ficgp;*/ /*Gnuplot File */
 5244:   struct stat info;
 5245:   double agedeb, agefin,hf;
 5246:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 5247: 
 5248:   double fret;
 5249:   double **xi,tmp,delta;
 5250: 
 5251:   double dum; /* Dummy variable */
 5252:   double ***p3mat;
 5253:   double ***mobaverage;
 5254:   int *indx;
 5255:   char line[MAXLINE], linepar[MAXLINE];
 5256:   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
 5257:   char pathr[MAXLINE], pathimach[MAXLINE]; 
 5258:   char **bp, *tok, *val; /* pathtot */
 5259:   int firstobs=1, lastobs=10;
 5260:   int sdeb, sfin; /* Status at beginning and end */
 5261:   int c,  h , cpt,l;
 5262:   int ju,jl, mi;
 5263:   int i1,j1, jk,aa,bb, stepsize, ij;
 5264:   int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
 5265:   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
 5266:   int mobilav=0,popforecast=0;
 5267:   int hstepm, nhstepm;
 5268:   int agemortsup;
 5269:   float  sumlpop=0.;
 5270:   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
 5271:   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
 5272: 
 5273:   double bage, fage, age, agelim, agebase;
 5274:   double ftolpl=FTOL;
 5275:   double **prlim;
 5276:   double ***param; /* Matrix of parameters */
 5277:   double  *p;
 5278:   double **matcov; /* Matrix of covariance */
 5279:   double ***delti3; /* Scale */
 5280:   double *delti; /* Scale */
 5281:   double ***eij, ***vareij;
 5282:   double **varpl; /* Variances of prevalence limits by age */
 5283:   double *epj, vepp;
 5284:   double kk1, kk2;
 5285:   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
 5286:   double **ximort;
 5287:   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
 5288:   int *dcwave;
 5289: 
 5290:   char z[1]="c", occ;
 5291: 
 5292:   /*char  *strt;*/
 5293:   char strtend[80];
 5294: 
 5295:   long total_usecs;
 5296:  
 5297: /*   setlocale (LC_ALL, ""); */
 5298: /*   bindtextdomain (PACKAGE, LOCALEDIR); */
 5299: /*   textdomain (PACKAGE); */
 5300: /*   setlocale (LC_CTYPE, ""); */
 5301: /*   setlocale (LC_MESSAGES, ""); */
 5302: 
 5303:   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
 5304:   (void) gettimeofday(&start_time,&tzp);
 5305:   curr_time=start_time;
 5306:   tm = *localtime(&start_time.tv_sec);
 5307:   tmg = *gmtime(&start_time.tv_sec);
 5308:   strcpy(strstart,asctime(&tm));
 5309: 
 5310: /*  printf("Localtime (at start)=%s",strstart); */
 5311: /*  tp.tv_sec = tp.tv_sec +86400; */
 5312: /*  tm = *localtime(&start_time.tv_sec); */
 5313: /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
 5314: /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
 5315: /*   tmg.tm_hour=tmg.tm_hour + 1; */
 5316: /*   tp.tv_sec = mktime(&tmg); */
 5317: /*   strt=asctime(&tmg); */
 5318: /*   printf("Time(after) =%s",strstart);  */
 5319: /*  (void) time (&time_value);
 5320: *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
 5321: *  tm = *localtime(&time_value);
 5322: *  strstart=asctime(&tm);
 5323: *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
 5324: */
 5325: 
 5326:   nberr=0; /* Number of errors and warnings */
 5327:   nbwarn=0;
 5328:   getcwd(pathcd, size);
 5329: 
 5330:   printf("\n%s\n%s",version,fullversion);
 5331:   if(argc <=1){
 5332:     printf("\nEnter the parameter file name: ");
 5333:     fgets(pathr,FILENAMELENGTH,stdin);
 5334:     i=strlen(pathr);
 5335:     if(pathr[i-1]=='\n')
 5336:       pathr[i-1]='\0';
 5337:    for (tok = pathr; tok != NULL; ){
 5338:       printf("Pathr |%s|\n",pathr);
 5339:       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
 5340:       printf("val= |%s| pathr=%s\n",val,pathr);
 5341:       strcpy (pathtot, val);
 5342:       if(pathr[0] == '\0') break; /* Dirty */
 5343:     }
 5344:   }
 5345:   else{
 5346:     strcpy(pathtot,argv[1]);
 5347:   }
 5348:   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
 5349:   /*cygwin_split_path(pathtot,path,optionfile);
 5350:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
 5351:   /* cutv(path,optionfile,pathtot,'\\');*/
 5352: 
 5353:   /* Split argv[0], imach program to get pathimach */
 5354:   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
 5355:   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
 5356:   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
 5357:  /*   strcpy(pathimach,argv[0]); */
 5358:   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
 5359:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
 5360:   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
 5361:   chdir(path); /* Can be a relative path */
 5362:   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
 5363:     printf("Current directory %s!\n",pathcd);
 5364:   strcpy(command,"mkdir ");
 5365:   strcat(command,optionfilefiname);
 5366:   if((outcmd=system(command)) != 0){
 5367:     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
 5368:     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
 5369:     /* fclose(ficlog); */
 5370: /*     exit(1); */
 5371:   }
 5372: /*   if((imk=mkdir(optionfilefiname))<0){ */
 5373: /*     perror("mkdir"); */
 5374: /*   } */
 5375: 
 5376:   /*-------- arguments in the command line --------*/
 5377: 
 5378:   /* Log file */
 5379:   strcat(filelog, optionfilefiname);
 5380:   strcat(filelog,".log");    /* */
 5381:   if((ficlog=fopen(filelog,"w"))==NULL)    {
 5382:     printf("Problem with logfile %s\n",filelog);
 5383:     goto end;
 5384:   }
 5385:   fprintf(ficlog,"Log filename:%s\n",filelog);
 5386:   fprintf(ficlog,"\n%s\n%s",version,fullversion);
 5387:   fprintf(ficlog,"\nEnter the parameter file name: \n");
 5388:   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
 5389:  path=%s \n\
 5390:  optionfile=%s\n\
 5391:  optionfilext=%s\n\
 5392:  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
 5393: 
 5394:   printf("Local time (at start):%s",strstart);
 5395:   fprintf(ficlog,"Local time (at start): %s",strstart);
 5396:   fflush(ficlog);
 5397: /*   (void) gettimeofday(&curr_time,&tzp); */
 5398: /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
 5399: 
 5400:   /* */
 5401:   strcpy(fileres,"r");
 5402:   strcat(fileres, optionfilefiname);
 5403:   strcat(fileres,".txt");    /* Other files have txt extension */
 5404: 
 5405:   /*---------arguments file --------*/
 5406: 
 5407:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
 5408:     printf("Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
 5409:     fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
 5410:     fflush(ficlog);
 5411:     /* goto end; */
 5412:     exit(70); 
 5413:   }
 5414: 
 5415: 
 5416: 
 5417:   strcpy(filereso,"o");
 5418:   strcat(filereso,fileres);
 5419:   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
 5420:     printf("Problem with Output resultfile: %s\n", filereso);
 5421:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
 5422:     fflush(ficlog);
 5423:     goto end;
 5424:   }
 5425: 
 5426:   /* Reads comments: lines beginning with '#' */
 5427:   numlinepar=0;
 5428:   while((c=getc(ficpar))=='#' && c!= EOF){
 5429:     ungetc(c,ficpar);
 5430:     fgets(line, MAXLINE, ficpar);
 5431:     numlinepar++;
 5432:     fputs(line,stdout);
 5433:     fputs(line,ficparo);
 5434:     fputs(line,ficlog);
 5435:   }
 5436:   ungetc(c,ficpar);
 5437: 
 5438:   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);
 5439:   numlinepar++;
 5440:   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);
 5441:   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);
 5442:   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);
 5443:   fflush(ficlog);
 5444:   while((c=getc(ficpar))=='#' && c!= EOF){
 5445:     ungetc(c,ficpar);
 5446:     fgets(line, MAXLINE, ficpar);
 5447:     numlinepar++;
 5448:     fputs(line, stdout);
 5449:     //puts(line);
 5450:     fputs(line,ficparo);
 5451:     fputs(line,ficlog);
 5452:   }
 5453:   ungetc(c,ficpar);
 5454: 
 5455:    
 5456:   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
 5457:   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
 5458:   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
 5459:      v1+v2*age+v2*v3 makes cptcovn = 3
 5460:   */
 5461:   if (strlen(model)>1) 
 5462:     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*/
 5463:   else
 5464:     ncovmodel=2;
 5465:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
 5466:   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
 5467:   npar= nforce*ncovmodel; /* Number of parameters like aij*/
 5468:   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
 5469:     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);
 5470:     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);
 5471:     fflush(stdout);
 5472:     fclose (ficlog);
 5473:     goto end;
 5474:   }
 5475:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 5476:   delti=delti3[1][1];
 5477:   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
 5478:   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
 5479:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
 5480:     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
 5481:     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
 5482:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
 5483:     fclose (ficparo);
 5484:     fclose (ficlog);
 5485:     goto end;
 5486:     exit(0);
 5487:   }
 5488:   else if(mle==-3) {
 5489:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
 5490:     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
 5491:     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
 5492:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 5493:     matcov=matrix(1,npar,1,npar);
 5494:   }
 5495:   else{
 5496:     /* Read guessed parameters */
 5497:     /* Reads comments: lines beginning with '#' */
 5498:     while((c=getc(ficpar))=='#' && c!= EOF){
 5499:       ungetc(c,ficpar);
 5500:       fgets(line, MAXLINE, ficpar);
 5501:       numlinepar++;
 5502:       fputs(line,stdout);
 5503:       fputs(line,ficparo);
 5504:       fputs(line,ficlog);
 5505:     }
 5506:     ungetc(c,ficpar);
 5507:     
 5508:     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 5509:     for(i=1; i <=nlstate; i++){
 5510:       j=0;
 5511:       for(jj=1; jj <=nlstate+ndeath; jj++){
 5512: 	if(jj==i) continue;
 5513: 	j++;
 5514: 	fscanf(ficpar,"%1d%1d",&i1,&j1);
 5515: 	if ((i1 != i) && (j1 != j)){
 5516: 	  printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
 5517: It might be a problem of design; if ncovcol and the model are correct\n \
 5518: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
 5519: 	  exit(1);
 5520: 	}
 5521: 	fprintf(ficparo,"%1d%1d",i1,j1);
 5522: 	if(mle==1)
 5523: 	  printf("%1d%1d",i,j);
 5524: 	fprintf(ficlog,"%1d%1d",i,j);
 5525: 	for(k=1; k<=ncovmodel;k++){
 5526: 	  fscanf(ficpar," %lf",&param[i][j][k]);
 5527: 	  if(mle==1){
 5528: 	    printf(" %lf",param[i][j][k]);
 5529: 	    fprintf(ficlog," %lf",param[i][j][k]);
 5530: 	  }
 5531: 	  else
 5532: 	    fprintf(ficlog," %lf",param[i][j][k]);
 5533: 	  fprintf(ficparo," %lf",param[i][j][k]);
 5534: 	}
 5535: 	fscanf(ficpar,"\n");
 5536: 	numlinepar++;
 5537: 	if(mle==1)
 5538: 	  printf("\n");
 5539: 	fprintf(ficlog,"\n");
 5540: 	fprintf(ficparo,"\n");
 5541:       }
 5542:     }  
 5543:     fflush(ficlog);
 5544: 
 5545:     /* Reads scales values */
 5546:     p=param[1][1];
 5547:     
 5548:     /* Reads comments: lines beginning with '#' */
 5549:     while((c=getc(ficpar))=='#' && c!= EOF){
 5550:       ungetc(c,ficpar);
 5551:       fgets(line, MAXLINE, ficpar);
 5552:       numlinepar++;
 5553:       fputs(line,stdout);
 5554:       fputs(line,ficparo);
 5555:       fputs(line,ficlog);
 5556:     }
 5557:     ungetc(c,ficpar);
 5558: 
 5559:     for(i=1; i <=nlstate; i++){
 5560:       for(j=1; j <=nlstate+ndeath-1; j++){
 5561: 	fscanf(ficpar,"%1d%1d",&i1,&j1);
 5562: 	if ((i1-i)*(j1-j)!=0){
 5563: 	  printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
 5564: 	  exit(1);
 5565: 	}
 5566: 	printf("%1d%1d",i,j);
 5567: 	fprintf(ficparo,"%1d%1d",i1,j1);
 5568: 	fprintf(ficlog,"%1d%1d",i1,j1);
 5569: 	for(k=1; k<=ncovmodel;k++){
 5570: 	  fscanf(ficpar,"%le",&delti3[i][j][k]);
 5571: 	  printf(" %le",delti3[i][j][k]);
 5572: 	  fprintf(ficparo," %le",delti3[i][j][k]);
 5573: 	  fprintf(ficlog," %le",delti3[i][j][k]);
 5574: 	}
 5575: 	fscanf(ficpar,"\n");
 5576: 	numlinepar++;
 5577: 	printf("\n");
 5578: 	fprintf(ficparo,"\n");
 5579: 	fprintf(ficlog,"\n");
 5580:       }
 5581:     }
 5582:     fflush(ficlog);
 5583: 
 5584:     /* Reads covariance matrix */
 5585:     delti=delti3[1][1];
 5586: 
 5587: 
 5588:     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
 5589:   
 5590:     /* Reads comments: lines beginning with '#' */
 5591:     while((c=getc(ficpar))=='#' && c!= EOF){
 5592:       ungetc(c,ficpar);
 5593:       fgets(line, MAXLINE, ficpar);
 5594:       numlinepar++;
 5595:       fputs(line,stdout);
 5596:       fputs(line,ficparo);
 5597:       fputs(line,ficlog);
 5598:     }
 5599:     ungetc(c,ficpar);
 5600:   
 5601:     matcov=matrix(1,npar,1,npar);
 5602:     for(i=1; i <=npar; i++)
 5603:       for(j=1; j <=npar; j++) matcov[i][j]=0.;
 5604:       
 5605:     for(i=1; i <=npar; i++){
 5606:       fscanf(ficpar,"%s",str);
 5607:       if(mle==1)
 5608: 	printf("%s",str);
 5609:       fprintf(ficlog,"%s",str);
 5610:       fprintf(ficparo,"%s",str);
 5611:       for(j=1; j <=i; j++){
 5612: 	fscanf(ficpar," %le",&matcov[i][j]);
 5613: 	if(mle==1){
 5614: 	  printf(" %.5le",matcov[i][j]);
 5615: 	}
 5616: 	fprintf(ficlog," %.5le",matcov[i][j]);
 5617: 	fprintf(ficparo," %.5le",matcov[i][j]);
 5618:       }
 5619:       fscanf(ficpar,"\n");
 5620:       numlinepar++;
 5621:       if(mle==1)
 5622: 	printf("\n");
 5623:       fprintf(ficlog,"\n");
 5624:       fprintf(ficparo,"\n");
 5625:     }
 5626:     for(i=1; i <=npar; i++)
 5627:       for(j=i+1;j<=npar;j++)
 5628: 	matcov[i][j]=matcov[j][i];
 5629:     
 5630:     if(mle==1)
 5631:       printf("\n");
 5632:     fprintf(ficlog,"\n");
 5633:     
 5634:     fflush(ficlog);
 5635:     
 5636:     /*-------- Rewriting parameter file ----------*/
 5637:     strcpy(rfileres,"r");    /* "Rparameterfile */
 5638:     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
 5639:     strcat(rfileres,".");    /* */
 5640:     strcat(rfileres,optionfilext);    /* Other files have txt extension */
 5641:     if((ficres =fopen(rfileres,"w"))==NULL) {
 5642:       printf("Problem writing new parameter file: %s\n", fileres);goto end;
 5643:       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
 5644:     }
 5645:     fprintf(ficres,"#%s\n",version);
 5646:   }    /* End of mle != -3 */
 5647: 
 5648: 
 5649:   n= lastobs;
 5650:   num=lvector(1,n);
 5651:   moisnais=vector(1,n);
 5652:   annais=vector(1,n);
 5653:   moisdc=vector(1,n);
 5654:   andc=vector(1,n);
 5655:   agedc=vector(1,n);
 5656:   cod=ivector(1,n);
 5657:   weight=vector(1,n);
 5658:   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
 5659:   mint=matrix(1,maxwav,1,n);
 5660:   anint=matrix(1,maxwav,1,n);
 5661:   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
 5662:   tab=ivector(1,NCOVMAX);
 5663:   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
 5664: 
 5665:   /* Reads data from file datafile */
 5666:   if (readdata(datafile, firstobs, lastobs, &imx)==1)
 5667:     goto end;
 5668: 
 5669:   /* Calculation of the number of parameters from char model */
 5670:     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
 5671: 	k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
 5672: 	k=3 V4 Tvar[k=3]= 4 (from V4)
 5673: 	k=2 V1 Tvar[k=2]= 1 (from V1)
 5674: 	k=1 Tvar[1]=2 (from V2)
 5675:     */
 5676:   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
 5677:   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
 5678:       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
 5679:       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
 5680:   */
 5681:   /* For model-covariate k tells which data-covariate to use but
 5682:     because this model-covariate is a construction we invent a new column
 5683:     ncovcol + k1
 5684:     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
 5685:     Tvar[3=V1*V4]=4+1 etc */
 5686:   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
 5687:   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
 5688:      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
 5689:   */
 5690:   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
 5691:   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
 5692: 			    * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
 5693: 			    * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
 5694:   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
 5695: 			 4 covariates (3 plus signs)
 5696: 			 Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
 5697: 		      */  
 5698: 
 5699:   if(decodemodel(model, lastobs) == 1)
 5700:     goto end;
 5701: 
 5702:   if((double)(lastobs-imx)/(double)imx > 1.10){
 5703:     nbwarn++;
 5704:     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); 
 5705:     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); 
 5706:   }
 5707:     /*  if(mle==1){*/
 5708:   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
 5709:     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
 5710:   }
 5711: 
 5712:     /*-calculation of age at interview from date of interview and age at death -*/
 5713:   agev=matrix(1,maxwav,1,imx);
 5714: 
 5715:   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
 5716:     goto end;
 5717: 
 5718: 
 5719:   agegomp=(int)agemin;
 5720:   free_vector(moisnais,1,n);
 5721:   free_vector(annais,1,n);
 5722:   /* free_matrix(mint,1,maxwav,1,n);
 5723:      free_matrix(anint,1,maxwav,1,n);*/
 5724:   free_vector(moisdc,1,n);
 5725:   free_vector(andc,1,n);
 5726:   /* */
 5727:   
 5728:   wav=ivector(1,imx);
 5729:   dh=imatrix(1,lastpass-firstpass+1,1,imx);
 5730:   bh=imatrix(1,lastpass-firstpass+1,1,imx);
 5731:   mw=imatrix(1,lastpass-firstpass+1,1,imx);
 5732:    
 5733:   /* Concatenates waves */
 5734:   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
 5735:   /* */
 5736:  
 5737:   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
 5738: 
 5739:   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
 5740:   ncodemax[1]=1;
 5741:   Ndum =ivector(-1,NCOVMAX);  
 5742:   if (ncovmodel > 2)
 5743:     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
 5744: 
 5745:   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
 5746:   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
 5747:   h=0;
 5748: 
 5749: 
 5750:   /*if (cptcovn > 0) */
 5751:       
 5752:  
 5753:   m=pow(2,cptcoveff);
 5754:  
 5755:   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
 5756:     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 */ 
 5757:       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
 5758: 	for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
 5759: 	  h++;
 5760: 	  if (h>m) 
 5761: 	    h=1;
 5762: 	  /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
 5763: 	   *     h     1     2     3     4
 5764: 	   *______________________________  
 5765: 	   *     1 i=1 1 i=1 1 i=1 1 i=1 1
 5766: 	   *     2     2     1     1     1
 5767: 	   *     3 i=2 1     2     1     1
 5768: 	   *     4     2     2     1     1
 5769: 	   *     5 i=3 1 i=2 1     2     1
 5770: 	   *     6     2     1     2     1
 5771: 	   *     7 i=4 1     2     2     1
 5772: 	   *     8     2     2     2     1
 5773: 	   *     9 i=5 1 i=3 1 i=2 1     1
 5774: 	   *    10     2     1     1     1
 5775: 	   *    11 i=6 1     2     1     1
 5776: 	   *    12     2     2     1     1
 5777: 	   *    13 i=7 1 i=4 1     2     1    
 5778: 	   *    14     2     1     2     1
 5779: 	   *    15 i=8 1     2     2     1
 5780: 	   *    16     2     2     2     1
 5781: 	   */
 5782: 	  codtab[h][k]=j;
 5783: 	  /*codtab[h][Tvar[k]]=j;*/
 5784: 	  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]]);
 5785: 	} 
 5786:       }
 5787:     }
 5788:   } 
 5789:   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
 5790:      codtab[1][2]=1;codtab[2][2]=2; */
 5791:   /* for(i=1; i <=m ;i++){ 
 5792:      for(k=1; k <=cptcovn; k++){
 5793:        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
 5794:      }
 5795:      printf("\n");
 5796:      }
 5797:      scanf("%d",i);*/
 5798: 
 5799:  free_ivector(Ndum,-1,NCOVMAX);
 5800: 
 5801: 
 5802:     
 5803:   /*------------ gnuplot -------------*/
 5804:   strcpy(optionfilegnuplot,optionfilefiname);
 5805:   if(mle==-3)
 5806:     strcat(optionfilegnuplot,"-mort");
 5807:   strcat(optionfilegnuplot,".gp");
 5808: 
 5809:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
 5810:     printf("Problem with file %s",optionfilegnuplot);
 5811:   }
 5812:   else{
 5813:     fprintf(ficgp,"\n# %s\n", version); 
 5814:     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
 5815:     //fprintf(ficgp,"set missing 'NaNq'\n");
 5816:     fprintf(ficgp,"set datafile missing 'NaNq'\n");
 5817:   }
 5818:   /*  fclose(ficgp);*/
 5819:   /*--------- index.htm --------*/
 5820: 
 5821:   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
 5822:   if(mle==-3)
 5823:     strcat(optionfilehtm,"-mort");
 5824:   strcat(optionfilehtm,".htm");
 5825:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
 5826:     printf("Problem with %s \n",optionfilehtm);
 5827:     exit(0);
 5828:   }
 5829: 
 5830:   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
 5831:   strcat(optionfilehtmcov,"-cov.htm");
 5832:   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
 5833:     printf("Problem with %s \n",optionfilehtmcov), exit(0);
 5834:   }
 5835:   else{
 5836:   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 5837: <hr size=\"2\" color=\"#EC5E5E\"> \n\
 5838: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
 5839: 	  optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
 5840:   }
 5841: 
 5842:   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 5843: <hr size=\"2\" color=\"#EC5E5E\"> \n\
 5844: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
 5845: \n\
 5846: <hr  size=\"2\" color=\"#EC5E5E\">\
 5847:  <ul><li><h4>Parameter files</h4>\n\
 5848:  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
 5849:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
 5850:  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
 5851:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
 5852:  - Date and time at start: %s</ul>\n",\
 5853: 	  optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
 5854: 	  optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
 5855: 	  fileres,fileres,\
 5856: 	  filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
 5857:   fflush(fichtm);
 5858: 
 5859:   strcpy(pathr,path);
 5860:   strcat(pathr,optionfilefiname);
 5861:   chdir(optionfilefiname); /* Move to directory named optionfile */
 5862:   
 5863:   /* Calculates basic frequencies. Computes observed prevalence at single age
 5864:      and prints on file fileres'p'. */
 5865:   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
 5866: 
 5867:   fprintf(fichtm,"\n");
 5868:   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
 5869: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
 5870: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
 5871: 	  imx,agemin,agemax,jmin,jmax,jmean);
 5872:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 5873:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 5874:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 5875:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 5876:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
 5877:     
 5878:    
 5879:   /* For Powell, parameters are in a vector p[] starting at p[1]
 5880:      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
 5881:   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
 5882: 
 5883:   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
 5884: 
 5885:   if (mle==-3){
 5886:     ximort=matrix(1,NDIM,1,NDIM); 
 5887: /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
 5888:     cens=ivector(1,n);
 5889:     ageexmed=vector(1,n);
 5890:     agecens=vector(1,n);
 5891:     dcwave=ivector(1,n);
 5892:  
 5893:     for (i=1; i<=imx; i++){
 5894:       dcwave[i]=-1;
 5895:       for (m=firstpass; m<=lastpass; m++)
 5896: 	if (s[m][i]>nlstate) {
 5897: 	  dcwave[i]=m;
 5898: 	  /*	printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
 5899: 	  break;
 5900: 	}
 5901:     }
 5902: 
 5903:     for (i=1; i<=imx; i++) {
 5904:       if (wav[i]>0){
 5905: 	ageexmed[i]=agev[mw[1][i]][i];
 5906: 	j=wav[i];
 5907: 	agecens[i]=1.; 
 5908: 
 5909: 	if (ageexmed[i]> 1 && wav[i] > 0){
 5910: 	  agecens[i]=agev[mw[j][i]][i];
 5911: 	  cens[i]= 1;
 5912: 	}else if (ageexmed[i]< 1) 
 5913: 	  cens[i]= -1;
 5914: 	if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
 5915: 	  cens[i]=0 ;
 5916:       }
 5917:       else cens[i]=-1;
 5918:     }
 5919:     
 5920:     for (i=1;i<=NDIM;i++) {
 5921:       for (j=1;j<=NDIM;j++)
 5922: 	ximort[i][j]=(i == j ? 1.0 : 0.0);
 5923:     }
 5924:     
 5925:     /*p[1]=0.0268; p[NDIM]=0.083;*/
 5926:     /*printf("%lf %lf", p[1], p[2]);*/
 5927:     
 5928:     
 5929: #ifdef GSL
 5930:     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
 5931: #elsedef
 5932:     printf("Powell\n");  fprintf(ficlog,"Powell\n");
 5933: #endif
 5934:     strcpy(filerespow,"pow-mort"); 
 5935:     strcat(filerespow,fileres);
 5936:     if((ficrespow=fopen(filerespow,"w"))==NULL) {
 5937:       printf("Problem with resultfile: %s\n", filerespow);
 5938:       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 5939:     }
 5940: #ifdef GSL
 5941:     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
 5942: #elsedef
 5943:     fprintf(ficrespow,"# Powell\n# iter -2*LL");
 5944: #endif
 5945:     /*  for (i=1;i<=nlstate;i++)
 5946: 	for(j=1;j<=nlstate+ndeath;j++)
 5947: 	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 5948:     */
 5949:     fprintf(ficrespow,"\n");
 5950: #ifdef GSL
 5951:     /* gsl starts here */ 
 5952:     T = gsl_multimin_fminimizer_nmsimplex;
 5953:     gsl_multimin_fminimizer *sfm = NULL;
 5954:     gsl_vector *ss, *x;
 5955:     gsl_multimin_function minex_func;
 5956: 
 5957:     /* Initial vertex size vector */
 5958:     ss = gsl_vector_alloc (NDIM);
 5959:     
 5960:     if (ss == NULL){
 5961:       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
 5962:     }
 5963:     /* Set all step sizes to 1 */
 5964:     gsl_vector_set_all (ss, 0.001);
 5965: 
 5966:     /* Starting point */
 5967:     
 5968:     x = gsl_vector_alloc (NDIM);
 5969:     
 5970:     if (x == NULL){
 5971:       gsl_vector_free(ss);
 5972:       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
 5973:     }
 5974:   
 5975:     /* Initialize method and iterate */
 5976:     /*     p[1]=0.0268; p[NDIM]=0.083; */
 5977: /*     gsl_vector_set(x, 0, 0.0268); */
 5978: /*     gsl_vector_set(x, 1, 0.083); */
 5979:     gsl_vector_set(x, 0, p[1]);
 5980:     gsl_vector_set(x, 1, p[2]);
 5981: 
 5982:     minex_func.f = &gompertz_f;
 5983:     minex_func.n = NDIM;
 5984:     minex_func.params = (void *)&p; /* ??? */
 5985:     
 5986:     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
 5987:     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
 5988:     
 5989:     printf("Iterations beginning .....\n\n");
 5990:     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
 5991: 
 5992:     iteri=0;
 5993:     while (rval == GSL_CONTINUE){
 5994:       iteri++;
 5995:       status = gsl_multimin_fminimizer_iterate(sfm);
 5996:       
 5997:       if (status) printf("error: %s\n", gsl_strerror (status));
 5998:       fflush(0);
 5999:       
 6000:       if (status) 
 6001:         break;
 6002:       
 6003:       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
 6004:       ssval = gsl_multimin_fminimizer_size (sfm);
 6005:       
 6006:       if (rval == GSL_SUCCESS)
 6007:         printf ("converged to a local maximum at\n");
 6008:       
 6009:       printf("%5d ", iteri);
 6010:       for (it = 0; it < NDIM; it++){
 6011: 	printf ("%10.5f ", gsl_vector_get (sfm->x, it));
 6012:       }
 6013:       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
 6014:     }
 6015:     
 6016:     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
 6017:     
 6018:     gsl_vector_free(x); /* initial values */
 6019:     gsl_vector_free(ss); /* inital step size */
 6020:     for (it=0; it<NDIM; it++){
 6021:       p[it+1]=gsl_vector_get(sfm->x,it);
 6022:       fprintf(ficrespow," %.12lf", p[it]);
 6023:     }
 6024:     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
 6025: #endif
 6026: #ifdef POWELL
 6027:      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
 6028: #endif  
 6029:     fclose(ficrespow);
 6030:     
 6031:     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
 6032: 
 6033:     for(i=1; i <=NDIM; i++)
 6034:       for(j=i+1;j<=NDIM;j++)
 6035: 	matcov[i][j]=matcov[j][i];
 6036:     
 6037:     printf("\nCovariance matrix\n ");
 6038:     for(i=1; i <=NDIM; i++) {
 6039:       for(j=1;j<=NDIM;j++){ 
 6040: 	printf("%f ",matcov[i][j]);
 6041:       }
 6042:       printf("\n ");
 6043:     }
 6044:     
 6045:     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
 6046:     for (i=1;i<=NDIM;i++) 
 6047:       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
 6048: 
 6049:     lsurv=vector(1,AGESUP);
 6050:     lpop=vector(1,AGESUP);
 6051:     tpop=vector(1,AGESUP);
 6052:     lsurv[agegomp]=100000;
 6053:     
 6054:     for (k=agegomp;k<=AGESUP;k++) {
 6055:       agemortsup=k;
 6056:       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
 6057:     }
 6058:     
 6059:     for (k=agegomp;k<agemortsup;k++)
 6060:       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
 6061:     
 6062:     for (k=agegomp;k<agemortsup;k++){
 6063:       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
 6064:       sumlpop=sumlpop+lpop[k];
 6065:     }
 6066:     
 6067:     tpop[agegomp]=sumlpop;
 6068:     for (k=agegomp;k<(agemortsup-3);k++){
 6069:       /*  tpop[k+1]=2;*/
 6070:       tpop[k+1]=tpop[k]-lpop[k];
 6071:     }
 6072:     
 6073:     
 6074:     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
 6075:     for (k=agegomp;k<(agemortsup-2);k++) 
 6076:       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]);
 6077:     
 6078:     
 6079:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
 6080:     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
 6081:     
 6082:     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
 6083: 		     stepm, weightopt,\
 6084: 		     model,imx,p,matcov,agemortsup);
 6085:     
 6086:     free_vector(lsurv,1,AGESUP);
 6087:     free_vector(lpop,1,AGESUP);
 6088:     free_vector(tpop,1,AGESUP);
 6089: #ifdef GSL
 6090:     free_ivector(cens,1,n);
 6091:     free_vector(agecens,1,n);
 6092:     free_ivector(dcwave,1,n);
 6093:     free_matrix(ximort,1,NDIM,1,NDIM);
 6094: #endif
 6095:   } /* Endof if mle==-3 */
 6096:   
 6097:   else{ /* For mle >=1 */
 6098:     globpr=0;/* debug */
 6099:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
 6100:     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
 6101:     for (k=1; k<=npar;k++)
 6102:       printf(" %d %8.5f",k,p[k]);
 6103:     printf("\n");
 6104:     globpr=1; /* to print the contributions */
 6105:     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
 6106:     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
 6107:     for (k=1; k<=npar;k++)
 6108:       printf(" %d %8.5f",k,p[k]);
 6109:     printf("\n");
 6110:     if(mle>=1){ /* Could be 1 or 2 */
 6111:       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
 6112:     }
 6113:     
 6114:     /*--------- results files --------------*/
 6115:     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);
 6116:     
 6117:     
 6118:     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 6119:     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 6120:     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 6121:     for(i=1,jk=1; i <=nlstate; i++){
 6122:       for(k=1; k <=(nlstate+ndeath); k++){
 6123: 	if (k != i) {
 6124: 	  printf("%d%d ",i,k);
 6125: 	  fprintf(ficlog,"%d%d ",i,k);
 6126: 	  fprintf(ficres,"%1d%1d ",i,k);
 6127: 	  for(j=1; j <=ncovmodel; j++){
 6128: 	    printf("%lf ",p[jk]);
 6129: 	    fprintf(ficlog,"%lf ",p[jk]);
 6130: 	    fprintf(ficres,"%lf ",p[jk]);
 6131: 	    jk++; 
 6132: 	  }
 6133: 	  printf("\n");
 6134: 	  fprintf(ficlog,"\n");
 6135: 	  fprintf(ficres,"\n");
 6136: 	}
 6137:       }
 6138:     }
 6139:     if(mle!=0){
 6140:       /* Computing hessian and covariance matrix */
 6141:       ftolhess=ftol; /* Usually correct */
 6142:       hesscov(matcov, p, npar, delti, ftolhess, func);
 6143:     }
 6144:     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
 6145:     printf("# Scales (for hessian or gradient estimation)\n");
 6146:     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
 6147:     for(i=1,jk=1; i <=nlstate; i++){
 6148:       for(j=1; j <=nlstate+ndeath; j++){
 6149: 	if (j!=i) {
 6150: 	  fprintf(ficres,"%1d%1d",i,j);
 6151: 	  printf("%1d%1d",i,j);
 6152: 	  fprintf(ficlog,"%1d%1d",i,j);
 6153: 	  for(k=1; k<=ncovmodel;k++){
 6154: 	    printf(" %.5e",delti[jk]);
 6155: 	    fprintf(ficlog," %.5e",delti[jk]);
 6156: 	    fprintf(ficres," %.5e",delti[jk]);
 6157: 	    jk++;
 6158: 	  }
 6159: 	  printf("\n");
 6160: 	  fprintf(ficlog,"\n");
 6161: 	  fprintf(ficres,"\n");
 6162: 	}
 6163:       }
 6164:     }
 6165:     
 6166:     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");
 6167:     if(mle>=1)
 6168:       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");
 6169:     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");
 6170:     /* # 121 Var(a12)\n\ */
 6171:     /* # 122 Cov(b12,a12) Var(b12)\n\ */
 6172:     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
 6173:     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
 6174:     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
 6175:     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
 6176:     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
 6177:     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
 6178:     
 6179:     
 6180:     /* Just to have a covariance matrix which will be more understandable
 6181:        even is we still don't want to manage dictionary of variables
 6182:     */
 6183:     for(itimes=1;itimes<=2;itimes++){
 6184:       jj=0;
 6185:       for(i=1; i <=nlstate; i++){
 6186: 	for(j=1; j <=nlstate+ndeath; j++){
 6187: 	  if(j==i) continue;
 6188: 	  for(k=1; k<=ncovmodel;k++){
 6189: 	    jj++;
 6190: 	    ca[0]= k+'a'-1;ca[1]='\0';
 6191: 	    if(itimes==1){
 6192: 	      if(mle>=1)
 6193: 		printf("#%1d%1d%d",i,j,k);
 6194: 	      fprintf(ficlog,"#%1d%1d%d",i,j,k);
 6195: 	      fprintf(ficres,"#%1d%1d%d",i,j,k);
 6196: 	    }else{
 6197: 	      if(mle>=1)
 6198: 		printf("%1d%1d%d",i,j,k);
 6199: 	      fprintf(ficlog,"%1d%1d%d",i,j,k);
 6200: 	      fprintf(ficres,"%1d%1d%d",i,j,k);
 6201: 	    }
 6202: 	    ll=0;
 6203: 	    for(li=1;li <=nlstate; li++){
 6204: 	      for(lj=1;lj <=nlstate+ndeath; lj++){
 6205: 		if(lj==li) continue;
 6206: 		for(lk=1;lk<=ncovmodel;lk++){
 6207: 		  ll++;
 6208: 		  if(ll<=jj){
 6209: 		    cb[0]= lk +'a'-1;cb[1]='\0';
 6210: 		    if(ll<jj){
 6211: 		      if(itimes==1){
 6212: 			if(mle>=1)
 6213: 			  printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
 6214: 			fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
 6215: 			fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
 6216: 		      }else{
 6217: 			if(mle>=1)
 6218: 			  printf(" %.5e",matcov[jj][ll]); 
 6219: 			fprintf(ficlog," %.5e",matcov[jj][ll]); 
 6220: 			fprintf(ficres," %.5e",matcov[jj][ll]); 
 6221: 		      }
 6222: 		    }else{
 6223: 		      if(itimes==1){
 6224: 			if(mle>=1)
 6225: 			  printf(" Var(%s%1d%1d)",ca,i,j);
 6226: 			fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
 6227: 			fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
 6228: 		      }else{
 6229: 			if(mle>=1)
 6230: 			  printf(" %.5e",matcov[jj][ll]); 
 6231: 			fprintf(ficlog," %.5e",matcov[jj][ll]); 
 6232: 			fprintf(ficres," %.5e",matcov[jj][ll]); 
 6233: 		      }
 6234: 		    }
 6235: 		  }
 6236: 		} /* end lk */
 6237: 	      } /* end lj */
 6238: 	    } /* end li */
 6239: 	    if(mle>=1)
 6240: 	      printf("\n");
 6241: 	    fprintf(ficlog,"\n");
 6242: 	    fprintf(ficres,"\n");
 6243: 	    numlinepar++;
 6244: 	  } /* end k*/
 6245: 	} /*end j */
 6246:       } /* end i */
 6247:     } /* end itimes */
 6248:     
 6249:     fflush(ficlog);
 6250:     fflush(ficres);
 6251:     
 6252:     while((c=getc(ficpar))=='#' && c!= EOF){
 6253:       ungetc(c,ficpar);
 6254:       fgets(line, MAXLINE, ficpar);
 6255:       fputs(line,stdout);
 6256:       fputs(line,ficparo);
 6257:     }
 6258:     ungetc(c,ficpar);
 6259:     
 6260:     estepm=0;
 6261:     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
 6262:     if (estepm==0 || estepm < stepm) estepm=stepm;
 6263:     if (fage <= 2) {
 6264:       bage = ageminpar;
 6265:       fage = agemaxpar;
 6266:     }
 6267:     
 6268:     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
 6269:     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
 6270:     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
 6271:     
 6272:     while((c=getc(ficpar))=='#' && c!= EOF){
 6273:       ungetc(c,ficpar);
 6274:       fgets(line, MAXLINE, ficpar);
 6275:       fputs(line,stdout);
 6276:       fputs(line,ficparo);
 6277:     }
 6278:     ungetc(c,ficpar);
 6279:     
 6280:     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);
 6281:     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);
 6282:     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);
 6283:     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
 6284:     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);
 6285:     
 6286:     while((c=getc(ficpar))=='#' && c!= EOF){
 6287:       ungetc(c,ficpar);
 6288:       fgets(line, MAXLINE, ficpar);
 6289:       fputs(line,stdout);
 6290:       fputs(line,ficparo);
 6291:     }
 6292:     ungetc(c,ficpar);
 6293:     
 6294:     
 6295:     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
 6296:     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
 6297:     
 6298:     fscanf(ficpar,"pop_based=%d\n",&popbased);
 6299:     fprintf(ficparo,"pop_based=%d\n",popbased);   
 6300:     fprintf(ficres,"pop_based=%d\n",popbased);   
 6301:     
 6302:     while((c=getc(ficpar))=='#' && c!= EOF){
 6303:       ungetc(c,ficpar);
 6304:       fgets(line, MAXLINE, ficpar);
 6305:       fputs(line,stdout);
 6306:       fputs(line,ficparo);
 6307:     }
 6308:     ungetc(c,ficpar);
 6309:     
 6310:     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);
 6311:     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);
 6312:     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);
 6313:     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);
 6314:     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);
 6315:     /* day and month of proj2 are not used but only year anproj2.*/
 6316:     
 6317:     
 6318:     
 6319:      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
 6320:     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
 6321:     
 6322:     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
 6323:     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
 6324:     
 6325:     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
 6326: 		 model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
 6327: 		 jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
 6328:       
 6329:    /*------------ free_vector  -------------*/
 6330:    /*  chdir(path); */
 6331:  
 6332:     free_ivector(wav,1,imx);
 6333:     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
 6334:     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
 6335:     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
 6336:     free_lvector(num,1,n);
 6337:     free_vector(agedc,1,n);
 6338:     /*free_matrix(covar,0,NCOVMAX,1,n);*/
 6339:     /*free_matrix(covar,1,NCOVMAX,1,n);*/
 6340:     fclose(ficparo);
 6341:     fclose(ficres);
 6342: 
 6343: 
 6344:     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
 6345: #include "prevlim.h"  /* Use ficrespl, ficlog */
 6346:     fclose(ficrespl);
 6347: 
 6348: #ifdef FREEEXIT2
 6349: #include "freeexit2.h"
 6350: #endif
 6351: 
 6352:     /*------------- h Pij x at various ages ------------*/
 6353: #include "hpijx.h"
 6354:     fclose(ficrespij);
 6355: 
 6356:   /*-------------- Variance of one-step probabilities---*/
 6357:     k=1;
 6358:     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
 6359: 
 6360: 
 6361:     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 6362:     for(i=1;i<=AGESUP;i++)
 6363:       for(j=1;j<=NCOVMAX;j++)
 6364: 	for(k=1;k<=NCOVMAX;k++)
 6365: 	  probs[i][j][k]=0.;
 6366: 
 6367:     /*---------- Forecasting ------------------*/
 6368:     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
 6369:     if(prevfcast==1){
 6370:       /*    if(stepm ==1){*/
 6371:       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
 6372:       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
 6373:       /*      }  */
 6374:       /*      else{ */
 6375:       /*        erreur=108; */
 6376:       /*        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); */
 6377:       /*        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); */
 6378:       /*      } */
 6379:     }
 6380:   
 6381: 
 6382:     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
 6383: 
 6384:     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
 6385:     /*  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",\
 6386: 	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
 6387:     */
 6388: 
 6389:     if (mobilav!=0) {
 6390:       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 6391:       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 6392: 	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 6393: 	printf(" Error in movingaverage mobilav=%d\n",mobilav);
 6394:       }
 6395:     }
 6396: 
 6397: 
 6398:     /*---------- Health expectancies, no variances ------------*/
 6399: 
 6400:     strcpy(filerese,"e");
 6401:     strcat(filerese,fileres);
 6402:     if((ficreseij=fopen(filerese,"w"))==NULL) {
 6403:       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
 6404:       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
 6405:     }
 6406:     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
 6407:     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
 6408:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
 6409:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
 6410:           
 6411:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
 6412: 	fprintf(ficreseij,"\n#****** ");
 6413: 	for(j=1;j<=cptcoveff;j++) {
 6414: 	  fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 6415: 	}
 6416: 	fprintf(ficreseij,"******\n");
 6417: 
 6418: 	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 6419: 	oldm=oldms;savm=savms;
 6420: 	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
 6421:       
 6422: 	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 6423:       /*}*/
 6424:     }
 6425:     fclose(ficreseij);
 6426: 
 6427: 
 6428:     /*---------- Health expectancies and variances ------------*/
 6429: 
 6430: 
 6431:     strcpy(filerest,"t");
 6432:     strcat(filerest,fileres);
 6433:     if((ficrest=fopen(filerest,"w"))==NULL) {
 6434:       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
 6435:       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
 6436:     }
 6437:     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
 6438:     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
 6439: 
 6440: 
 6441:     strcpy(fileresstde,"stde");
 6442:     strcat(fileresstde,fileres);
 6443:     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
 6444:       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
 6445:       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
 6446:     }
 6447:     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
 6448:     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
 6449: 
 6450:     strcpy(filerescve,"cve");
 6451:     strcat(filerescve,fileres);
 6452:     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
 6453:       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
 6454:       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
 6455:     }
 6456:     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
 6457:     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
 6458: 
 6459:     strcpy(fileresv,"v");
 6460:     strcat(fileresv,fileres);
 6461:     if((ficresvij=fopen(fileresv,"w"))==NULL) {
 6462:       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
 6463:       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
 6464:     }
 6465:     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
 6466:     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
 6467: 
 6468:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
 6469:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
 6470:           
 6471:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
 6472:     	fprintf(ficrest,"\n#****** ");
 6473: 	for(j=1;j<=cptcoveff;j++) 
 6474: 	  fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 6475: 	fprintf(ficrest,"******\n");
 6476: 
 6477: 	fprintf(ficresstdeij,"\n#****** ");
 6478: 	fprintf(ficrescveij,"\n#****** ");
 6479: 	for(j=1;j<=cptcoveff;j++) {
 6480: 	  fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 6481: 	  fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 6482: 	}
 6483: 	fprintf(ficresstdeij,"******\n");
 6484: 	fprintf(ficrescveij,"******\n");
 6485: 
 6486: 	fprintf(ficresvij,"\n#****** ");
 6487: 	for(j=1;j<=cptcoveff;j++) 
 6488: 	  fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 6489: 	fprintf(ficresvij,"******\n");
 6490: 
 6491: 	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 6492: 	oldm=oldms;savm=savms;
 6493: 	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
 6494: 	/*
 6495: 	 */
 6496: 	/* goto endfree; */
 6497:  
 6498: 	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 6499: 	pstamp(ficrest);
 6500: 
 6501: 
 6502: 	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
 6503: 	  oldm=oldms;savm=savms; /* Segmentation fault */
 6504: 	  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
 6505: 	  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 ");
 6506: 	  if(vpopbased==1)
 6507: 	    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);
 6508: 	  else
 6509: 	    fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
 6510: 	  fprintf(ficrest,"# Age e.. (std) ");
 6511: 	  for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
 6512: 	  fprintf(ficrest,"\n");
 6513: 
 6514: 	  epj=vector(1,nlstate+1);
 6515: 	  for(age=bage; age <=fage ;age++){
 6516: 	    prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
 6517: 	    if (vpopbased==1) {
 6518: 	      if(mobilav ==0){
 6519: 		for(i=1; i<=nlstate;i++)
 6520: 		  prlim[i][i]=probs[(int)age][i][k];
 6521: 	      }else{ /* mobilav */ 
 6522: 		for(i=1; i<=nlstate;i++)
 6523: 		  prlim[i][i]=mobaverage[(int)age][i][k];
 6524: 	      }
 6525: 	    }
 6526: 	
 6527: 	    fprintf(ficrest," %4.0f",age);
 6528: 	    for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
 6529: 	      for(i=1, epj[j]=0.;i <=nlstate;i++) {
 6530: 		epj[j] += prlim[i][i]*eij[i][j][(int)age];
 6531: 		/*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
 6532: 	      }
 6533: 	      epj[nlstate+1] +=epj[j];
 6534: 	    }
 6535: 
 6536: 	    for(i=1, vepp=0.;i <=nlstate;i++)
 6537: 	      for(j=1;j <=nlstate;j++)
 6538: 		vepp += vareij[i][j][(int)age];
 6539: 	    fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
 6540: 	    for(j=1;j <=nlstate;j++){
 6541: 	      fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
 6542: 	    }
 6543: 	    fprintf(ficrest,"\n");
 6544: 	  }
 6545: 	}
 6546: 	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 6547: 	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 6548: 	free_vector(epj,1,nlstate+1);
 6549:       /*}*/
 6550:     }
 6551:     free_vector(weight,1,n);
 6552:     free_imatrix(Tvard,1,NCOVMAX,1,2);
 6553:     free_imatrix(s,1,maxwav+1,1,n);
 6554:     free_matrix(anint,1,maxwav,1,n); 
 6555:     free_matrix(mint,1,maxwav,1,n);
 6556:     free_ivector(cod,1,n);
 6557:     free_ivector(tab,1,NCOVMAX);
 6558:     fclose(ficresstdeij);
 6559:     fclose(ficrescveij);
 6560:     fclose(ficresvij);
 6561:     fclose(ficrest);
 6562:     fclose(ficpar);
 6563:   
 6564:     /*------- Variance of period (stable) prevalence------*/   
 6565: 
 6566:     strcpy(fileresvpl,"vpl");
 6567:     strcat(fileresvpl,fileres);
 6568:     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
 6569:       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
 6570:       exit(0);
 6571:     }
 6572:     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
 6573: 
 6574:     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
 6575:       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
 6576:           
 6577:     for (k=1; k <= (int) pow(2,cptcoveff); k++){
 6578:     	fprintf(ficresvpl,"\n#****** ");
 6579: 	for(j=1;j<=cptcoveff;j++) 
 6580: 	  fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 6581: 	fprintf(ficresvpl,"******\n");
 6582:       
 6583: 	varpl=matrix(1,nlstate,(int) bage, (int) fage);
 6584: 	oldm=oldms;savm=savms;
 6585: 	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
 6586: 	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
 6587:       /*}*/
 6588:     }
 6589: 
 6590:     fclose(ficresvpl);
 6591: 
 6592:     /*---------- End : free ----------------*/
 6593:     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 6594:     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 6595:   }  /* mle==-3 arrives here for freeing */
 6596:  endfree:
 6597:     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
 6598:     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
 6599:     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
 6600:     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
 6601:     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
 6602:     free_matrix(covar,0,NCOVMAX,1,n);
 6603:     free_matrix(matcov,1,npar,1,npar);
 6604:     /*free_vector(delti,1,npar);*/
 6605:     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
 6606:     free_matrix(agev,1,maxwav,1,imx);
 6607:     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 6608: 
 6609:     free_ivector(ncodemax,1,NCOVMAX);
 6610:     free_ivector(Tvar,1,NCOVMAX);
 6611:     free_ivector(Tprod,1,NCOVMAX);
 6612:     free_ivector(Tvaraff,1,NCOVMAX);
 6613:     free_ivector(Tage,1,NCOVMAX);
 6614: 
 6615:     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
 6616:     free_imatrix(codtab,1,100,1,10);
 6617:   fflush(fichtm);
 6618:   fflush(ficgp);
 6619:   
 6620: 
 6621:   if((nberr >0) || (nbwarn>0)){
 6622:     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
 6623:     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
 6624:   }else{
 6625:     printf("End of Imach\n");
 6626:     fprintf(ficlog,"End of Imach\n");
 6627:   }
 6628:   printf("See log file on %s\n",filelog);
 6629:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
 6630:   (void) gettimeofday(&end_time,&tzp);
 6631:   tm = *localtime(&end_time.tv_sec);
 6632:   tmg = *gmtime(&end_time.tv_sec);
 6633:   strcpy(strtend,asctime(&tm));
 6634:   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
 6635:   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
 6636:   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
 6637: 
 6638:   printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
 6639:   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
 6640:   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
 6641:   /*  printf("Total time was %d uSec.\n", total_usecs);*/
 6642: /*   if(fileappend(fichtm,optionfilehtm)){ */
 6643:   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
 6644:   fclose(fichtm);
 6645:   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
 6646:   fclose(fichtmcov);
 6647:   fclose(ficgp);
 6648:   fclose(ficlog);
 6649:   /*------ End -----------*/
 6650: 
 6651: 
 6652:    printf("Before Current directory %s!\n",pathcd);
 6653:    if(chdir(pathcd) != 0)
 6654:     printf("Can't move to directory %s!\n",path);
 6655:   if(getcwd(pathcd,MAXLINE) > 0)
 6656:     printf("Current directory %s!\n",pathcd);
 6657:   /*strcat(plotcmd,CHARSEPARATOR);*/
 6658:   sprintf(plotcmd,"gnuplot");
 6659: #ifndef UNIX
 6660:   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
 6661: #endif
 6662:   if(!stat(plotcmd,&info)){
 6663:     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
 6664:     if(!stat(getenv("GNUPLOTBIN"),&info)){
 6665:       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
 6666:     }else
 6667:       strcpy(pplotcmd,plotcmd);
 6668: #ifdef UNIX
 6669:     strcpy(plotcmd,GNUPLOTPROGRAM);
 6670:     if(!stat(plotcmd,&info)){
 6671:       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
 6672:     }else
 6673:       strcpy(pplotcmd,plotcmd);
 6674: #endif
 6675:   }else
 6676:     strcpy(pplotcmd,plotcmd);
 6677:   
 6678:   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
 6679:   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
 6680: 
 6681:   if((outcmd=system(plotcmd)) != 0){
 6682:     printf("\n Problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
 6683:     printf("\n Trying on same directory\n");
 6684:     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
 6685:     if((outcmd=system(plotcmd)) != 0)
 6686:       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
 6687:   }
 6688:   printf(" Wait...");
 6689:   while (z[0] != 'q') {
 6690:     /* chdir(path); */
 6691:     printf("\nType e to edit output files, g to graph again and q for exiting: ");
 6692:     scanf("%s",z);
 6693: /*     if (z[0] == 'c') system("./imach"); */
 6694:     if (z[0] == 'e') {
 6695: #ifdef OSX
 6696:       sprintf(pplotcmd, "open %s", optionfilehtm);
 6697: #else
 6698:       sprintf(pplotcmd, "%s", optionfilehtm);
 6699: #endif
 6700:       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
 6701:       system(pplotcmd);
 6702:     }
 6703:     else if (z[0] == 'g') system(plotcmd);
 6704:     else if (z[0] == 'q') exit(0);
 6705:   }
 6706:   end:
 6707:   while (z[0] != 'q') {
 6708:     printf("\nType  q for exiting: ");
 6709:     scanf("%s",z);
 6710:   }
 6711: }
 6712: 
 6713: 
 6714: 

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