Diff for /imach/src/imach.c between versions 1.49 and 1.148

version 1.49, 2002/06/20 14:03:39 version 1.148, 2014/06/17 17:38:48
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.148  2014/06/17 17:38:48  brouard
      Summary: Nothing new
   This program computes Healthy Life Expectancies from    Author: Brouard
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Just a new packaging for OS/X version 0.98nS
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.147  2014/06/16 10:33:11  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.146  2014/06/16 10:20:28  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Merge
   Maximum Likelihood of the parameters involved in the model.  The    Author: Brouard
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Merge, before building revised version.
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.145  2014/06/10 21:23:15  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Summary: Debugging with valgrind
   complex model than "constant and age", you should modify the program    Author: Nicolas Brouard
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Lot of changes in order to output the results with some covariates
   convergence.    After the Edimburgh REVES conference 2014, it seems mandatory to
     improve the code.
   The advantage of this computer programme, compared to a simple    No more memory valgrind error but a lot has to be done in order to
   multinomial logistic model, is clear when the delay between waves is not    continue the work of splitting the code into subroutines.
   identical for each individual. Also, if a individual missed an    Also, decodemodel has been improved. Tricode is still not
   intermediate interview, the information is lost, but taken into    optimal. nbcode should be improved. Documentation has been added in
   account using an interpolation or extrapolation.      the source code.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.143  2014/01/26 09:45:38  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   semester or year) is model as a multinomial logistic.  The hPx    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.142  2014/01/26 03:57:36  brouard
   hPijx.    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
   Also this programme outputs the covariance matrix of the parameters but also    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.141  2014/01/26 02:42:01  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.140  2011/09/02 10:37:54  brouard
   from the European Union.    Summary: times.h is ok with mingw32 now.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.139  2010/06/14 07:50:17  brouard
   can be accessed at http://euroreves.ined.fr/imach .    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   **********************************************************************/    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
    
 #include <math.h>    Revision 1.138  2010/04/30 18:19:40  brouard
 #include <stdio.h>    *** empty log message ***
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 #define MAXLINE 256    than V1+V2. A lot of change to be done. Unstable.
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.136  2010/04/26 20:30:53  brouard
 #define FILENAMELENGTH 80    (Module): merging some libgsl code. Fixing computation
 /*#define DEBUG*/    of likelione (using inter/intrapolation if mle = 0) in order to
 #define windows    get same likelihood as if mle=1.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Some cleaning of code and comments added.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.135  2009/10/29 15:33:14  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.134  2009/10/29 13:18:53  brouard
 #define NINTERVMAX 8    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.133  2009/07/06 10:21:25  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    just nforces
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.132  2009/07/06 08:22:05  brouard
 #define AGESUP 130    Many tings
 #define AGEBASE 40  
 #ifdef windows    Revision 1.131  2009/06/20 16:22:47  brouard
 #define DIRSEPARATOR '\\'    Some dimensions resccaled
 #else  
 #define DIRSEPARATOR '/'    Revision 1.130  2009/05/26 06:44:34  brouard
 #endif    (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 int erreur; /* Error number */  
 int nvar;    Revision 1.129  2007/08/31 13:49:27  lievre
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.128  2006/06/30 13:02:05  brouard
 int ndeath=1; /* Number of dead states */    (Module): Clarifications on computing e.j
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 int *wav; /* Number of waves for this individuual 0 is possible */    imach-114 because nhstepm was no more computed in the age
 int maxwav; /* Maxim number of waves */    loop. Now we define nhstepma in the age loop.
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): In order to speed up (in case of numerous covariates) we
 int mle, weightopt;    compute health expectancies (without variances) in a first step
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    and then all the health expectancies with variances or standard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    deviation (needs data from the Hessian matrices) which slows the
 double jmean; /* Mean space between 2 waves */    computation.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    In the future we should be able to stop the program is only health
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    expectancies and graph are needed without standard deviations.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Revision 1.126  2006/04/28 17:23:28  brouard
 FILE *fichtm; /* Html File */    (Module): Yes the sum of survivors was wrong since
 FILE *ficreseij;    imach-114 because nhstepm was no more computed in the age
 char filerese[FILENAMELENGTH];    loop. Now we define nhstepma in the age loop.
 FILE  *ficresvij;    Version 0.98h
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    Revision 1.125  2006/04/04 15:20:31  lievre
 char fileresvpl[FILENAMELENGTH];    Errors in calculation of health expectancies. Age was not initialized.
 char title[MAXLINE];    Forecasting file added.
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    The log-likelihood is printed in the log file
   
 char filerest[FILENAMELENGTH];    Revision 1.123  2006/03/20 10:52:43  brouard
 char fileregp[FILENAMELENGTH];    * imach.c (Module): <title> changed, corresponds to .htm file
 char popfile[FILENAMELENGTH];    name. <head> headers where missing.
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define NR_END 1    otherwise the weight is truncated).
 #define FREE_ARG char*    Modification of warning when the covariates values are not 0 or
 #define FTOL 1.0e-10    1.
     Version 0.98g
 #define NRANSI  
 #define ITMAX 200    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 #define TOL 2.0e-4    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 #define CGOLD 0.3819660    Modification of warning when the covariates values are not 0 or
 #define ZEPS 1.0e-10    1.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Version 0.98g
   
 #define GOLD 1.618034    Revision 1.121  2006/03/16 17:45:01  lievre
 #define GLIMIT 100.0    * imach.c (Module): Comments concerning covariates added
 #define TINY 1.0e-20  
     * imach.c (Module): refinements in the computation of lli if
 static double maxarg1,maxarg2;    status=-2 in order to have more reliable computation if stepm is
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    not 1 month. Version 0.98f
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.120  2006/03/16 15:10:38  lievre
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): refinements in the computation of lli if
 #define rint(a) floor(a+0.5)    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.119  2006/03/15 17:42:26  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 int imx;  
 int stepm;    Revision 1.118  2006/03/14 18:20:07  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 int estepm;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (Module): Function pstamp added
     (Module): Version 0.98d
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.117  2006/03/14 17:16:22  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): varevsij Comments added explaining the second
 double **pmmij, ***probs, ***mobaverage;    table of variances if popbased=1 .
 double dateintmean=0;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 double *weight;    (Module): Version 0.98d
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.116  2006/03/06 10:29:27  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.114  2006/02/26 12:57:58  brouard
 {    (Module): Some improvements in processing parameter
    char *s;                             /* pointer */    filename with strsep.
    int  l1, l2;                         /* length counters */  
     Revision 1.113  2006/02/24 14:20:24  brouard
    l1 = strlen( path );                 /* length of path */    (Module): Memory leaks checks with valgrind and:
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    datafile was not closed, some imatrix were not freed and on matrix
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */    allocation too.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.112  2006/01/30 09:55:26  brouard
       extern char       *getwd( );    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.111  2006/01/25 20:38:18  brouard
 #else    (Module): Lots of cleaning and bugs added (Gompertz)
       extern char       *getcwd( );    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.110  2006/01/25 00:51:50  brouard
          return( GLOCK_ERROR_GETCWD );    (Module): Lots of cleaning and bugs added (Gompertz)
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.109  2006/01/24 19:37:15  brouard
    } else {                             /* strip direcotry from path */    (Module): Comments (lines starting with a #) are allowed in data.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.108  2006/01/19 18:05:42  lievre
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Gnuplot problem appeared...
       strcpy( name, s );                /* save file name */    To be fixed
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.107  2006/01/19 16:20:37  brouard
    }    Test existence of gnuplot in imach path
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.106  2006/01/19 13:24:36  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Some cleaning and links added in html output
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.105  2006/01/05 20:23:19  lievre
 #endif    *** empty log message ***
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.104  2005/09/30 16:11:43  lievre
    strcpy(ext,s);                       /* save extension */    (Module): sump fixed, loop imx fixed, and simplifications.
    l1= strlen( name);    (Module): If the status is missing at the last wave but we know
    l2= strlen( s)+1;    that the person is alive, then we can code his/her status as -2
    strncpy( finame, name, l1-l2);    (instead of missing=-1 in earlier versions) and his/her
    finame[l1-l2]= 0;    contributions to the likelihood is 1 - Prob of dying from last
    return( 0 );                         /* we're done */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 }    the healthy state at last known wave). Version is 0.98
   
     Revision 1.103  2005/09/30 15:54:49  lievre
 /******************************************/    (Module): sump fixed, loop imx fixed, and simplifications.
   
 void replace(char *s, char*t)    Revision 1.102  2004/09/15 17:31:30  brouard
 {    Add the possibility to read data file including tab characters.
   int i;  
   int lg=20;    Revision 1.101  2004/09/15 10:38:38  brouard
   i=0;    Fix on curr_time
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.100  2004/07/12 18:29:06  brouard
     (s[i] = t[i]);    Add version for Mac OS X. Just define UNIX in Makefile
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.99  2004/06/05 08:57:40  brouard
 }    *** empty log message ***
   
 int nbocc(char *s, char occ)    Revision 1.98  2004/05/16 15:05:56  brouard
 {    New version 0.97 . First attempt to estimate force of mortality
   int i,j=0;    directly from the data i.e. without the need of knowing the health
   int lg=20;    state at each age, but using a Gompertz model: log u =a + b*age .
   i=0;    This is the basic analysis of mortality and should be done before any
   lg=strlen(s);    other analysis, in order to test if the mortality estimated from the
   for(i=0; i<= lg; i++) {    cross-longitudinal survey is different from the mortality estimated
   if  (s[i] == occ ) j++;    from other sources like vital statistic data.
   }  
   return j;    The same imach parameter file can be used but the option for mle should be -3.
 }  
     Agnès, who wrote this part of the code, tried to keep most of the
 void cutv(char *u,char *v, char*t, char occ)    former routines in order to include the new code within the former code.
 {  
   int i,lg,j,p=0;    The output is very simple: only an estimate of the intercept and of
   i=0;    the slope with 95% confident intervals.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Current limitations:
   }    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   lg=strlen(t);    B) There is no computation of Life Expectancy nor Life Table.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.97  2004/02/20 13:25:42  lievre
   }    Version 0.96d. Population forecasting command line is (temporarily)
      u[p]='\0';    suppressed.
   
    for(j=0; j<= lg; j++) {    Revision 1.96  2003/07/15 15:38:55  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   }    rewritten within the same printf. Workaround: many printfs.
 }  
     Revision 1.95  2003/07/08 07:54:34  brouard
 /********************** nrerror ********************/    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 void nrerror(char error_text[])    matrix (cov(a12,c31) instead of numbers.
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.94  2003/06/27 13:00:02  brouard
   fprintf(stderr,"%s\n",error_text);    Just cleaning
   exit(1);  
 }    Revision 1.93  2003/06/25 16:33:55  brouard
 /*********************** vector *******************/    (Module): On windows (cygwin) function asctime_r doesn't
 double *vector(int nl, int nh)    exist so I changed back to asctime which exists.
 {    (Module): Version 0.96b
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.92  2003/06/25 16:30:45  brouard
   if (!v) nrerror("allocation failure in vector");    (Module): On windows (cygwin) function asctime_r doesn't
   return v-nl+NR_END;    exist so I changed back to asctime which exists.
 }  
     Revision 1.91  2003/06/25 15:30:29  brouard
 /************************ free vector ******************/    * imach.c (Repository): Duplicated warning errors corrected.
 void free_vector(double*v, int nl, int nh)    (Repository): Elapsed time after each iteration is now output. It
 {    helps to forecast when convergence will be reached. Elapsed time
   free((FREE_ARG)(v+nl-NR_END));    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 /************************ivector *******************************/    Revision 1.90  2003/06/24 12:34:15  brouard
 int *ivector(long nl,long nh)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   int *v;    of the covariance matrix to be input.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.89  2003/06/24 12:30:52  brouard
   return v-nl+NR_END;    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.88  2003/06/23 17:54:56  brouard
 {    * 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.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.86  2003/06/17 20:04:08  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): Change position of html and gnuplot routines and added
 {    routine fileappend.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.85  2003/06/17 13:12:43  brouard
      * imach.c (Repository): Check when date of death was earlier that
   /* allocate pointers to rows */    current date of interview. It may happen when the death was just
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    prior to the death. In this case, dh was negative and likelihood
   if (!m) nrerror("allocation failure 1 in matrix()");    was wrong (infinity). We still send an "Error" but patch by
   m += NR_END;    assuming that the date of death was just one stepm after the
   m -= nrl;    interview.
      (Repository): Because some people have very long ID (first column)
      we changed int to long in num[] and we added a new lvector for
   /* allocate rows and set pointers to them */    memory allocation. But we also truncated to 8 characters (left
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    truncation)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Repository): No more line truncation errors.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.84  2003/06/13 21:44:43  brouard
      * imach.c (Repository): Replace "freqsummary" at a correct
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    place. It differs from routine "prevalence" which may be called
      many times. Probs is memory consuming and must be used with
   /* return pointer to array of pointers to rows */    parcimony.
   return m;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 }  
     Revision 1.83  2003/06/10 13:39:11  lievre
 /****************** free_imatrix *************************/    *** empty log message ***
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.82  2003/06/05 15:57:20  brouard
       long nch,ncl,nrh,nrl;    Add log in  imach.c and  fullversion number is now printed.
      /* free an int matrix allocated by imatrix() */  
 {  */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /*
   free((FREE_ARG) (m+nrl-NR_END));     Interpolated Markov Chain
 }  
     Short summary of the programme:
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    first survey ("cross") where individuals from different ages are
   double **m;    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    second wave of interviews ("longitudinal") which measure each change
   if (!m) nrerror("allocation failure 1 in matrix()");    (if any) in individual health status.  Health expectancies are
   m += NR_END;    computed from the time spent in each health state according to a
   m -= nrl;    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    simplest model is the multinomial logistic model where pij is the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    probability to be observed in state j at the second wave
   m[nrl] += NR_END;    conditional to be observed in state i at the first wave. Therefore
   m[nrl] -= ncl;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    complex model than "constant and age", you should modify the program
   return m;    where the markup *Covariates have to be included here again* invites
 }    you to do it.  More covariates you add, slower the
     convergence.
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    identical for each individual. Also, if a individual missed an
   free((FREE_ARG)(m+nrl-NR_END));    intermediate interview, the information is lost, but taken into
 }    account using an interpolation or extrapolation.  
   
 /******************* ma3x *******************************/    hPijx is the probability to be observed in state i at age x+h
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    conditional to the observed state i at age x. The delay 'h' can be
 {    split into an exact number (nh*stepm) of unobserved intermediate
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    states. This elementary transition (by month, quarter,
   double ***m;    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    and the contribution of each individual to the likelihood is simply
   if (!m) nrerror("allocation failure 1 in matrix()");    hPijx.
   m += NR_END;  
   m -= nrl;    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m[nrl] += NR_END;             Institut national d'études démographiques, Paris.
   m[nrl] -= ncl;    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    can be accessed at http://euroreves.ined.fr/imach .
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   m[nrl][ncl] -= nll;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   for (j=ncl+1; j<=nch; j++)    
     m[nrl][j]=m[nrl][j-1]+nlay;    **********************************************************************/
    /*
   for (i=nrl+1; i<=nrh; i++) {    main
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    read parameterfile
     for (j=ncl+1; j<=nch; j++)    read datafile
       m[i][j]=m[i][j-1]+nlay;    concatwav
   }    freqsummary
   return m;    if (mle >= 1)
 }      mlikeli
     print results files
 /*************************free ma3x ************************/    if mle==1 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)       computes hessian
 {    read end of parameter file: agemin, agemax, bage, fage, estepm
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));        begin-prev-date,...
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    open gnuplot file
   free((FREE_ARG)(m+nrl-NR_END));    open html file
 }    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
      for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 /***************** f1dim *************************/                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 extern int ncom;      freexexit2 possible for memory heap.
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    h Pij x                         | pij_nom  ficrestpij
       # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 double f1dim(double x)         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
 {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   int j;  
   double f;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   double *xt;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
      variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   xt=vector(1,ncom);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    forecasting if prevfcast==1 prevforecast call prevalence()
   return f;    health expectancies
 }    Variance-covariance of DFLE
     prevalence()
 /*****************brent *************************/     movingaverage()
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   int iter;    total life expectancies
   double a,b,d,etemp;    Variance of period (stable) prevalence
   double fu,fv,fw,fx;   end
   double ftemp;  */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  
    
   a=(ax < cx ? ax : cx);   
   b=(ax > cx ? ax : cx);  #include <math.h>
   x=w=v=bx;  #include <stdio.h>
   fw=fv=fx=(*f)(x);  #include <stdlib.h>
   for (iter=1;iter<=ITMAX;iter++) {  #include <string.h>
     xm=0.5*(a+b);  #include <unistd.h>
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #include <limits.h>
     printf(".");fflush(stdout);  #include <sys/types.h>
 #ifdef DEBUG  #include <sys/stat.h>
     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);  #include <errno.h>
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  extern int errno;
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #ifdef LINUX
       *xmin=x;  #include <time.h>
       return fx;  #include "timeval.h"
     }  #else
     ftemp=fu;  #include <sys/time.h>
     if (fabs(e) > tol1) {  #endif
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  #ifdef GSL
       p=(x-v)*q-(x-w)*r;  #include <gsl/gsl_errno.h>
       q=2.0*(q-r);  #include <gsl/gsl_multimin.h>
       if (q > 0.0) p = -p;  #endif
       q=fabs(q);  
       etemp=e;  /* #include <libintl.h> */
       e=d;  /* #define _(String) gettext (String) */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       else {  
         d=p/q;  #define GNUPLOTPROGRAM "gnuplot"
         u=x+d;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         if (u-a < tol2 || b-u < tol2)  #define FILENAMELENGTH 132
           d=SIGN(tol1,xm-x);  
       }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     } else {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     fu=(*f)(u);  
     if (fu <= fx) {  #define NINTERVMAX 8
       if (u >= x) a=x; else b=x;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       SHFT(v,w,x,u)  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
         SHFT(fv,fw,fx,fu)  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
         } else {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
           if (u < x) a=u; else b=u;  #define MAXN 20000
           if (fu <= fw || w == x) {  #define YEARM 12. /**< Number of months per year */
             v=w;  #define AGESUP 130
             w=u;  #define AGEBASE 40
             fv=fw;  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
             fw=fu;  #ifdef UNIX
           } else if (fu <= fv || v == x || v == w) {  #define DIRSEPARATOR '/'
             v=u;  #define CHARSEPARATOR "/"
             fv=fu;  #define ODIRSEPARATOR '\\'
           }  #else
         }  #define DIRSEPARATOR '\\'
   }  #define CHARSEPARATOR "\\"
   nrerror("Too many iterations in brent");  #define ODIRSEPARATOR '/'
   *xmin=x;  #endif
   return fx;  
 }  /* $Id$ */
   /* $State$ */
 /****************** mnbrak ***********************/  
   char version[]="Imach version 0.98nS, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char fullversion[]="$Revision$ $Date$"; 
             double (*func)(double))  char strstart[80];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double ulim,u,r,q, dum;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double fu;  int nvar=0, nforce=0; /* Number of variables, number of forces */
    /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   *fa=(*func)(*ax);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   *fb=(*func)(*bx);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   if (*fb > *fa) {  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     SHFT(dum,*ax,*bx,dum)  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       SHFT(dum,*fb,*fa,dum)  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   *cx=(*bx)+GOLD*(*bx-*ax);  int cptcov=0; /* Working variable */
   *fc=(*func)(*cx);  int npar=NPARMAX;
   while (*fb > *fc) {  int nlstate=2; /* Number of live states */
     r=(*bx-*ax)*(*fb-*fc);  int ndeath=1; /* Number of dead states */
     q=(*bx-*cx)*(*fb-*fa);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int popbased=0;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int *wav; /* Number of waves for this individuual 0 is possible */
     if ((*bx-u)*(u-*cx) > 0.0) {  int maxwav=0; /* Maxim number of waves */
       fu=(*func)(u);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       fu=(*func)(u);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       if (fu < *fc) {                     to the likelihood and the sum of weights (done by funcone)*/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int mle=1, weightopt=0;
           SHFT(*fb,*fc,fu,(*func)(u))  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
           }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       u=ulim;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       fu=(*func)(u);  double jmean=1; /* Mean space between 2 waves */
     } else {  double **matprod2(); /* test */
       u=(*cx)+GOLD*(*cx-*bx);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       fu=(*func)(u);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     }  /*FILE *fic ; */ /* Used in readdata only */
     SHFT(*ax,*bx,*cx,u)  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       SHFT(*fa,*fb,*fc,fu)  FILE *ficlog, *ficrespow;
       }  int globpr=0; /* Global variable for printing or not */
 }  double fretone; /* Only one call to likelihood */
   long ipmx=0; /* Number of contributions */
 /*************** linmin ************************/  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 int ncom;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 double *pcom,*xicom;  FILE *ficresilk;
 double (*nrfunc)(double []);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    FILE *ficresprobmorprev;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  FILE *fichtm, *fichtmcov; /* Html File */
 {  FILE *ficreseij;
   double brent(double ax, double bx, double cx,  char filerese[FILENAMELENGTH];
                double (*f)(double), double tol, double *xmin);  FILE *ficresstdeij;
   double f1dim(double x);  char fileresstde[FILENAMELENGTH];
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  FILE *ficrescveij;
               double *fc, double (*func)(double));  char filerescve[FILENAMELENGTH];
   int j;  FILE  *ficresvij;
   double xx,xmin,bx,ax;  char fileresv[FILENAMELENGTH];
   double fx,fb,fa;  FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
   ncom=n;  char title[MAXLINE];
   pcom=vector(1,n);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   xicom=vector(1,n);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   nrfunc=func;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   for (j=1;j<=n;j++) {  char command[FILENAMELENGTH];
     pcom[j]=p[j];  int  outcmd=0;
     xicom[j]=xi[j];  
   }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   ax=0.0;  
   xx=1.0;  char filelog[FILENAMELENGTH]; /* Log file */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  char filerest[FILENAMELENGTH];
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  char fileregp[FILENAMELENGTH];
 #ifdef DEBUG  char popfile[FILENAMELENGTH];
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     p[j] += xi[j];  struct timezone tzp;
   }  extern int gettimeofday();
   free_vector(xicom,1,n);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free_vector(pcom,1,n);  long time_value;
 }  extern long time();
   char strcurr[80], strfor[80];
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  char *endptr;
             double (*func)(double []))  long lval;
 {  double dval;
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  #define NR_END 1
   int i,ibig,j;  #define FREE_ARG char*
   double del,t,*pt,*ptt,*xit;  #define FTOL 1.0e-10
   double fp,fptt;  
   double *xits;  #define NRANSI 
   pt=vector(1,n);  #define ITMAX 200 
   ptt=vector(1,n);  
   xit=vector(1,n);  #define TOL 2.0e-4 
   xits=vector(1,n);  
   *fret=(*func)(p);  #define CGOLD 0.3819660 
   for (j=1;j<=n;j++) pt[j]=p[j];  #define ZEPS 1.0e-10 
   for (*iter=1;;++(*iter)) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     fp=(*fret);  
     ibig=0;  #define GOLD 1.618034 
     del=0.0;  #define GLIMIT 100.0 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define TINY 1.0e-20 
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  static double maxarg1,maxarg2;
     printf("\n");  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     for (i=1;i<=n;i++) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    
       fptt=(*fret);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #ifdef DEBUG  #define rint(a) floor(a+0.5)
       printf("fret=%lf \n",*fret);  
 #endif  static double sqrarg;
       printf("%d",i);fflush(stdout);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       linmin(p,xit,n,fret,func);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       if (fabs(fptt-(*fret)) > del) {  int agegomp= AGEGOMP;
         del=fabs(fptt-(*fret));  
         ibig=i;  int imx; 
       }  int stepm=1;
 #ifdef DEBUG  /* Stepm, step in month: minimum step interpolation*/
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  int estepm;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  int m,nb;
       for(j=1;j<=n;j++)  long *num;
         printf(" p=%.12e",p[j]);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       printf("\n");  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #endif  double **pmmij, ***probs;
     }  double *ageexmed,*agecens;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double dateintmean=0;
 #ifdef DEBUG  
       int k[2],l;  double *weight;
       k[0]=1;  int **s; /* Status */
       k[1]=-1;  double *agedc;
       printf("Max: %.12e",(*func)(p));  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       for (j=1;j<=n;j++)                    * covar=matrix(0,NCOVMAX,1,n); 
         printf(" %.12e",p[j]);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       printf("\n");  double  idx; 
       for(l=0;l<=1;l++) {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         for (j=1;j<=n;j++) {  int *Ndum; /** Freq of modality (tricode */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  int **codtab; /**< codtab=imatrix(1,100,1,10); */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
         }  double *lsurv, *lpop, *tpop;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 #endif  double ftolhess; /**< Tolerance for computing hessian */
   
   /**************** split *************************/
       free_vector(xit,1,n);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       free_vector(xits,1,n);  {
       free_vector(ptt,1,n);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       free_vector(pt,1,n);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       return;    */ 
     }    char  *ss;                            /* pointer */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    int   l1, l2;                         /* length counters */
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];    l1 = strlen(path );                   /* length of path */
       xit[j]=p[j]-pt[j];    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       pt[j]=p[j];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     fptt=(*func)(ptt);      strcpy( name, path );               /* we got the fullname name because no directory */
     if (fptt < fp) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       if (t < 0.0) {      /* get current working directory */
         linmin(p,xit,n,fret,func);      /*    extern  char* getcwd ( char *buf , int len);*/
         for (j=1;j<=n;j++) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
           xi[j][ibig]=xi[j][n];        return( GLOCK_ERROR_GETCWD );
           xi[j][n]=xit[j];      }
         }      /* got dirc from getcwd*/
 #ifdef DEBUG      printf(" DIRC = %s \n",dirc);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    } else {                              /* strip direcotry from path */
         for(j=1;j<=n;j++)      ss++;                               /* after this, the filename */
           printf(" %.12e",xit[j]);      l2 = strlen( ss );                  /* length of filename */
         printf("\n");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 #endif      strcpy( name, ss );         /* save file name */
       }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     }      dirc[l1-l2] = 0;                    /* add zero */
   }      printf(" DIRC2 = %s \n",dirc);
 }    }
     /* We add a separator at the end of dirc if not exists */
 /**** Prevalence limit ****************/    l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      dirc[l1] =  DIRSEPARATOR;
 {      dirc[l1+1] = 0; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      printf(" DIRC3 = %s \n",dirc);
      matrix by transitions matrix until convergence is reached */    }
     ss = strrchr( name, '.' );            /* find last / */
   int i, ii,j,k;    if (ss >0){
   double min, max, maxmin, maxmax,sumnew=0.;      ss++;
   double **matprod2();      strcpy(ext,ss);                     /* save extension */
   double **out, cov[NCOVMAX], **pmij();      l1= strlen( name);
   double **newm;      l2= strlen(ss)+1;
   double agefin, delaymax=50 ; /* Max number of years to converge */      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
   for (ii=1;ii<=nlstate+ndeath;ii++)    }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return( 0 );                          /* we're done */
     }  }
   
    cov[1]=1.;  
    /******************************************/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  void replace_back_to_slash(char *s, char*t)
     newm=savm;  {
     /* Covariates have to be included here again */    int i;
      cov[2]=agefin;    int lg=0;
      i=0;
       for (k=1; k<=cptcovn;k++) {    lg=strlen(t);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for(i=0; i<= lg; i++) {
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/      (s[i] = t[i]);
       }      if (t[i]== '\\') s[i]='/';
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    }
       for (k=1; k<=cptcovprod;k++)  }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   char *trimbb(char *out, char *in)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    char *s;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    s=out;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     savm=oldm;        in++;
     oldm=newm;      }
     maxmax=0.;      *out++ = *in++;
     for(j=1;j<=nlstate;j++){    }
       min=1.;    *out='\0';
       max=0.;    return s;
       for(i=1; i<=nlstate; i++) {  }
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  char *cutl(char *blocc, char *alocc, char *in, char occ)
         prlim[i][j]= newm[i][j]/(1-sumnew);  {
         max=FMAX(max,prlim[i][j]);    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
         min=FMIN(min,prlim[i][j]);       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       }       gives blocc="abcdef2ghi" and alocc="j".
       maxmin=max-min;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
       maxmax=FMAX(maxmax,maxmin);    */
     }    char *s, *t, *bl;
     if(maxmax < ftolpl){    t=in;s=in;
       return prlim;    while ((*in != occ) && (*in != '\0')){
     }      *alocc++ = *in++;
   }    }
 }    if( *in == occ){
       *(alocc)='\0';
 /*************** transition probabilities ***************/      s=++in;
     }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )   
 {    if (s == t) {/* occ not found */
   double s1, s2;      *(alocc-(in-s))='\0';
   /*double t34;*/      in=s;
   int i,j,j1, nc, ii, jj;    }
     while ( *in != '\0'){
     for(i=1; i<= nlstate; i++){      *blocc++ = *in++;
     for(j=1; j<i;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/    *blocc='\0';
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    return t;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  }
       }  char *cutv(char *blocc, char *alocc, char *in, char occ)
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     for(j=i+1; j<=nlstate+ndeath;j++){       gives blocc="abcdef2ghi" and alocc="j".
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    char *s, *t;
       }    t=in;s=in;
       ps[i][j]=s2;    while (*in != '\0'){
     }      while( *in == occ){
   }        *blocc++ = *in++;
     /*ps[3][2]=1;*/        s=in;
       }
   for(i=1; i<= nlstate; i++){      *blocc++ = *in++;
      s1=0;    }
     for(j=1; j<i; j++)    if (s == t) /* occ not found */
       s1+=exp(ps[i][j]);      *(blocc-(in-s))='\0';
     for(j=i+1; j<=nlstate+ndeath; j++)    else
       s1+=exp(ps[i][j]);      *(blocc-(in-s)-1)='\0';
     ps[i][i]=1./(s1+1.);    in=s;
     for(j=1; j<i; j++)    while ( *in != '\0'){
       ps[i][j]= exp(ps[i][j])*ps[i][i];      *alocc++ = *in++;
     for(j=i+1; j<=nlstate+ndeath; j++)    }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    *alocc='\0';
   } /* end i */    return s;
   }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  int nbocc(char *s, char occ)
       ps[ii][jj]=0;  {
       ps[ii][ii]=1;    int i,j=0;
     }    int lg=20;
   }    i=0;
     lg=strlen(s);
     for(i=0; i<= lg; i++) {
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    if  (s[i] == occ ) j++;
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
      printf("%lf ",ps[ii][jj]);    return j;
    }  }
     printf("\n ");  
     }  /* void cutv(char *u,char *v, char*t, char occ) */
     printf("\n ");printf("%lf ",cov[2]);*/  /* { */
 /*  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   goto end;*/  /*      gives u="abcdef2ghi" and v="j" *\/ */
     return ps;  /*   int i,lg,j,p=0; */
 }  /*   i=0; */
   /*   lg=strlen(t); */
 /**************** Product of 2 matrices ******************/  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /*   } */
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*   for(j=0; j<p; j++) { */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /*     (u[j] = t[j]); */
   /* in, b, out are matrice of pointers which should have been initialized  /*   } */
      before: only the contents of out is modified. The function returns  /*      u[p]='\0'; */
      a pointer to pointers identical to out */  
   long i, j, k;  /*    for(j=0; j<= lg; j++) { */
   for(i=nrl; i<= nrh; i++)  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     for(k=ncolol; k<=ncoloh; k++)  /*   } */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /* } */
         out[i][k] +=in[i][j]*b[j][k];  
   /********************** nrerror ********************/
   return out;  
 }  void nrerror(char error_text[])
   {
     fprintf(stderr,"ERREUR ...\n");
 /************* Higher Matrix Product ***************/    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  }
 {  /*********************** vector *******************/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  double *vector(int nl, int nh)
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    double *v;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      (typically every 2 years instead of every month which is too big).    if (!v) nrerror("allocation failure in vector");
      Model is determined by parameters x and covariates have to be    return v-nl+NR_END;
      included manually here.  }
   
      */  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
   int i, j, d, h, k;  {
   double **out, cov[NCOVMAX];    free((FREE_ARG)(v+nl-NR_END));
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  /************************ivector *******************************/
   for (i=1;i<=nlstate+ndeath;i++)  int *ivector(long nl,long nh)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[i][j]=(i==j ? 1.0 : 0.0);    int *v;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     }    if (!v) nrerror("allocation failure in ivector");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    return v-nl+NR_END;
   for(h=1; h <=nhstepm; h++){  }
     for(d=1; d <=hstepm; d++){  
       newm=savm;  /******************free ivector **************************/
       /* Covariates have to be included here again */  void free_ivector(int *v, long nl, long nh)
       cov[1]=1.;  {
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    free((FREE_ARG)(v+nl-NR_END));
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /************************lvector *******************************/
       for (k=1; k<=cptcovprod;k++)  long *lvector(long nl,long nh)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    if (!v) nrerror("allocation failure in ivector");
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    return v-nl+NR_END;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  /******************free lvector **************************/
       oldm=newm;  void free_lvector(long *v, long nl, long nh)
     }  {
     for(i=1; i<=nlstate+ndeath; i++)    free((FREE_ARG)(v+nl-NR_END));
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /******************* imatrix *******************************/
          */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   } /* end h */  { 
   return po;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 }    int **m; 
     
     /* allocate pointers to rows */ 
 /*************** log-likelihood *************/    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 double func( double *x)    if (!m) nrerror("allocation failure 1 in matrix()"); 
 {    m += NR_END; 
   int i, ii, j, k, mi, d, kk;    m -= nrl; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    
   double **out;    
   double sw; /* Sum of weights */    /* allocate rows and set pointers to them */ 
   double lli; /* Individual log likelihood */    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   long ipmx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   /*extern weight */    m[nrl] += NR_END; 
   /* We are differentiating ll according to initial status */    m[nrl] -= ncl; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    
   /*for(i=1;i<imx;i++)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     printf(" %d\n",s[4][i]);    
   */    /* return pointer to array of pointers to rows */ 
   cov[1]=1.;    return m; 
   } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /****************** free_imatrix *************************/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(mi=1; mi<= wav[i]-1; mi++){        int **m;
       for (ii=1;ii<=nlstate+ndeath;ii++)        long nch,ncl,nrh,nrl; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       /* free an int matrix allocated by imatrix() */ 
       for(d=0; d<dh[mi][i]; d++){  { 
         newm=savm;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    free((FREE_ARG) (m+nrl-NR_END)); 
         for (kk=1; kk<=cptcovage;kk++) {  } 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  /******************* matrix *******************************/
          double **matrix(long nrl, long nrh, long ncl, long nch)
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         savm=oldm;    double **m;
         oldm=newm;  
            m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
            if (!m) nrerror("allocation failure 1 in matrix()");
       } /* end mult */    m += NR_END;
          m -= nrl;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       ipmx +=1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       sw += weight[i];    m[nrl] += NR_END;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    m[nrl] -= ncl;
     } /* end of wave */  
   } /* end of individual */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   return -l;     */
 }  }
   
   /*************************free matrix ************************/
 /*********** Maximum Likelihood Estimation ***************/  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  /******************* ma3x *******************************/
   xi=matrix(1,npar,1,npar);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       xi[i][j]=(i==j ? 1.0 : 0.0);    double ***m;
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    m += NR_END;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    m -= nrl;
   
 }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /**** Computes Hessian and covariance matrix ***/    m[nrl] += NR_END;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    m[nrl] -= ncl;
 {  
   double  **a,**y,*x,pd;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double **hess;  
   int i, j,jk;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   int *indx;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   double hessii(double p[], double delta, int theta, double delti[]);    m[nrl][ncl] -= nll;
   double hessij(double p[], double delti[], int i, int j);    for (j=ncl+1; j<=nch; j++) 
   void lubksb(double **a, int npar, int *indx, double b[]) ;      m[nrl][j]=m[nrl][j-1]+nlay;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    
     for (i=nrl+1; i<=nrh; i++) {
   hess=matrix(1,npar,1,npar);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
   printf("\nCalculation of the hessian matrix. Wait...\n");        m[i][j]=m[i][j-1]+nlay;
   for (i=1;i<=npar;i++){    }
     printf("%d",i);fflush(stdout);    return m; 
     hess[i][i]=hessii(p,ftolhess,i,delti);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /*printf(" %f ",p[i]);*/             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     /*printf(" %lf ",hess[i][i]);*/    */
   }  }
    
   for (i=1;i<=npar;i++) {  /*************************free ma3x ************************/
     for (j=1;j<=npar;j++)  {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       if (j>i) {  {
         printf(".%d%d",i,j);fflush(stdout);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         hess[i][j]=hessij(p,delti,i,j);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         hess[j][i]=hess[i][j];        free((FREE_ARG)(m+nrl-NR_END));
         /*printf(" %lf ",hess[i][j]);*/  }
       }  
     }  /*************** function subdirf ***********/
   }  char *subdirf(char fileres[])
   printf("\n");  {
     /* Caution optionfilefiname is hidden */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/"); /* Add to the right */
   a=matrix(1,npar,1,npar);    strcat(tmpout,fileres);
   y=matrix(1,npar,1,npar);    return tmpout;
   x=vector(1,npar);  }
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)  /*************** function subdirf2 ***********/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  char *subdirf2(char fileres[], char *preop)
   ludcmp(a,npar,indx,&pd);  {
     
   for (j=1;j<=npar;j++) {    /* Caution optionfilefiname is hidden */
     for (i=1;i<=npar;i++) x[i]=0;    strcpy(tmpout,optionfilefiname);
     x[j]=1;    strcat(tmpout,"/");
     lubksb(a,npar,indx,x);    strcat(tmpout,preop);
     for (i=1;i<=npar;i++){    strcat(tmpout,fileres);
       matcov[i][j]=x[i];    return tmpout;
     }  }
   }  
   /*************** function subdirf3 ***********/
   printf("\n#Hessian matrix#\n");  char *subdirf3(char fileres[], char *preop, char *preop2)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++) {    
       printf("%.3e ",hess[i][j]);    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     printf("\n");    strcat(tmpout,"/");
   }    strcat(tmpout,preop);
     strcat(tmpout,preop2);
   /* Recompute Inverse */    strcat(tmpout,fileres);
   for (i=1;i<=npar;i++)    return tmpout;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /***************** f1dim *************************/
   /*  printf("\n#Hessian matrix recomputed#\n");  extern int ncom; 
   extern double *pcom,*xicom;
   for (j=1;j<=npar;j++) {  extern double (*nrfunc)(double []); 
     for (i=1;i<=npar;i++) x[i]=0;   
     x[j]=1;  double f1dim(double x) 
     lubksb(a,npar,indx,x);  { 
     for (i=1;i<=npar;i++){    int j; 
       y[i][j]=x[i];    double f;
       printf("%.3e ",y[i][j]);    double *xt; 
     }   
     printf("\n");    xt=vector(1,ncom); 
   }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   */    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
   free_matrix(a,1,npar,1,npar);    return f; 
   free_matrix(y,1,npar,1,npar);  } 
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  /*****************brent *************************/
   free_matrix(hess,1,npar,1,npar);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
     int iter; 
 }    double a,b,d,etemp;
     double fu,fv,fw,fx;
 /*************** hessian matrix ****************/    double ftemp;
 double hessii( double x[], double delta, int theta, double delti[])    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 {    double e=0.0; 
   int i;   
   int l=1, lmax=20;    a=(ax < cx ? ax : cx); 
   double k1,k2;    b=(ax > cx ? ax : cx); 
   double p2[NPARMAX+1];    x=w=v=bx; 
   double res;    fw=fv=fx=(*f)(x); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for (iter=1;iter<=ITMAX;iter++) { 
   double fx;      xm=0.5*(a+b); 
   int k=0,kmax=10;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double l1;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
   fx=func(x);      fprintf(ficlog,".");fflush(ficlog);
   for (i=1;i<=npar;i++) p2[i]=x[i];  #ifdef DEBUG
   for(l=0 ; l <=lmax; l++){      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);
     l1=pow(10,l);      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);
     delts=delt;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(k=1 ; k <kmax; k=k+1){  #endif
       delt = delta*(l1*k);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       p2[theta]=x[theta] +delt;        *xmin=x; 
       k1=func(p2)-fx;        return fx; 
       p2[theta]=x[theta]-delt;      } 
       k2=func(p2)-fx;      ftemp=fu;
       /*res= (k1-2.0*fx+k2)/delt/delt; */      if (fabs(e) > tol1) { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        r=(x-w)*(fx-fv); 
              q=(x-v)*(fx-fw); 
 #ifdef DEBUG        p=(x-v)*q-(x-w)*r; 
       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);        q=2.0*(q-r); 
 #endif        if (q > 0.0) p = -p; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        q=fabs(q); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        etemp=e; 
         k=kmax;        e=d; 
       }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         k=kmax; l=lmax*10.;        else { 
       }          d=p/q; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          u=x+d; 
         delts=delt;          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
     }        } 
   }      } else { 
   delti[theta]=delts;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   return res;      } 
        u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 }      fu=(*f)(u); 
       if (fu <= fx) { 
 double hessij( double x[], double delti[], int thetai,int thetaj)        if (u >= x) a=x; else b=x; 
 {        SHFT(v,w,x,u) 
   int i;          SHFT(fv,fw,fx,fu) 
   int l=1, l1, lmax=20;          } else { 
   double k1,k2,k3,k4,res,fx;            if (u < x) a=u; else b=u; 
   double p2[NPARMAX+1];            if (fu <= fw || w == x) { 
   int k;              v=w; 
               w=u; 
   fx=func(x);              fv=fw; 
   for (k=1; k<=2; k++) {              fw=fu; 
     for (i=1;i<=npar;i++) p2[i]=x[i];            } else if (fu <= fv || v == x || v == w) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;              v=u; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              fv=fu; 
     k1=func(p2)-fx;            } 
            } 
     p2[thetai]=x[thetai]+delti[thetai]/k;    } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    nrerror("Too many iterations in brent"); 
     k2=func(p2)-fx;    *xmin=x; 
      return fx; 
     p2[thetai]=x[thetai]-delti[thetai]/k;  } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  /****************** mnbrak ***********************/
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;              double (*func)(double)) 
     k4=func(p2)-fx;  { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double ulim,u,r,q, dum;
 #ifdef DEBUG    double fu; 
     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);   
 #endif    *fa=(*func)(*ax); 
   }    *fb=(*func)(*bx); 
   return res;    if (*fb > *fa) { 
 }      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
 /************** Inverse of matrix **************/        } 
 void ludcmp(double **a, int n, int *indx, double *d)    *cx=(*bx)+GOLD*(*bx-*ax); 
 {    *fc=(*func)(*cx); 
   int i,imax,j,k;    while (*fb > *fc) { 
   double big,dum,sum,temp;      r=(*bx-*ax)*(*fb-*fc); 
   double *vv;      q=(*bx-*cx)*(*fb-*fa); 
        u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   vv=vector(1,n);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   *d=1.0;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for (i=1;i<=n;i++) {      if ((*bx-u)*(u-*cx) > 0.0) { 
     big=0.0;        fu=(*func)(u); 
     for (j=1;j<=n;j++)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       if ((temp=fabs(a[i][j])) > big) big=temp;        fu=(*func)(u); 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        if (fu < *fc) { 
     vv[i]=1.0/big;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   }            SHFT(*fb,*fc,fu,(*func)(u)) 
   for (j=1;j<=n;j++) {            } 
     for (i=1;i<j;i++) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       sum=a[i][j];        u=ulim; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        fu=(*func)(u); 
       a[i][j]=sum;      } else { 
     }        u=(*cx)+GOLD*(*cx-*bx); 
     big=0.0;        fu=(*func)(u); 
     for (i=j;i<=n;i++) {      } 
       sum=a[i][j];      SHFT(*ax,*bx,*cx,u) 
       for (k=1;k<j;k++)        SHFT(*fa,*fb,*fc,fu) 
         sum -= a[i][k]*a[k][j];        } 
       a[i][j]=sum;  } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  /*************** linmin ************************/
         imax=i;  
       }  int ncom; 
     }  double *pcom,*xicom;
     if (j != imax) {  double (*nrfunc)(double []); 
       for (k=1;k<=n;k++) {   
         dum=a[imax][k];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         a[imax][k]=a[j][k];  { 
         a[j][k]=dum;    double brent(double ax, double bx, double cx, 
       }                 double (*f)(double), double tol, double *xmin); 
       *d = -(*d);    double f1dim(double x); 
       vv[imax]=vv[j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     }                double *fc, double (*func)(double)); 
     indx[j]=imax;    int j; 
     if (a[j][j] == 0.0) a[j][j]=TINY;    double xx,xmin,bx,ax; 
     if (j != n) {    double fx,fb,fa;
       dum=1.0/(a[j][j]);   
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    ncom=n; 
     }    pcom=vector(1,n); 
   }    xicom=vector(1,n); 
   free_vector(vv,1,n);  /* Doesn't work */    nrfunc=func; 
 ;    for (j=1;j<=n;j++) { 
 }      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
 void lubksb(double **a, int n, int *indx, double b[])    } 
 {    ax=0.0; 
   int i,ii=0,ip,j;    xx=1.0; 
   double sum;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (i=1;i<=n;i++) {  #ifdef DEBUG
     ip=indx[i];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     sum=b[ip];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     b[ip]=b[i];  #endif
     if (ii)    for (j=1;j<=n;j++) { 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      xi[j] *= xmin; 
     else if (sum) ii=i;      p[j] += xi[j]; 
     b[i]=sum;    } 
   }    free_vector(xicom,1,n); 
   for (i=n;i>=1;i--) {    free_vector(pcom,1,n); 
     sum=b[i];  } 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  char *asc_diff_time(long time_sec, char ascdiff[])
   }  {
 }    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
 /************ Frequencies ********************/    sec_left = (time_sec) % (60*60*24);
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    hours = (sec_left) / (60*60) ;
 {  /* Some frequencies */    sec_left = (sec_left) %(60*60);
      minutes = (sec_left) /60;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    sec_left = (sec_left) % (60);
   double ***freq; /* Frequencies */    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   double *pp;    return ascdiff;
   double pos, k2, dateintsum=0,k2cpt=0;  }
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  /*************** powell ************************/
    void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   pp=vector(1,nlstate);              double (*func)(double [])) 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  { 
   strcpy(fileresp,"p");    void linmin(double p[], double xi[], int n, double *fret, 
   strcat(fileresp,fileres);                double (*func)(double [])); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    int i,ibig,j; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double del,t,*pt,*ptt,*xit;
     exit(0);    double fp,fptt;
   }    double *xits;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int niterf, itmp;
   j1=0;  
      pt=vector(1,n); 
   j=cptcoveff;    ptt=vector(1,n); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    xit=vector(1,n); 
      xits=vector(1,n); 
   for(k1=1; k1<=j;k1++){    *fret=(*func)(p); 
     for(i1=1; i1<=ncodemax[k1];i1++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       j1++;    for (*iter=1;;++(*iter)) { 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      fp=(*fret); 
         scanf("%d", i);*/      ibig=0; 
       for (i=-1; i<=nlstate+ndeath; i++)        del=0.0; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        last_time=curr_time;
           for(m=agemin; m <= agemax+3; m++)      (void) gettimeofday(&curr_time,&tzp);
             freq[i][jk][m]=0;      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);
            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);
       dateintsum=0;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       k2cpt=0;     for (i=1;i<=n;i++) {
       for (i=1; i<=imx; i++) {        printf(" %d %.12f",i, p[i]);
         bool=1;        fprintf(ficlog," %d %.12lf",i, p[i]);
         if  (cptcovn>0) {        fprintf(ficrespow," %.12lf", p[i]);
           for (z1=1; z1<=cptcoveff; z1++)      }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      printf("\n");
               bool=0;      fprintf(ficlog,"\n");
         }      fprintf(ficrespow,"\n");fflush(ficrespow);
         if (bool==1) {      if(*iter <=3){
           for(m=firstpass; m<=lastpass; m++){        tm = *localtime(&curr_time.tv_sec);
             k2=anint[m][i]+(mint[m][i]/12.);        strcpy(strcurr,asctime(&tm));
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  /*       asctime_r(&tm,strcurr); */
               if(agev[m][i]==0) agev[m][i]=agemax+1;        forecast_time=curr_time; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        itmp = strlen(strcurr);
               if (m<lastpass) {        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          strcurr[itmp-1]='\0';
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
               }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                      for(niterf=10;niterf<=30;niterf+=10){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                 dateintsum=dateintsum+k2;          tmf = *localtime(&forecast_time.tv_sec);
                 k2cpt++;  /*      asctime_r(&tmf,strfor); */
               }          strcpy(strfor,asctime(&tmf));
             }          itmp = strlen(strfor);
           }          if(strfor[itmp-1]=='\n')
         }          strfor[itmp-1]='\0';
       }          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);
                  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);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
       }
       if  (cptcovn>0) {      for (i=1;i<=n;i++) { 
         fprintf(ficresp, "\n#********** Variable ");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        fptt=(*fret); 
         fprintf(ficresp, "**********\n#");  #ifdef DEBUG
       }        printf("fret=%lf \n",*fret);
       for(i=1; i<=nlstate;i++)        fprintf(ficlog,"fret=%lf \n",*fret);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  #endif
       fprintf(ficresp, "\n");        printf("%d",i);fflush(stdout);
              fprintf(ficlog,"%d",i);fflush(ficlog);
       for(i=(int)agemin; i <= (int)agemax+3; i++){        linmin(p,xit,n,fret,func); 
         if(i==(int)agemax+3)        if (fabs(fptt-(*fret)) > del) { 
           printf("Total");          del=fabs(fptt-(*fret)); 
         else          ibig=i; 
           printf("Age %d", i);        } 
         for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUG
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        printf("%d %.12e",i,(*fret));
             pp[jk] += freq[jk][m][i];        fprintf(ficlog,"%d %.12e",i,(*fret));
         }        for (j=1;j<=n;j++) {
         for(jk=1; jk <=nlstate ; jk++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           for(m=-1, pos=0; m <=0 ; m++)          printf(" x(%d)=%.12e",j,xit[j]);
             pos += freq[jk][m][i];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
           if(pp[jk]>=1.e-10)        }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for(j=1;j<=n;j++) {
           else          printf(" p=%.12e",p[j]);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          fprintf(ficlog," p=%.12e",p[j]);
         }        }
         printf("\n");
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog,"\n");
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  #endif
             pp[jk] += freq[jk][m][i];      } 
         }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
         for(jk=1,pos=0; jk <=nlstate ; jk++)        int k[2],l;
           pos += pp[jk];        k[0]=1;
         for(jk=1; jk <=nlstate ; jk++){        k[1]=-1;
           if(pos>=1.e-5)        printf("Max: %.12e",(*func)(p));
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        fprintf(ficlog,"Max: %.12e",(*func)(p));
           else        for (j=1;j<=n;j++) {
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          printf(" %.12e",p[j]);
           if( i <= (int) agemax){          fprintf(ficlog," %.12e",p[j]);
             if(pos>=1.e-5){        }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        printf("\n");
               probs[i][jk][j1]= pp[jk]/pos;        fprintf(ficlog,"\n");
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        for(l=0;l<=1;l++) {
             }          for (j=1;j<=n;j++) {
             else            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         }          }
                  printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         for(jk=-1; jk <=nlstate+ndeath; jk++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           for(m=-1; m <=nlstate+ndeath; m++)        }
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  #endif
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");  
         printf("\n");        free_vector(xit,1,n); 
       }        free_vector(xits,1,n); 
     }        free_vector(ptt,1,n); 
   }        free_vector(pt,1,n); 
   dateintmean=dateintsum/k2cpt;        return; 
        } 
   fclose(ficresp);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (j=1;j<=n;j++) { 
   free_vector(pp,1,nlstate);        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
   /* End of Freq */        pt[j]=p[j]; 
 }      } 
       fptt=(*func)(ptt); 
 /************ Prevalence ********************/      if (fptt < fp) { 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 {  /* Some frequencies */        if (t < 0.0) { 
            linmin(p,xit,n,fret,func); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          for (j=1;j<=n;j++) { 
   double ***freq; /* Frequencies */            xi[j][ibig]=xi[j][n]; 
   double *pp;            xi[j][n]=xit[j]; 
   double pos, k2;          }
   #ifdef DEBUG
   pp=vector(1,nlstate);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            for(j=1;j<=n;j++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            printf(" %.12e",xit[j]);
   j1=0;            fprintf(ficlog," %.12e",xit[j]);
            }
   j=cptcoveff;          printf("\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          fprintf(ficlog,"\n");
    #endif
   for(k1=1; k1<=j;k1++){        }
     for(i1=1; i1<=ncodemax[k1];i1++){      } 
       j1++;    } 
        } 
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    /**** Prevalence limit (stable or period prevalence)  ****************/
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
        {
       for (i=1; i<=imx; i++) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         bool=1;       matrix by transitions matrix until convergence is reached */
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)    int i, ii,j,k;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double min, max, maxmin, maxmax,sumnew=0.;
               bool=0;    /* double **matprod2(); */ /* test */
         }    double **out, cov[NCOVMAX+1], **pmij();
         if (bool==1) {    double **newm;
           for(m=firstpass; m<=lastpass; m++){    double agefin, delaymax=50 ; /* Max number of years to converge */
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    for (ii=1;ii<=nlstate+ndeath;ii++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for (j=1;j<=nlstate+ndeath;j++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if (m<lastpass) {      }
                 if (calagedate>0)  
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];     cov[1]=1.;
                 else   
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
               }      newm=savm;
             }      /* Covariates have to be included here again */
           }      cov[2]=agefin;
         }      
       }      for (k=1; k<=cptcovn;k++) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for(jk=1; jk <=nlstate ; jk++){        /*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]]);*/
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
             pp[jk] += freq[jk][m][i];      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         }      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
         for(jk=1; jk <=nlstate ; jk++){      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
           for(m=-1, pos=0; m <=0 ; m++)      
             pos += freq[jk][m][i];      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         }      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
              /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         for(jk=1; jk <=nlstate ; jk++){      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
             pp[jk] += freq[jk][m][i];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
         }      
              savm=oldm;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      oldm=newm;
              maxmax=0.;
         for(jk=1; jk <=nlstate ; jk++){          for(j=1;j<=nlstate;j++){
           if( i <= (int) agemax){        min=1.;
             if(pos>=1.e-5){        max=0.;
               probs[i][jk][j1]= pp[jk]/pos;        for(i=1; i<=nlstate; i++) {
             }          sumnew=0;
           }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         }          prlim[i][j]= newm[i][j]/(1-sumnew);
                  /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
       }          max=FMAX(max,prlim[i][j]);
     }          min=FMIN(min,prlim[i][j]);
   }        }
         maxmin=max-min;
          maxmax=FMAX(maxmax,maxmin);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);      if(maxmax < ftolpl){
          return prlim;
 }  /* End of Freq */      }
     }
 /************* Waves Concatenation ***************/  }
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  /*************** transition probabilities ***************/ 
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      Death is a valid wave (if date is known).  {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    /* According to parameters values stored in x and the covariate's values stored in cov,
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]       computes the probability to be observed in state j being in state i by appying the
      and mw[mi+1][i]. dh depends on stepm.       model to the ncovmodel covariates (including constant and age).
      */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   int i, mi, m;       ncth covariate in the global vector x is given by the formula:
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
      double sum=0., jmean=0.;*/       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   int j, k=0,jk, ju, jl;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   double sum=0.;       Outputs ps[i][j] the probability to be observed in j being in j according to
   jmin=1e+5;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   jmax=-1;    */
   jmean=0.;    double s1, lnpijopii;
   for(i=1; i<=imx; i++){    /*double t34;*/
     mi=0;    int i,j,j1, nc, ii, jj;
     m=firstpass;  
     while(s[m][i] <= nlstate){      for(i=1; i<= nlstate; i++){
       if(s[m][i]>=1)        for(j=1; j<i;j++){
         mw[++mi][i]=m;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       if(m >=lastpass)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         break;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       else  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         m++;          }
     }/* end while */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     if (s[m][i] > nlstate){  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       mi++;     /* Death is another wave */        }
       /* if(mi==0)  never been interviewed correctly before death */        for(j=i+1; j<=nlstate+ndeath;j++){
          /* Only death is a correct wave */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       mw[mi][i]=m;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     wav[i]=mi;          }
     if(mi==0)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        }
   }      }
       
   for(i=1; i<=imx; i++){      for(i=1; i<= nlstate; i++){
     for(mi=1; mi<wav[i];mi++){        s1=0;
       if (stepm <=0)        for(j=1; j<i; j++){
         dh[mi][i]=1;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       else{          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         if (s[mw[mi+1][i]][i] > nlstate) {        }
           if (agedc[i] < 2*AGESUP) {        for(j=i+1; j<=nlstate+ndeath; j++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           if(j==0) j=1;  /* Survives at least one month after exam */          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           k=k+1;        }
           if (j >= jmax) jmax=j;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           if (j <= jmin) jmin=j;        ps[i][i]=1./(s1+1.);
           sum=sum+j;        /* Computing other pijs */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(j=1; j<i; j++)
           }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         }        for(j=i+1; j<=nlstate+ndeath; j++)
         else{          ps[i][j]= exp(ps[i][j])*ps[i][i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           k=k+1;      } /* end i */
           if (j >= jmax) jmax=j;      
           else if (j <= jmin)jmin=j;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        for(jj=1; jj<= nlstate+ndeath; jj++){
           sum=sum+j;          ps[ii][jj]=0;
         }          ps[ii][ii]=1;
         jk= j/stepm;        }
         jl= j -jk*stepm;      }
         ju= j -(jk+1)*stepm;      
         if(jl <= -ju)      
           dh[mi][i]=jk;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         else      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           dh[mi][i]=jk+1;      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         if(dh[mi][i]==0)      /*   } */
           dh[mi][i]=1; /* At least one step */      /*   printf("\n "); */
       }      /* } */
     }      /* printf("\n ");printf("%lf ",cov[2]);*/
   }      /*
   jmean=sum/k;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        goto end;*/
  }      return ps;
 /*********** Tricode ****************************/  }
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  /**************** Product of 2 matrices ******************/
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   cptcoveff=0;  {
      /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   for (k=0; k<19; k++) Ndum[k]=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   for (k=1; k<=7; k++) ncodemax[k]=0;    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {       a pointer to pointers identical to out */
     for (i=1; i<=imx; i++) {    int i, j, k;
       ij=(int)(covar[Tvar[j]][i]);    for(i=nrl; i<= nrh; i++)
       Ndum[ij]++;      for(k=ncolol; k<=ncoloh; k++){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        out[i][k]=0.;
       if (ij > cptcode) cptcode=ij;        for(j=ncl; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
       }
     for (i=0; i<=cptcode; i++) {    return out;
       if(Ndum[i]!=0) ncodemax[j]++;  }
     }  
     ij=1;  
   /************* Higher Matrix Product ***************/
   
     for (i=1; i<=ncodemax[j]; i++) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       for (k=0; k<=19; k++) {  {
         if (Ndum[k] != 0) {    /* Computes the transition matrix starting at age 'age' over 
           nbcode[Tvar[j]][ij]=k;       'nhstepm*hstepm*stepm' months (i.e. until
                 age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           ij++;       nhstepm*hstepm matrices. 
         }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         if (ij > ncodemax[j]) break;       (typically every 2 years instead of every month which is too big 
       }         for the memory).
     }       Model is determined by parameters x and covariates have to be 
   }         included manually here. 
   
  for (k=0; k<19; k++) Ndum[k]=0;       */
   
  for (i=1; i<=ncovmodel-2; i++) {    int i, j, d, h, k;
       ij=Tvar[i];    double **out, cov[NCOVMAX+1];
       Ndum[ij]++;    double **newm;
     }  
     /* Hstepm could be zero and should return the unit matrix */
  ij=1;    for (i=1;i<=nlstate+ndeath;i++)
  for (i=1; i<=10; i++) {      for (j=1;j<=nlstate+ndeath;j++){
    if((Ndum[i]!=0) && (i<=ncovcol)){        oldm[i][j]=(i==j ? 1.0 : 0.0);
      Tvaraff[ij]=i;        po[i][j][0]=(i==j ? 1.0 : 0.0);
      ij++;      }
    }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  }    for(h=1; h <=nhstepm; h++){
        for(d=1; d <=hstepm; d++){
     cptcoveff=ij-1;        newm=savm;
 }        /* Covariates have to be included here again */
         cov[1]=1.;
 /*********** Health Expectancies ****************/        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* Health expectancies */        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double age, agelim, hf;  
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double *xp;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double **gp, **gm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double ***gradg, ***trgradg;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int theta;        savm=oldm;
         oldm=newm;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);      }
   xp=vector(1,npar);      for(i=1; i<=nlstate+ndeath; i++)
   dnewm=matrix(1,nlstate*2,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   doldm=matrix(1,nlstate*2,1,nlstate*2);          po[i][j][h]=newm[i][j];
            /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   fprintf(ficreseij,"# Health expectancies\n");        }
   fprintf(ficreseij,"# Age");      /*printf("h=%d ",h);*/
   for(i=1; i<=nlstate;i++)    } /* end h */
     for(j=1; j<=nlstate;j++)  /*     printf("\n H=%d \n",h); */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    return po;
   fprintf(ficreseij,"\n");  }
   
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  /*************** log-likelihood *************/
   }  double func( double *x)
   else  hstepm=estepm;    {
   /* We compute the life expectancy from trapezoids spaced every estepm months    int i, ii, j, k, mi, d, kk;
    * This is mainly to measure the difference between two models: for example    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    * if stepm=24 months pijx are given only every 2 years and by summing them    double **out;
    * we are calculating an estimate of the Life Expectancy assuming a linear    double sw; /* Sum of weights */
    * progression inbetween and thus overestimating or underestimating according    double lli; /* Individual log likelihood */
    * to the curvature of the survival function. If, for the same date, we    int s1, s2;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    double bbh, survp;
    * to compare the new estimate of Life expectancy with the same linear    long ipmx;
    * hypothesis. A more precise result, taking into account a more precise    /*extern weight */
    * curvature will be obtained if estepm is as small as stepm. */    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /* For example we decided to compute the life expectancy with the smallest unit */    /*for(i=1;i<imx;i++) 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      printf(" %d\n",s[4][i]);
      nhstepm is the number of hstepm from age to agelim    */
      nstepm is the number of stepm from age to agelin.    cov[1]=1.;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  
      survival function given by stepm (the optimization length). Unfortunately it    if(mle==1){
      means that if the survival funtion is printed only each two years of age and if      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        /* Computes the values of the ncovmodel covariates of the model
      results. So we changed our mind and took the option of the best precision.           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */           to be observed in j being in i according to the model.
          */
   agelim=AGESUP;        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          cov[2+k]=covar[Tvar[k]][i];
     /* nhstepm age range expressed in number of stepm */        }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     /* if (stepm >= YEARM) hstepm=1;*/           has been calculated etc */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        for(mi=1; mi<= wav[i]-1; mi++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (ii=1;ii<=nlstate+ndeath;ii++)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            for (j=1;j<=nlstate+ndeath;j++){
     gp=matrix(0,nhstepm,1,nlstate*2);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     gm=matrix(0,nhstepm,1,nlstate*2);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          for(d=0; d<dh[mi][i]; d++){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            newm=savm;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* Computing Variances of health expectancies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
      for(theta=1; theta <=npar; theta++){            oldm=newm;
       for(i=1; i<=npar; i++){          } /* end mult */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        
       }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            /* But now since version 0.9 we anticipate for bias at large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
       cptj=0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for(j=1; j<= nlstate; j++){           * the nearest (and in case of equal distance, to the lowest) interval but now
         for(i=1; i<=nlstate; i++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           cptj=cptj+1;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){           * probability in order to take into account the bias as a fraction of the way
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           }           * -stepm/2 to stepm/2 .
         }           * For stepm=1 the results are the same as for previous versions of Imach.
       }           * For stepm > 1 the results are less biased than in previous versions. 
                 */
                s1=s[mw[mi][i]][i];
       for(i=1; i<=npar; i++)          s2=s[mw[mi+1][i]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          bbh=(double)bh[mi][i]/(double)stepm; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            /* bias bh is positive if real duration
                 * is higher than the multiple of stepm and negative otherwise.
       cptj=0;           */
       for(j=1; j<= nlstate; j++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         for(i=1;i<=nlstate;i++){          if( s2 > nlstate){ 
           cptj=cptj+1;            /* i.e. if s2 is a death state and if the date of death is known 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){               then the contribution to the likelihood is the probability to 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;               die between last step unit time and current  step unit time, 
           }               which is also equal to probability to die before dh 
         }               minus probability to die before dh-stepm . 
       }               In version up to 0.92 likelihood was computed
       for(j=1; j<= nlstate*2; j++)          as if date of death was unknown. Death was treated as any other
         for(h=0; h<=nhstepm-1; h++){          health state: the date of the interview describes the actual state
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          and not the date of a change in health state. The former idea was
         }          to consider that at each interview the state was recorded
      }          (healthy, disable or death) and IMaCh was corrected; but when we
              introduced the exact date of death then we should have modified
 /* End theta */          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
      for(h=0; h<=nhstepm-1; h++)          interview up to one month before death multiplied by the
       for(j=1; j<=nlstate*2;j++)          probability to die within a month. Thanks to Chris
         for(theta=1; theta <=npar; theta++)          Jackson for correcting this bug.  Former versions increased
           trgradg[h][j][theta]=gradg[h][theta][j];          mortality artificially. The bad side is that we add another loop
                which slows down the processing. The difference can be up to 10%
           lower mortality.
      for(i=1;i<=nlstate*2;i++)            */
       for(j=1;j<=nlstate*2;j++)            lli=log(out[s1][s2] - savm[s1][s2]);
         varhe[i][j][(int)age] =0.;  
   
      printf("%d|",(int)age);fflush(stdout);          } else if  (s2==-2) {
      for(h=0;h<=nhstepm-1;h++){            for (j=1,survp=0. ; j<=nlstate; j++) 
       for(k=0;k<=nhstepm-1;k++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);            /*survp += out[s1][j]; */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            lli= log(survp);
         for(i=1;i<=nlstate*2;i++)          }
           for(j=1;j<=nlstate*2;j++)          
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          else if  (s2==-4) { 
       }            for (j=3,survp=0. ; j<=nlstate; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     /* Computing expectancies */            lli= log(survp); 
     for(i=1; i<=nlstate;i++)          } 
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          else if  (s2==-5) { 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            for (j=1,survp=0. ; j<=2; j++)  
                        survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /* 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]);*/            lli= log(survp); 
           } 
         }          
           else{
     fprintf(ficreseij,"%3.0f",age );            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     cptj=0;            /*  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 */
     for(i=1; i<=nlstate;i++)          } 
       for(j=1; j<=nlstate;j++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         cptj++;          /*if(lli ==000.0)*/
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          /*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); */
       }          ipmx +=1;
     fprintf(ficreseij,"\n");          sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_matrix(gm,0,nhstepm,1,nlstate*2);        } /* end of wave */
     free_matrix(gp,0,nhstepm,1,nlstate*2);      } /* end of individual */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    }  else if(mle==2){
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   printf("\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   free_vector(xp,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(dnewm,1,nlstate*2,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);            }
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          for(d=0; d<=dh[mi][i]; d++){
 }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /************ Variance ******************/            for (kk=1; kk<=cptcovage;kk++) {
 void varevsij(char fileres[], 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)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   /* Variance of health expectancies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **newm;            savm=oldm;
   double **dnewm,**doldm;            oldm=newm;
   int i, j, nhstepm, hstepm, h, nstepm ;          } /* end mult */
   int k, cptcode;        
   double *xp;          s1=s[mw[mi][i]][i];
   double **gp, **gm;          s2=s[mw[mi+1][i]][i];
   double ***gradg, ***trgradg;          bbh=(double)bh[mi][i]/(double)stepm; 
   double ***p3mat;          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 */
   double age,agelim, hf;          ipmx +=1;
   int theta;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");        } /* end of wave */
   fprintf(ficresvij,"# Age");      } /* end of individual */
   for(i=1; i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
     for(j=1; j<=nlstate;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficresvij,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   xp=vector(1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   dnewm=matrix(1,nlstate,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   if(estepm < stepm){          for(d=0; d<dh[mi][i]; d++){
     printf ("Problem %d lower than %d\n",estepm, stepm);            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   else  hstepm=estepm;              for (kk=1; kk<=cptcovage;kk++) {
   /* For example we decided to compute the life expectancy with the smallest unit */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            }
      nhstepm is the number of hstepm from age to agelim            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      nstepm is the number of stepm from age to agelin.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      Look at hpijx to understand the reason of that which relies in memory size            savm=oldm;
      and note for a fixed period like k years */            oldm=newm;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          } /* end mult */
      survival function given by stepm (the optimization length). Unfortunately it        
      means that if the survival funtion is printed only each two years of age and if          s1=s[mw[mi][i]][i];
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          s2=s[mw[mi+1][i]][i];
      results. So we changed our mind and took the option of the best precision.          bbh=(double)bh[mi][i]/(double)stepm; 
   */          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 */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          ipmx +=1;
   agelim = AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /* end of wave */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      } /* end of individual */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gp=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gm=matrix(0,nhstepm,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){ /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (popbased==1) {            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<= nlstate; j++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(h=0; h<=nhstepm; h++){            savm=oldm;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            oldm=newm;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          } /* end mult */
         }        
       }          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */          if( s2 > nlstate){ 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            lli=log(out[s1][s2] - savm[s1][s2]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }else{
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
       if (popbased==1) {          ipmx +=1;
         for(i=1; i<=nlstate;i++)          sw += weight[i];
           prlim[i][i]=probs[(int)age][i][ij];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }  /*      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]); */
         } /* end of wave */
       for(j=1; j<= nlstate; j++){      } /* end of individual */
         for(h=0; h<=nhstepm; h++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<= nlstate; j++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(h=0; h<=nhstepm; h++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            }
         }          for(d=0; d<dh[mi][i]; d++){
     } /* End theta */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(h=0; h<=nhstepm; h++)            }
       for(j=1; j<=nlstate;j++)          
         for(theta=1; theta <=npar; theta++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           trgradg[h][j][theta]=gradg[h][theta][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            oldm=newm;
     for(i=1;i<=nlstate;i++)          } /* end mult */
       for(j=1;j<=nlstate;j++)        
         vareij[i][j][(int)age] =0.;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     for(h=0;h<=nhstepm;h++){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(k=0;k<=nhstepm;k++){          ipmx +=1;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          sw += weight[i];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1;i<=nlstate;i++)          /*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]);*/
           for(j=1;j<=nlstate;j++)        } /* end of wave */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      } /* end of individual */
       }    } /* End of if */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     fprintf(ficresvij,"%.0f ",age );    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(i=1; i<=nlstate;i++)    return -l;
       for(j=1; j<=nlstate;j++){  }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  
       }  /*************** log-likelihood *************/
     fprintf(ficresvij,"\n");  double funcone( double *x)
     free_matrix(gp,0,nhstepm,1,nlstate);  {
     free_matrix(gm,0,nhstepm,1,nlstate);    /* Same as likeli but slower because of a lot of printf and if */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    int i, ii, j, k, mi, d, kk;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **out;
   } /* End age */    double lli; /* Individual log likelihood */
      double llt;
   free_vector(xp,1,npar);    int s1, s2;
   free_matrix(doldm,1,nlstate,1,npar);    double bbh, survp;
   free_matrix(dnewm,1,nlstate,1,nlstate);    /*extern weight */
     /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 /************ Variance of prevlim ******************/      printf(" %d\n",s[4][i]);
 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)    */
 {    cov[1]=1.;
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double **newm;  
   double **dnewm,**doldm;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j, nhstepm, hstepm;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int k, cptcode;      for(mi=1; mi<= wav[i]-1; mi++){
   double *xp;        for (ii=1;ii<=nlstate+ndeath;ii++)
   double *gp, *gm;          for (j=1;j<=nlstate+ndeath;j++){
   double **gradg, **trgradg;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age,agelim;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int theta;          }
            for(d=0; d<dh[mi][i]; d++){
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          newm=savm;
   fprintf(ficresvpl,"# Age");          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=nlstate;i++)          for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresvpl," %1d-%1d",i,i);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficresvpl,"\n");          }
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   xp=vector(1,npar);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   dnewm=matrix(1,nlstate,1,npar);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   doldm=matrix(1,nlstate,1,nlstate);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
            /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   hstepm=1*YEARM; /* Every year of age */          savm=oldm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          oldm=newm;
   agelim = AGESUP;        } /* end mult */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        s1=s[mw[mi][i]][i];
     if (stepm >= YEARM) hstepm=1;        s2=s[mw[mi+1][i]][i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        bbh=(double)bh[mi][i]/(double)stepm; 
     gradg=matrix(1,npar,1,nlstate);        /* bias is positive if real duration
     gp=vector(1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
     gm=vector(1,nlstate);         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
     for(theta=1; theta <=npar; theta++){          lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=npar; i++){ /* Computes gradient */        } else if  (s2==-2) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (j=1,survp=0. ; j<=nlstate; j++) 
       }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli= log(survp);
       for(i=1;i<=nlstate;i++)        }else if (mle==1){
         gp[i] = prlim[i][i];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            } else if(mle==2){
       for(i=1; i<=npar; i++) /* Computes gradient */          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 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } else if(mle==3){  /* exponential inter-extrapolation */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          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 */
       for(i=1;i<=nlstate;i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         gm[i] = prlim[i][i];          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
       for(i=1;i<=nlstate;i++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          /*lli=log(out[s1][s2]); */ /* Original formula */
     } /* End theta */        } /* End of if */
         ipmx +=1;
     trgradg =matrix(1,nlstate,1,npar);        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(j=1; j<=nlstate;j++)        /*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]); */
       for(theta=1; theta <=npar; theta++)        if(globpr){
         trgradg[j][theta]=gradg[theta][j];          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
     for(i=1;i<=nlstate;i++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       varpl[i][(int)age] =0.;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            llt +=ll[k]*gipmx/gsw;
     for(i=1;i<=nlstate;i++)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          }
           fprintf(ficresilk," %10.6f\n", -llt);
     fprintf(ficresvpl,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)      } /* end of wave */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    } /* end of individual */
     fprintf(ficresvpl,"\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     free_vector(gp,1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     free_vector(gm,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_matrix(gradg,1,npar,1,nlstate);    if(globpr==0){ /* First time we count the contributions and weights */
     free_matrix(trgradg,1,nlstate,1,npar);      gipmx=ipmx;
   } /* End age */      gsw=sw;
     }
   free_vector(xp,1,npar);    return -l;
   free_matrix(doldm,1,nlstate,1,npar);  }
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   
 }  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 /************ Variance of one-step probabilities  ******************/  {
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    /* This routine should help understanding what is done with 
 {       the selection of individuals/waves and
   int i, j=0,  i1, k1, l1, t, tj;       to check the exact contribution to the likelihood.
   int k2, l2, j1,  z1;       Plotting could be done.
   int k=0,l, cptcode;     */
   int first=1;    int k;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;  
   double **dnewm,**doldm;    if(*globpri !=0){ /* Just counts and sums, no printings */
   double *xp;      strcpy(fileresilk,"ilk"); 
   double *gp, *gm;      strcat(fileresilk,fileres);
   double **gradg, **trgradg;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double **mu;        printf("Problem with resultfile: %s\n", fileresilk);
   double age,agelim, cov[NCOVMAX];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      }
   int theta;      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");
   char fileresprob[FILENAMELENGTH];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   char fileresprobcov[FILENAMELENGTH];      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   char fileresprobcor[FILENAMELENGTH];      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   double ***varpij;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);    *fretone=(*funcone)(p);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    if(*globpri !=0){
     printf("Problem with resultfile: %s\n", fileresprob);      fclose(ficresilk);
   }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   strcpy(fileresprobcov,"probcov");      fflush(fichtm); 
   strcat(fileresprobcov,fileres);    } 
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    return;
     printf("Problem with resultfile: %s\n", fileresprobcov);  }
   }  
   strcpy(fileresprobcor,"probcor");  
   strcat(fileresprobcor,fileres);  /*********** Maximum Likelihood Estimation ***************/
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcor);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    int i,j, iter;
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    double **xi;
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    double fret;
      double fretone; /* Only one call to likelihood */
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    /*  char filerespow[FILENAMELENGTH];*/
   fprintf(ficresprob,"# Age");    xi=matrix(1,npar,1,npar);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    for (i=1;i<=npar;i++)
   fprintf(ficresprobcov,"# Age");      for (j=1;j<=npar;j++)
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
   fprintf(ficresprobcov,"# Age");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
   for(i=1; i<=nlstate;i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(j=1; j<=(nlstate+ndeath);j++){      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    }
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     }      for (i=1;i<=nlstate;i++)
   fprintf(ficresprob,"\n");      for(j=1;j<=nlstate+ndeath;j++)
   fprintf(ficresprobcov,"\n");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficresprobcor,"\n");    fprintf(ficrespow,"\n");
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    powell(p,xi,npar,ftol,&iter,&fret,func);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    free_matrix(xi,1,npar,1,npar);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    fclose(ficrespow);
   first=1;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     exit(0);  
   }  }
   else{  
     fprintf(ficgp,"\n# Routine varprob");  /**** Computes Hessian and covariance matrix ***/
   }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  {
     printf("Problem with html file: %s\n", optionfilehtm);    double  **a,**y,*x,pd;
     exit(0);    double **hess;
   }    int i, j,jk;
   else{    int *indx;
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");  
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
   }    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
      hess=matrix(1,npar,1,npar);
   cov[1]=1;  
   tj=cptcoveff;    printf("\nCalculation of the hessian matrix. Wait...\n");
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   j1=0;    for (i=1;i<=npar;i++){
   for(t=1; t<=tj;t++){      printf("%d",i);fflush(stdout);
     for(i1=1; i1<=ncodemax[t];i1++){      fprintf(ficlog,"%d",i);fflush(ficlog);
       j1++;     
             hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       if  (cptcovn>0) {      
         fprintf(ficresprob, "\n#********** Variable ");      /*  printf(" %f ",p[i]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         fprintf(ficresprob, "**********\n#");    }
         fprintf(ficresprobcov, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (i=1;i<=npar;i++) {
         fprintf(ficresprobcov, "**********\n#");      for (j=1;j<=npar;j++)  {
                if (j>i) { 
         fprintf(ficgp, "\n#********** Variable ");          printf(".%d%d",i,j);fflush(stdout);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         fprintf(ficgp, "**********\n#");          hess[i][j]=hessij(p,delti,i,j,func,npar);
                  
                  hess[j][i]=hess[i][j];    
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          /*printf(" %lf ",hess[i][j]);*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");      }
            }
         fprintf(ficresprobcor, "\n#********** Variable ");        printf("\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\n");
         fprintf(ficgp, "**********\n#");      
       }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
          fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for (age=bage; age<=fage; age ++){    
         cov[2]=age;    a=matrix(1,npar,1,npar);
         for (k=1; k<=cptcovn;k++) {    y=matrix(1,npar,1,npar);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    x=vector(1,npar);
         }    indx=ivector(1,npar);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for (i=1;i<=npar;i++)
         for (k=1; k<=cptcovprod;k++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    ludcmp(a,npar,indx,&pd);
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    for (j=1;j<=npar;j++) {
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      for (i=1;i<=npar;i++) x[i]=0;
         gp=vector(1,(nlstate)*(nlstate+ndeath));      x[j]=1;
         gm=vector(1,(nlstate)*(nlstate+ndeath));      lubksb(a,npar,indx,x);
          for (i=1;i<=npar;i++){ 
         for(theta=1; theta <=npar; theta++){        matcov[i][j]=x[i];
           for(i=1; i<=npar; i++)      }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("\n#Hessian matrix#\n");
              fprintf(ficlog,"\n#Hessian matrix#\n");
           k=0;    for (i=1;i<=npar;i++) { 
           for(i=1; i<= (nlstate); i++){      for (j=1;j<=npar;j++) { 
             for(j=1; j<=(nlstate+ndeath);j++){        printf("%.3e ",hess[i][j]);
               k=k+1;        fprintf(ficlog,"%.3e ",hess[i][j]);
               gp[k]=pmmij[i][j];      }
             }      printf("\n");
           }      fprintf(ficlog,"\n");
              }
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* Recompute Inverse */
        for (i=1;i<=npar;i++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           k=0;    ludcmp(a,npar,indx,&pd);
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){    /*  printf("\n#Hessian matrix recomputed#\n");
               k=k+1;  
               gm[k]=pmmij[i][j];    for (j=1;j<=npar;j++) {
             }      for (i=1;i<=npar;i++) x[i]=0;
           }      x[j]=1;
            lubksb(a,npar,indx,x);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      for (i=1;i<=npar;i++){ 
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          y[i][j]=x[i];
         }        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      }
           for(theta=1; theta <=npar; theta++)      printf("\n");
             trgradg[j][theta]=gradg[theta][j];      fprintf(ficlog,"\n");
            }
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    */
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
            free_matrix(a,1,npar,1,npar);
         pmij(pmmij,cov,ncovmodel,x,nlstate);    free_matrix(y,1,npar,1,npar);
            free_vector(x,1,npar);
         k=0;    free_ivector(indx,1,npar);
         for(i=1; i<=(nlstate); i++){    free_matrix(hess,1,npar,1,npar);
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;  
             mu[k][(int) age]=pmmij[i][j];  }
           }  
         }  /*************** hessian matrix ****************/
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  {
             varpij[i][j][(int)age] = doldm[i][j];    int i;
     int l=1, lmax=20;
         /*printf("\n%d ",(int)age);    double k1,k2;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    double p2[MAXPARM+1]; /* identical to x */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double res;
      }*/    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
         fprintf(ficresprob,"\n%d ",(int)age);    int k=0,kmax=10;
         fprintf(ficresprobcov,"\n%d ",(int)age);    double l1;
         fprintf(ficresprobcor,"\n%d ",(int)age);  
     fx=func(x);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      l1=pow(10,l);
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      delts=delt;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      for(k=1 ; k <kmax; k=k+1){
         }        delt = delta*(l1*k);
         i=0;        p2[theta]=x[theta] +delt;
         for (k=1; k<=(nlstate);k++){        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
           for (l=1; l<=(nlstate+ndeath);l++){        p2[theta]=x[theta]-delt;
             i=i++;        k2=func(p2)-fx;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        /*res= (k1-2.0*fx+k2)/delt/delt; */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             for (j=1; j<=i;j++){        
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);  #ifdef DEBUGHESS
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        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);
             }        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);
           }  #endif
         }/* end of loop for state */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       } /* end of loop for age */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          k=kmax;
       for (k1=1; k1<=(nlstate);k1++){        }
         for (l1=1; l1<=(nlstate+ndeath);l1++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           if(l1==k1) continue;          k=kmax; l=lmax*10.;
           i=(k1-1)*(nlstate+ndeath)+l1;        }
           for (k2=1; k2<=(nlstate);k2++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             for (l2=1; l2<=(nlstate+ndeath);l2++){          delts=delt;
               if(l2==k2) continue;        }
               j=(k2-1)*(nlstate+ndeath)+l2;      }
               if(j<=i) continue;    }
               for (age=bage; age<=fage; age ++){    delti[theta]=delts;
                 if ((int)age %5==0){    return res; 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  }
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   mu1=mu[i][(int) age]/stepm*YEARM ;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
                   mu2=mu[j][(int) age]/stepm*YEARM;  {
                   /* Computing eigen value of matrix of covariance */    int i;
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    int l=1, l1, lmax=20;
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    double k1,k2,k3,k4,res,fx;
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    double p2[MAXPARM+1];
                   /* Eigen vectors */    int k;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  
                   v21=sqrt(1.-v11*v11);    fx=func(x);
                   v12=-v21;    for (k=1; k<=2; k++) {
                   v22=v11;      for (i=1;i<=npar;i++) p2[i]=x[i];
                   /*printf(fignu*/      p2[thetai]=x[thetai]+delti[thetai]/k;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */      k1=func(p2)-fx;
                   if(first==1){    
                     first=0;      p2[thetai]=x[thetai]+delti[thetai]/k;
                     fprintf(ficgp,"\nset parametric;set nolabel");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);      k2=func(p2)-fx;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);      p2[thetai]=x[thetai]-delti[thetai]/k;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);      k3=func(p2)-fx;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      p2[thetai]=x[thetai]-delti[thetai]/k;
                     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)) t \"%d\"",\      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      k4=func(p2)-fx;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                   }else{  #ifdef DEBUG
                     first=0;      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);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      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);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  #endif
                     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)) t \"%d\"",\    }
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    return res;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  }
                   }/* if first */  
                 } /* age mod 5 */  /************** Inverse of matrix **************/
               } /* end loop age */  void ludcmp(double **a, int n, int *indx, double *d) 
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);  { 
               first=1;    int i,imax,j,k; 
             } /*l12 */    double big,dum,sum,temp; 
           } /* k12 */    double *vv; 
         } /*l1 */   
       }/* k1 */    vv=vector(1,n); 
     } /* loop covariates */    *d=1.0; 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    for (i=1;i<=n;i++) { 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      big=0.0; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=n;j++) 
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      vv[i]=1.0/big; 
   }    } 
   free_vector(xp,1,npar);    for (j=1;j<=n;j++) { 
   fclose(ficresprob);      for (i=1;i<j;i++) { 
   fclose(ficresprobcov);        sum=a[i][j]; 
   fclose(ficresprobcor);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   fclose(ficgp);        a[i][j]=sum; 
   fclose(fichtm);      } 
 }      big=0.0; 
       for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
 /******************* Printing html file ***********/        for (k=1;k<j;k++) 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          sum -= a[i][k]*a[k][j]; 
                   int lastpass, int stepm, int weightopt, char model[],\        a[i][j]=sum; 
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   int popforecast, int estepm ,\          big=dum; 
                   double jprev1, double mprev1,double anprev1, \          imax=i; 
                   double jprev2, double mprev2,double anprev2){        } 
   int jj1, k1, i1, cpt;      } 
   /*char optionfilehtm[FILENAMELENGTH];*/      if (j != imax) { 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {        for (k=1;k<=n;k++) { 
     printf("Problem with %s \n",optionfilehtm), exit(0);          dum=a[imax][k]; 
   }          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n        } 
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n        *d = -(*d); 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        vv[imax]=vv[j]; 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      } 
  - Life expectancies by age and initial health status (estepm=%2d months):      indx[j]=imax; 
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      if (a[j][j] == 0.0) a[j][j]=TINY; 
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      if (j != n) { 
         dum=1.0/(a[j][j]); 
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      } 
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    } 
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    free_vector(vv,1,n);  /* Doesn't work */
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  ;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  } 
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
  if(popforecast==1) fprintf(fichtm,"\n    int i,ii=0,ip,j; 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    double sum; 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n   
         <br>",fileres,fileres,fileres,fileres);    for (i=1;i<=n;i++) { 
  else      ip=indx[i]; 
    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);      sum=b[ip]; 
 fprintf(fichtm," <li><b>Graphs</b></li><p>");      b[ip]=b[i]; 
       if (ii) 
  m=cptcoveff;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      else if (sum) ii=i; 
       b[i]=sum; 
  jj1=0;    } 
  for(k1=1; k1<=m;k1++){    for (i=n;i>=1;i--) { 
    for(i1=1; i1<=ncodemax[k1];i1++){      sum=b[i]; 
      jj1++;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
      if (cptcovn > 0) {      b[i]=sum/a[i][i]; 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    } 
        for (cpt=1; cpt<=cptcoveff;cpt++)  } 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  void pstamp(FILE *fichier)
      }  {
      /* Pij */    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>  }
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      
      /* Quasi-incidences */  /************ Frequencies ********************/
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>  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[])
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  {  /* Some frequencies */
        /* Stable prevalence in each health state */    
        for(cpt=1; cpt<nlstate;cpt++){    int i, m, jk, k1,i1, j1, bool, z1,j;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    int first;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double ***freq; /* Frequencies */
        }    double *pp, **prop;
     for(cpt=1; cpt<=nlstate;cpt++) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    char fileresp[FILENAMELENGTH];
 interval) in state (%d): v%s%d%d.png <br>    
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      pp=vector(1,nlstate);
      }    prop=matrix(1,nlstate,iagemin,iagemax+3);
      for(cpt=1; cpt<=nlstate;cpt++) {    strcpy(fileresp,"p");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    strcat(fileresp,fileres);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if((ficresp=fopen(fileresp,"w"))==NULL) {
      }      printf("Problem with prevalence resultfile: %s\n", fileresp);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 health expectancies in states (1) and (2): e%s%d.png<br>      exit(0);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
    }    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
  }    j1=0;
 fclose(fichtm);    
 }    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    first=1;
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
   int ng;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /*    j1++;
     printf("Problem with file %s",optionfilegnuplot);  */
   }    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 #ifdef windows          scanf("%d", i);*/
     fprintf(ficgp,"cd \"%s\" \n",pathc);        for (i=-5; i<=nlstate+ndeath; i++)  
 #endif          for (jk=-5; jk<=nlstate+ndeath; jk++)  
 m=pow(2,cptcoveff);            for(m=iagemin; m <= iagemax+3; m++)
                freq[i][jk][m]=0;
  /* 1eme*/        
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for (i=1; i<=nlstate; i++)  
    for (k1=1; k1<= m ; k1 ++) {          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
 #ifdef windows        
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        dateintsum=0;
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);        k2cpt=0;
 #endif        for (i=1; i<=imx; i++) {
 #ifdef unix          bool=1;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);            for (z1=1; z1<=cptcoveff; z1++)       
 #endif              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                   /* Tests if the value of each of the covariates of i is equal to filter j1 */
 for (i=1; i<= nlstate ; i ++) {                bool=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                /* 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", 
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
 }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
     for (i=1; i<= nlstate ; i ++) {              } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }          if (bool==1){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            for(m=firstpass; m<=lastpass; m++){
      for (i=1; i<= nlstate ; i ++) {              k2=anint[m][i]+(mint[m][i]/12.);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 #ifdef unix                if (m<lastpass) {
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 #endif                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    }                }
   }                
   /*2 eme*/                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   for (k1=1; k1<= m ; k1 ++) {                  k2cpt++;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);                }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);                /*}*/
                }
     for (i=1; i<= nlstate+1 ; i ++) {          }
       k=2*i;        } /* end i */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);         
       for (j=1; j<= nlstate+1 ; j ++) {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        pstamp(ficresp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        if  (cptcovn>0) {
 }            fprintf(ficresp, "\n#********** Variable "); 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          fprintf(ficresp, "**********\n#");
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficlog, "\n#********** Variable "); 
       for (j=1; j<= nlstate+1 ; j ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficlog, "**********\n#");
         else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }          for(i=1; i<=nlstate;i++) 
       fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresp, "\n");
       for (j=1; j<= nlstate+1 ; j ++) {        
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=iagemin; i <= iagemax+3; i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(i==iagemax+3){
 }              fprintf(ficlog,"Total");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          }else{
       else fprintf(ficgp,"\" t\"\" w l 0,");            if(first==1){
     }              first=0;
   }              printf("See log file for details...\n");
              }
   /*3eme*/            fprintf(ficlog,"Age %d", i);
           }
   for (k1=1; k1<= m ; k1 ++) {          for(jk=1; jk <=nlstate ; jk++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       k=2+nlstate*(2*cpt-2);              pp[jk] += freq[jk][m][i]; 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          }
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          for(jk=1; jk <=nlstate ; jk++){
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            for(m=-1, pos=0; m <=0 ; m++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              pos += freq[jk][m][i];
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            if(pp[jk]>=1.e-10){
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              if(first==1){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 */            }else{
       for (i=1; i< nlstate ; i ++) {              if(first==1)
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
     }          }
   }  
            for(jk=1; jk <=nlstate ; jk++){
   /* CV preval stat */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     for (k1=1; k1<= m ; k1 ++) {              pp[jk] += freq[jk][m][i];
     for (cpt=1; cpt<nlstate ; cpt ++) {          }       
       k=3;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            pos += pp[jk];
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);            posprop += prop[jk][i];
           }
       for (i=1; i< nlstate ; i ++)          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficgp,"+$%d",k+i+1);            if(pos>=1.e-5){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              if(first==1)
                      printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       l=3+(nlstate+ndeath)*cpt;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            }else{
       for (i=1; i< nlstate ; i ++) {              if(first==1)
         l=3+(nlstate+ndeath)*cpt;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficgp,"+$%d",l+i+1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              if( i <= iagemax){
     }              if(pos>=1.e-5){
   }                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  /*probs[i][jk][j1]= pp[jk]/pos;*/
   /* proba elementaires */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
    for(i=1,jk=1; i <=nlstate; i++){              }
     for(k=1; k <=(nlstate+ndeath); k++){              else
       if (k != i) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         for(j=1; j <=ncovmodel; j++){            }
                  }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          
           jk++;          for(jk=-1; jk <=nlstate+ndeath; jk++)
           fprintf(ficgp,"\n");            for(m=-1; m <=nlstate+ndeath; m++)
         }              if(freq[jk][m][i] !=0 ) {
       }              if(first==1)
     }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
    }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/          if(i <= iagemax)
      for(jk=1; jk <=m; jk++) {            fprintf(ficresp,"\n");
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          if(first==1)
        if (ng==2)            printf("Others in log...\n");
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          fprintf(ficlog,"\n");
        else        }
          fprintf(ficgp,"\nset title \"Probability\"\n");        /*}*/
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    }
        i=1;    dateintmean=dateintsum/k2cpt; 
        for(k2=1; k2<=nlstate; k2++) {   
          k3=i;    fclose(ficresp);
          for(k=1; k<=(nlstate+ndeath); k++) {    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
            if (k != k2){    free_vector(pp,1,nlstate);
              if(ng==2)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    /* End of Freq */
              else  }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
              ij=1;  /************ Prevalence ********************/
              for(j=3; j <=ncovmodel; j++) {  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)
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  {  
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                  ij++;       in each health status at the date of interview (if between dateprev1 and dateprev2).
                }       We still use firstpass and lastpass as another selection.
                else    */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   
              }    int i, m, jk, k1, i1, j1, bool, z1,j;
              fprintf(ficgp,")/(1");    double ***freq; /* Frequencies */
                  double *pp, **prop;
              for(k1=1; k1 <=nlstate; k1++){      double pos,posprop; 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double  y2; /* in fractional years */
                ij=1;    int iagemin, iagemax;
                for(j=3; j <=ncovmodel; j++){    int first; /** to stop verbosity which is redirected to log file */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    iagemin= (int) agemin;
                    ij++;    iagemax= (int) agemax;
                  }    /*pp=vector(1,nlstate);*/
                  else    prop=matrix(1,nlstate,iagemin,iagemax+3); 
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                }    j1=0;
                fprintf(ficgp,")");    
              }    /*j=cptcoveff;*/
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    
              i=i+ncovmodel;    first=1;
            }    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
          }      /*for(i1=1; i1<=ncodemax[k1];i1++){
        }        j1++;*/
      }        
    }        for (i=1; i<=nlstate; i++)  
    fclose(ficgp);          for(m=iagemin; m <= iagemax+3; m++)
 }  /* end gnuplot */            prop[i][m]=0.0;
        
         for (i=1; i<=imx; i++) { /* Each individual */
 /*************** Moving average **************/          bool=1;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   int i, cpt, cptcod;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                bool=0;
       for (i=1; i<=nlstate;i++)          } 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          if (bool==1) { 
           mobaverage[(int)agedeb][i][cptcod]=0.;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                  y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for (i=1; i<=nlstate;i++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           for (cpt=0;cpt<=4;cpt++){                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); 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           }                  /*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]]);*/
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
       }                } 
     }              }
                } /* end selection of waves */
 }          }
         }
         for(i=iagemin; i <= iagemax+3; i++){  
 /************** Forecasting ******************/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            posprop += prop[jk][i]; 
            } 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          
   int *popage;          for(jk=1; jk <=nlstate ; jk++){     
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            if( i <=  iagemax){ 
   double *popeffectif,*popcount;              if(posprop>=1.e-5){ 
   double ***p3mat;                probs[i][jk][j1]= prop[jk][i]/posprop;
   char fileresf[FILENAMELENGTH];              } else{
                 if(first==1){
  agelim=AGESUP;                  first=0;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                  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]);
                 }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              }
              } 
            }/* end jk */ 
   strcpy(fileresf,"f");        }/* end i */ 
   strcat(fileresf,fileres);      /*} *//* end i1 */
   if((ficresf=fopen(fileresf,"w"))==NULL) {    } /* end j1 */
     printf("Problem with forecast resultfile: %s\n", fileresf);    
   }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   printf("Computing forecasting: result on file '%s' \n", fileresf);    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  }  /* End of prevalence */
   
   if (mobilav==1) {  /************* Waves Concatenation ***************/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);  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)
   }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   stepsize=(int) (stepm+YEARM-1)/YEARM;       Death is a valid wave (if date is known).
   if (stepm<=12) stepsize=1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   agelim=AGESUP;       and mw[mi+1][i]. dh depends on stepm.
         */
   hstepm=1;  
   hstepm=hstepm/stepm;    int i, mi, m;
   yp1=modf(dateintmean,&yp);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   anprojmean=yp;       double sum=0., jmean=0.;*/
   yp2=modf((yp1*12),&yp);    int first;
   mprojmean=yp;    int j, k=0,jk, ju, jl;
   yp1=modf((yp2*30.5),&yp);    double sum=0.;
   jprojmean=yp;    first=0;
   if(jprojmean==0) jprojmean=1;    jmin=1e+5;
   if(mprojmean==0) jprojmean=1;    jmax=-1;
      jmean=0.;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    for(i=1; i<=imx; i++){
        mi=0;
   for(cptcov=1;cptcov<=i2;cptcov++){      m=firstpass;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      while(s[m][i] <= nlstate){
       k=k+1;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       fprintf(ficresf,"\n#******");          mw[++mi][i]=m;
       for(j=1;j<=cptcoveff;j++) {        if(m >=lastpass)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          break;
       }        else
       fprintf(ficresf,"******\n");          m++;
       fprintf(ficresf,"# StartingAge FinalAge");      }/* end while */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      if (s[m][i] > nlstate){
              mi++;     /* Death is another wave */
              /* if(mi==0)  never been interviewed correctly before death */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           /* Only death is a correct wave */
         fprintf(ficresf,"\n");        mw[mi][i]=m;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        }
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      wav[i]=mi;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      if(mi==0){
           nhstepm = nhstepm/hstepm;        nbwarn++;
                  if(first==0){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           oldm=oldms;savm=savms;          first=1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
                if(first==1){
           for (h=0; h<=nhstepm; h++){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      } /* end mi==0 */
             }    } /* End individuals */
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    for(i=1; i<=imx; i++){
               for(i=1; i<=nlstate;i++) {                    for(mi=1; mi<wav[i];mi++){
                 if (mobilav==1)        if (stepm <=0)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          dh[mi][i]=1;
                 else {        else{
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                 }            if (agedc[i] < 2*AGESUP) {
                              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               }              if(j==0) j=1;  /* Survives at least one month after exam */
               if (h==(int)(calagedate+12*cpt)){              else if(j<0){
                 fprintf(ficresf," %.3f", kk1);                nberr++;
                                        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]);
               }                j=1; /* Temporary Dangerous patch */
             }                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);
           }                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]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                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);
         }              }
       }              k=k+1;
     }              if (j >= jmax){
   }                jmax=j;
                        ijmax=i;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              }
               if (j <= jmin){
   fclose(ficresf);                jmin=j;
 }                ijmin=i;
 /************** Forecasting ******************/              }
 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){              sum=sum+j;
                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   int *popage;            }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }
   double *popeffectif,*popcount;          else{
   double ***p3mat,***tabpop,***tabpopprev;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   char filerespop[FILENAMELENGTH];  /*        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]); */
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            k=k+1;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if (j >= jmax) {
   agelim=AGESUP;              jmax=j;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              ijmax=i;
              }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            else if (j <= jmin){
                jmin=j;
                ijmin=i;
   strcpy(filerespop,"pop");            }
   strcat(filerespop,fileres);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {            /*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]);*/
     printf("Problem with forecast resultfile: %s\n", filerespop);            if(j<0){
   }              nberr++;
   printf("Computing forecasting: result on file '%s' \n", filerespop);              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]);
               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]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            }
             sum=sum+j;
   if (mobilav==1) {          }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          jk= j/stepm;
     movingaverage(agedeb, fage, ageminpar, mobaverage);          jl= j -jk*stepm;
   }          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   stepsize=(int) (stepm+YEARM-1)/YEARM;            if(jl==0){
   if (stepm<=12) stepsize=1;              dh[mi][i]=jk;
                bh[mi][i]=0;
   agelim=AGESUP;            }else{ /* We want a negative bias in order to only have interpolation ie
                      * to avoid the price of an extra matrix product in likelihood */
   hstepm=1;              dh[mi][i]=jk+1;
   hstepm=hstepm/stepm;              bh[mi][i]=ju;
              }
   if (popforecast==1) {          }else{
     if((ficpop=fopen(popfile,"r"))==NULL) {            if(jl <= -ju){
       printf("Problem with population file : %s\n",popfile);exit(0);              dh[mi][i]=jk;
     }              bh[mi][i]=jl;       /* bias is positive if real duration
     popage=ivector(0,AGESUP);                                   * is higher than the multiple of stepm and negative otherwise.
     popeffectif=vector(0,AGESUP);                                   */
     popcount=vector(0,AGESUP);            }
                else{
     i=1;                dh[mi][i]=jk+1;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              bh[mi][i]=ju;
                }
     imx=i;            if(dh[mi][i]==0){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              dh[mi][i]=1; /* At least one step */
   }              bh[mi][i]=ju; /* At least one step */
               /*  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);*/
   for(cptcov=1;cptcov<=i2;cptcov++){            }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          } /* end if mle */
       k=k+1;        }
       fprintf(ficrespop,"\n#******");      } /* end wave */
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    jmean=sum/k;
       }    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);
       fprintf(ficrespop,"******\n");    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);
       fprintf(ficrespop,"# Age");   }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");  /*********** Tricode ****************************/
        void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       for (cpt=0; cpt<=0;cpt++) {  {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /**< Uses cptcovn+2*cptcovprod as the number of covariates */
            /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
           nhstepm = nhstepm/hstepm;    /* nbcode[Tvar[j]][1]= 
              */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int modmaxcovj=0; /* Modality max of covariates j */
            int cptcode=0; /* Modality max of covariates j */
           for (h=0; h<=nhstepm; h++){    int modmincovj=0; /* Modality min of covariates j */
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    cptcoveff=0; 
             for(j=1; j<=nlstate+ndeath;j++) {   
               kk1=0.;kk2=0;    for (k=-1; k < maxncov; k++) Ndum[k]=0;
               for(i=1; i<=nlstate;i++) {                  for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Loop on covariates without age and products */
                 else {    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
                 }                                 modality of this covariate Vj*/ 
               }        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
               if (h==(int)(calagedate+12*cpt)){                                      * If product of Vn*Vm, still boolean *:
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                   /*fprintf(ficrespop," %.3f", kk1);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
               }                                        modality of the nth covariate of individual i. */
             }        if (ij > modmaxcovj)
             for(i=1; i<=nlstate;i++){          modmaxcovj=ij; 
               kk1=0.;        else if (ij < modmincovj) 
                 for(j=1; j<=nlstate;j++){          modmincovj=ij; 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        if ((ij < -1) && (ij > NCOVMAX)){
                 }          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          exit(1);
             }        }else
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           }        /* getting the maximum value of the modality of the covariate
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         }           female is 1, then modmaxcovj=1.*/
       }      }
        printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   /******/      cptcode=modmaxcovj;
       /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {     /*for (i=0; i<=cptcode; i++) {*/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           nhstepm = nhstepm/hstepm;          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
                  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
           oldm=oldms;savm=savms;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        } /* Ndum[-1] number of undefined modalities */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
             }      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
             for(j=1; j<=nlstate+ndeath;j++) {         modmincovj=3; modmaxcovj = 7;
               kk1=0.;kk2=0;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
               for(i=1; i<=nlstate;i++) {                       which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];             variables V1_1 and V1_2.
               }         nbcode[Tvar[j]][ij]=k;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);         nbcode[Tvar[j]][1]=0;
             }         nbcode[Tvar[j]][2]=1;
           }         nbcode[Tvar[j]][3]=2;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      */
         }      ij=1; /* ij is similar to i but can jumps over null modalities */
       }      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
    }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   }          /*recode from 0 */
            if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                        k is a modality. If we have model=V1+V1*sex 
   if (popforecast==1) {                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     free_ivector(popage,0,AGESUP);            ij++;
     free_vector(popeffectif,0,AGESUP);          }
     free_vector(popcount,0,AGESUP);          if (ij > ncodemax[j]) break; 
   }        }  /* end of loop on */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end of loop on modality */ 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   fclose(ficrespop);    
 }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     
 /***********************************************/    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
 /**************** Main Program *****************/     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
 /***********************************************/     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; 
 int main(int argc, char *argv[])   } 
 {  
    ij=1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   double agedeb, agefin,hf;     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;     if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   double fret;       Tvaraff[ij]=i; /*For printing (unclear) */
   double **xi,tmp,delta;       ij++;
      }else
   double dum; /* Dummy variable */         Tvaraff[ij]=0;
   double ***p3mat;   }
   int *indx;   ij--;
   char line[MAXLINE], linepar[MAXLINE];   cptcoveff=ij; /*Number of total covariates*/
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;  }
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  
   int ju,jl, mi;  /*********** Health Expectancies ****************/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  {
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   double bage, fage, age, agelim, agebase;    int nhstepma, nstepma; /* Decreasing with age */
   double ftolpl=FTOL;    double age, agelim, hf;
   double **prlim;    double ***p3mat;
   double *severity;    double eip;
   double ***param; /* Matrix of parameters */  
   double  *p;    pstamp(ficreseij);
   double **matcov; /* Matrix of covariance */    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   double ***delti3; /* Scale */    fprintf(ficreseij,"# Age");
   double *delti; /* Scale */    for(i=1; i<=nlstate;i++){
   double ***eij, ***vareij;      for(j=1; j<=nlstate;j++){
   double **varpl; /* Variances of prevalence limits by age */        fprintf(ficreseij," e%1d%1d ",i,j);
   double *epj, vepp;      }
   double kk1, kk2;      fprintf(ficreseij," e%1d. ",i);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    }
      fprintf(ficreseij,"\n");
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   char z[1]="c", occ;    }
 #include <sys/time.h>    else  hstepm=estepm;   
 #include <time.h>    /* We compute the life expectancy from trapezoids spaced every estepm months
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];     * This is mainly to measure the difference between two models: for example
       * if stepm=24 months pijx are given only every 2 years and by summing them
   /* long total_usecs;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   struct timeval start_time, end_time;     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   getcwd(pathcd, size);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   printf("\n%s",version);     * curvature will be obtained if estepm is as small as stepm. */
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    /* For example we decided to compute the life expectancy with the smallest unit */
     scanf("%s",pathtot);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   }       nhstepm is the number of hstepm from age to agelim 
   else{       nstepm is the number of stepm from age to agelin. 
     strcpy(pathtot,argv[1]);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /*cygwin_split_path(pathtot,path,optionfile);       survival function given by stepm (the optimization length). Unfortunately it
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       means that if the survival funtion is printed only each two years of age and if
   /* cutv(path,optionfile,pathtot,'\\');*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   chdir(path);  
   replace(pathc,path);    agelim=AGESUP;
     /* If stepm=6 months */
 /*-------- arguments in the command line --------*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   strcpy(fileres,"r");      
   strcat(fileres, optionfilefiname);  /* nhstepm age range expressed in number of stepm */
   strcat(fileres,".txt");    /* Other files have txt extension */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /*---------arguments file --------*/    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    for (age=bage; age<=fage; age ++){ 
   }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   strcpy(filereso,"o");      /* if (stepm >= YEARM) hstepm=1;*/
   strcat(filereso,fileres);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      /* If stepm=6 months */
   }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     puts(line);      
     fputs(line,ficparo);      printf("%d|",(int)age);fflush(stdout);
   }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   ungetc(c,ficpar);      
       /* Computing expectancies */
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      for(i=1; i<=nlstate;i++)
   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);        for(j=1; j<=nlstate;j++)
   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);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 while((c=getc(ficpar))=='#' && c!= EOF){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);            /* 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]);*/
     puts(line);  
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);      fprintf(ficreseij,"%3.0f",age );
        for(i=1; i<=nlstate;i++){
            eip=0;
   covar=matrix(0,NCOVMAX,1,n);        for(j=1; j<=nlstate;j++){
   cptcovn=0;          eip +=eij[i][j][(int)age];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
   ncovmodel=2+cptcovn;        fprintf(ficreseij,"%9.4f", eip );
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      }
        fprintf(ficreseij,"\n");
   /* Read guess parameters */      
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);    printf("\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\n");
     puts(line);    
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  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[] )
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  {
     for(i=1; i <=nlstate; i++)    /* Covariances of health expectancies eij and of total life expectancies according
     for(j=1; j <=nlstate+ndeath-1; j++){     to initial status i, ei. .
       fscanf(ficpar,"%1d%1d",&i1,&j1);    */
       fprintf(ficparo,"%1d%1d",i1,j1);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       printf("%1d%1d",i,j);    int nhstepma, nstepma; /* Decreasing with age */
       for(k=1; k<=ncovmodel;k++){    double age, agelim, hf;
         fscanf(ficpar," %lf",&param[i][j][k]);    double ***p3matp, ***p3matm, ***varhe;
         printf(" %lf",param[i][j][k]);    double **dnewm,**doldm;
         fprintf(ficparo," %lf",param[i][j][k]);    double *xp, *xm;
       }    double **gp, **gm;
       fscanf(ficpar,"\n");    double ***gradg, ***trgradg;
       printf("\n");    int theta;
       fprintf(ficparo,"\n");  
     }    double eip, vip;
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
   p=param[1][1];    xm=vector(1,npar);
      dnewm=matrix(1,nlstate*nlstate,1,npar);
   /* Reads comments: lines beginning with '#' */    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    pstamp(ficresstdeij);
     fgets(line, MAXLINE, ficpar);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     puts(line);    fprintf(ficresstdeij,"# Age");
     fputs(line,ficparo);    for(i=1; i<=nlstate;i++){
   }      for(j=1; j<=nlstate;j++)
   ungetc(c,ficpar);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(ficresstdeij,"\n");
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){    pstamp(ficrescveij);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       printf("%1d%1d",i,j);    fprintf(ficrescveij,"# Age");
       fprintf(ficparo,"%1d%1d",i1,j1);    for(i=1; i<=nlstate;i++)
       for(k=1; k<=ncovmodel;k++){      for(j=1; j<=nlstate;j++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);        cptj= (j-1)*nlstate+i;
         printf(" %le",delti3[i][j][k]);        for(i2=1; i2<=nlstate;i2++)
         fprintf(ficparo," %le",delti3[i][j][k]);          for(j2=1; j2<=nlstate;j2++){
       }            cptj2= (j2-1)*nlstate+i2;
       fscanf(ficpar,"\n");            if(cptj2 <= cptj)
       printf("\n");              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       fprintf(ficparo,"\n");          }
     }      }
   }    fprintf(ficrescveij,"\n");
   delti=delti3[1][1];    
      if(estepm < stepm){
   /* Reads comments: lines beginning with '#' */      printf ("Problem %d lower than %d\n",estepm, stepm);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    else  hstepm=estepm;   
     fgets(line, MAXLINE, ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
     puts(line);     * This is mainly to measure the difference between two models: for example
     fputs(line,ficparo);     * if stepm=24 months pijx are given only every 2 years and by summing them
   }     * we are calculating an estimate of the Life Expectancy assuming a linear 
   ungetc(c,ficpar);     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   matcov=matrix(1,npar,1,npar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   for(i=1; i <=npar; i++){     * to compare the new estimate of Life expectancy with the same linear 
     fscanf(ficpar,"%s",&str);     * hypothesis. A more precise result, taking into account a more precise
     printf("%s",str);     * curvature will be obtained if estepm is as small as stepm. */
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){    /* For example we decided to compute the life expectancy with the smallest unit */
       fscanf(ficpar," %le",&matcov[i][j]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       printf(" %.5le",matcov[i][j]);       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficparo," %.5le",matcov[i][j]);       nstepm is the number of stepm from age to agelin. 
     }       Look at hpijx to understand the reason of that which relies in memory size
     fscanf(ficpar,"\n");       and note for a fixed period like estepm months */
     printf("\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fprintf(ficparo,"\n");       survival function given by stepm (the optimization length). Unfortunately it
   }       means that if the survival funtion is printed only each two years of age and if
   for(i=1; i <=npar; i++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     for(j=i+1;j<=npar;j++)       results. So we changed our mind and took the option of the best precision.
       matcov[i][j]=matcov[j][i];    */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   printf("\n");  
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     /*-------- Rewriting paramater file ----------*/    agelim=AGESUP;
      strcpy(rfileres,"r");    /* "Rparameterfile */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      strcat(rfileres,".");    /* */    /* if (stepm >= YEARM) hstepm=1;*/
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     if((ficres =fopen(rfileres,"w"))==NULL) {    
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"#%s\n",version);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     /*-------- data file ----------*/    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     if((fic=fopen(datafile,"r"))==NULL)    {    gm=matrix(0,nhstepm,1,nlstate*nlstate);
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     n= lastobs;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     severity = vector(1,maxwav);      /* if (stepm >= YEARM) hstepm=1;*/
     outcome=imatrix(1,maxwav+1,1,n);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     num=ivector(1,n);  
     moisnais=vector(1,n);      /* If stepm=6 months */
     annais=vector(1,n);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     moisdc=vector(1,n);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     andc=vector(1,n);      
     agedc=vector(1,n);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     cod=ivector(1,n);  
     weight=vector(1,n);      /* Computing  Variances of health expectancies */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     mint=matrix(1,maxwav,1,n);         decrease memory allocation */
     anint=matrix(1,maxwav,1,n);      for(theta=1; theta <=npar; theta++){
     s=imatrix(1,maxwav+1,1,n);        for(i=1; i<=npar; i++){ 
     adl=imatrix(1,maxwav+1,1,n);              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     tab=ivector(1,NCOVMAX);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     ncodemax=ivector(1,8);        }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     i=1;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     while (fgets(line, MAXLINE, fic) != NULL)    {    
       if ((i >= firstobs) && (i <=lastobs)) {        for(j=1; j<= nlstate; j++){
                  for(i=1; i<=nlstate; i++){
         for (j=maxwav;j>=1;j--){            for(h=0; h<=nhstepm-1; h++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           strcpy(line,stra);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }        }
               
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(ij=1; ij<= nlstate*nlstate; ij++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      }/* End theta */
       
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      
         for (j=ncovcol;j>=1;j--){      for(h=0; h<=nhstepm-1; h++)
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<=nlstate*nlstate;j++)
         }          for(theta=1; theta <=npar; theta++)
         num[i]=atol(stra);            trgradg[h][j][theta]=gradg[h][theta][j];
              
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.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;}*/       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
         i=i+1;          varhe[ij][ji][(int)age] =0.;
       }  
     }       printf("%d|",(int)age);fflush(stdout);
     /* printf("ii=%d", ij);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        scanf("%d",i);*/       for(h=0;h<=nhstepm-1;h++){
   imx=i-1; /* Number of individuals */        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   /* for (i=1; i<=imx; i++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          for(ij=1;ij<=nlstate*nlstate;ij++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            for(ji=1;ji<=nlstate*nlstate;ji++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     }*/        }
    /*  for (i=1; i<=imx; i++){      }
      if (s[4][i]==9)  s[4][i]=-1;  
      printf("%d %.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]));}*/      /* Computing expectancies */
        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        for(i=1; i<=nlstate;i++)
   /* Calculation of the number of parameter from char model*/        for(j=1; j<=nlstate;j++)
   Tvar=ivector(1,15);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   Tprod=ivector(1,15);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   Tvaraff=ivector(1,15);            
   Tvard=imatrix(1,15,1,2);            /* 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]);*/
   Tage=ivector(1,15);        
              }
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;      fprintf(ficresstdeij,"%3.0f",age );
     j=nbocc(model,'+');      for(i=1; i<=nlstate;i++){
     j1=nbocc(model,'*');        eip=0.;
     cptcovn=j+1;        vip=0.;
     cptcovprod=j1;        for(j=1; j<=nlstate;j++){
              eip += eij[i][j][(int)age];
     strcpy(modelsav,model);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
       printf("Error. Non available option model=%s ",model);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       goto end;        }
     }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
          }
     for(i=(j+1); i>=1;i--){      fprintf(ficresstdeij,"\n");
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      fprintf(ficrescveij,"%3.0f",age );
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      for(i=1; i<=nlstate;i++)
       /*scanf("%d",i);*/        for(j=1; j<=nlstate;j++){
       if (strchr(strb,'*')) {          cptj= (j-1)*nlstate+i;
         cutv(strd,strc,strb,'*');          for(i2=1; i2<=nlstate;i2++)
         if (strcmp(strc,"age")==0) {            for(j2=1; j2<=nlstate;j2++){
           cptcovprod--;              cptj2= (j2-1)*nlstate+i2;
           cutv(strb,stre,strd,'V');              if(cptj2 <= cptj)
           Tvar[i]=atoi(stre);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           cptcovage++;            }
             Tage[cptcovage]=i;        }
             /*printf("stre=%s ", stre);*/      fprintf(ficrescveij,"\n");
         }     
         else if (strcmp(strd,"age")==0) {    }
           cptcovprod--;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           cutv(strb,stre,strc,'V');    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           Tvar[i]=atoi(stre);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           cptcovage++;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           Tage[cptcovage]=i;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         else {    printf("\n");
           cutv(strb,stre,strc,'V');    fprintf(ficlog,"\n");
           Tvar[i]=ncovcol+k1;  
           cutv(strb,strc,strd,'V');    free_vector(xm,1,npar);
           Tprod[k1]=i;    free_vector(xp,1,npar);
           Tvard[k1][1]=atoi(strc);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           Tvard[k1][2]=atoi(stre);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           Tvar[cptcovn+k2]=Tvard[k1][1];    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  }
           for (k=1; k<=lastobs;k++)  
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  /************ Variance ******************/
           k1++;  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[])
           k2=k2+2;  {
         }    /* Variance of health expectancies */
       }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       else {    /* double **newm;*/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double **dnewm,**doldm;
        /*  scanf("%d",i);*/    double **dnewmp,**doldmp;
       cutv(strd,strc,strb,'V');    int i, j, nhstepm, hstepm, h, nstepm ;
       Tvar[i]=atoi(strc);    int k, cptcode;
       }    double *xp;
       strcpy(modelsav,stra);      double **gp, **gm;  /* for var eij */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    double ***gradg, ***trgradg; /*for var eij */
         scanf("%d",i);*/    double **gradgp, **trgradgp; /* for var p point j */
     }    double *gpp, *gmp; /* for var p point j */
 }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      double ***p3mat;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double age,agelim, hf;
   printf("cptcovprod=%d ", cptcovprod);    double ***mobaverage;
   scanf("%d ",i);*/    int theta;
     fclose(fic);    char digit[4];
     char digitp[25];
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    char fileresprobmorprev[FILENAMELENGTH];
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }    if(popbased==1){
     /*-calculation of age at interview from date of interview and age at death -*/      if(mobilav!=0)
     agev=matrix(1,maxwav,1,imx);        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     for (i=1; i<=imx; i++) {    }
       for(m=2; (m<= maxwav); m++) {    else 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      strcpy(digitp,"-stablbased-");
          anint[m][i]=9999;  
          s[m][i]=-1;    if (mobilav!=0) {
        }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     for (i=1; i<=imx; i++)  {    }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){    strcpy(fileresprobmorprev,"prmorprev"); 
         if(s[m][i] >0){    sprintf(digit,"%-d",ij);
           if (s[m][i] >= nlstate+1) {    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
             if(agedc[i]>0)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
               if(moisdc[i]!=99 && andc[i]!=9999)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                 agev[m][i]=agedc[i];    strcat(fileresprobmorprev,fileres);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
            else {      printf("Problem with resultfile: %s\n", fileresprobmorprev);
               if (andc[i]!=9999){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    }
               agev[m][i]=-1;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
               }   
             }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           }    pstamp(ficresprobmorprev);
           else if(s[m][i] !=9){ /* Should no more exist */    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);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
             if(mint[m][i]==99 || anint[m][i]==9999)    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
               agev[m][i]=1;      fprintf(ficresprobmorprev," p.%-d SE",j);
             else if(agev[m][i] <agemin){      for(i=1; i<=nlstate;i++)
               agemin=agev[m][i];        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    }  
             }    fprintf(ficresprobmorprev,"\n");
             else if(agev[m][i] >agemax){    fprintf(ficgp,"\n# Routine varevsij");
               agemax=agev[m][i];    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    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");
             }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
             /*agev[m][i]=anint[m][i]-annais[i];*/  /*   } */
             /*   agev[m][i] = age[i]+2*m;*/    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }    pstamp(ficresvij);
           else { /* =9 */    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
             agev[m][i]=1;    if(popbased==1)
             s[m][i]=-1;      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);
           }    else
         }      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
         else /*= 0 Unknown */    fprintf(ficresvij,"# Age");
           agev[m][i]=1;    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=nlstate;j++)
            fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     }    fprintf(ficresvij,"\n");
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){    xp=vector(1,npar);
         if (s[m][i] > (nlstate+ndeath)) {    dnewm=matrix(1,nlstate,1,npar);
           printf("Error: Wrong value in nlstate or ndeath\n");      doldm=matrix(1,nlstate,1,nlstate);
           goto end;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }  
     }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_vector(severity,1,maxwav);    
     free_imatrix(outcome,1,maxwav+1,1,n);    if(estepm < stepm){
     free_vector(moisnais,1,n);      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_vector(annais,1,n);    }
     /* free_matrix(mint,1,maxwav,1,n);    else  hstepm=estepm;   
        free_matrix(anint,1,maxwav,1,n);*/    /* For example we decided to compute the life expectancy with the smallest unit */
     free_vector(moisdc,1,n);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     free_vector(andc,1,n);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
           Look at function hpijx to understand why (it is linked to memory size questions) */
     wav=ivector(1,imx);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       survival function given by stepm (the optimization length). Unfortunately it
     mw=imatrix(1,lastpass-firstpass+1,1,imx);       means that if the survival funtion is printed every two years of age and if
           you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     /* Concatenates waves */       results. So we changed our mind and took the option of the best precision.
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
       Tcode=ivector(1,100);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       ncodemax[1]=1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
    codtab=imatrix(1,100,1,10);      gp=matrix(0,nhstepm,1,nlstate);
    h=0;      gm=matrix(0,nhstepm,1,nlstate);
    m=pow(2,cptcoveff);  
    
    for(k=1;k<=cptcoveff; k++){      for(theta=1; theta <=npar; theta++){
      for(i=1; i <=(m/pow(2,k));i++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
        for(j=1; j <= ncodemax[k]; j++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        }
            h++;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  
          }        if (popbased==1) {
        }          if(mobilav ==0){
      }            for(i=1; i<=nlstate;i++)
    }              prlim[i][i]=probs[(int)age][i][ij];
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          }else{ /* mobilav */ 
       codtab[1][2]=1;codtab[2][2]=2; */            for(i=1; i<=nlstate;i++)
    /* for(i=1; i <=m ;i++){              prlim[i][i]=mobaverage[(int)age][i][ij];
       for(k=1; k <=cptcovn; k++){          }
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        }
       }    
       printf("\n");        for(j=1; j<= nlstate; j++){
       }          for(h=0; h<=nhstepm; h++){
       scanf("%d",i);*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                  gp[h][j] += prlim[i][i]*p3mat[i][j][h];
    /* Calculates basic frequencies. Computes observed prevalence at single age          }
        and prints on file fileres'p'. */        }
         /* This for computing probability of death (h=1 means
               computed over hstepm matrices product = hstepm*stepm months) 
               as a weighted average of prlim.
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        }    
              /* end probability of death */
     /* For Powell, parameters are in a vector p[] starting at p[1]  
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     if(mle==1){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);   
     }        if (popbased==1) {
              if(mobilav ==0){
     /*--------- results files --------------*/            for(i=1; i<=nlstate;i++)
     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);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
    jk=1;              prlim[i][i]=mobaverage[(int)age][i][ij];
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          }
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        }
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
        if (k != i)          for(h=0; h<=nhstepm; h++){
          {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
            printf("%d%d ",i,k);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            fprintf(ficres,"%1d%1d ",i,k);          }
            for(j=1; j <=ncovmodel; j++){        }
              printf("%f ",p[jk]);        /* This for computing probability of death (h=1 means
              fprintf(ficres,"%f ",p[jk]);           computed over hstepm matrices product = hstepm*stepm months) 
              jk++;           as a weighted average of prlim.
            }        */
            printf("\n");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            fprintf(ficres,"\n");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
          }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
      }        }    
    }        /* end probability of death */
  if(mle==1){  
     /* Computing hessian and covariance matrix */        for(j=1; j<= nlstate; j++) /* vareij */
     ftolhess=ftol; /* Usually correct */          for(h=0; h<=nhstepm; h++){
     hesscov(matcov, p, npar, delti, ftolhess, func);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
  }          }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
      for(i=1,jk=1; i <=nlstate; i++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       for(j=1; j <=nlstate+ndeath; j++){        }
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);      } /* End theta */
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);      for(h=0; h<=nhstepm; h++) /* veij */
             jk++;        for(j=1; j<=nlstate;j++)
           }          for(theta=1; theta <=npar; theta++)
           printf("\n");            trgradg[h][j][theta]=gradg[h][theta][j];
           fprintf(ficres,"\n");  
         }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       }        for(theta=1; theta <=npar; theta++)
      }          trgradgp[j][theta]=gradgp[theta][j];
        
     k=1;  
     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");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     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");      for(i=1;i<=nlstate;i++)
     for(i=1;i<=npar;i++){        for(j=1;j<=nlstate;j++)
       /*  if (k>nlstate) k=1;          vareij[i][j][(int)age] =0.;
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      for(h=0;h<=nhstepm;h++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for(k=0;k<=nhstepm;k++){
       fprintf(ficres,"%3d",i);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       printf("%3d",i);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       for(j=1; j<=i;j++){          for(i=1;i<=nlstate;i++)
         fprintf(ficres," %.5e",matcov[i][j]);            for(j=1;j<=nlstate;j++)
         printf(" %.5e",matcov[i][j]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
       fprintf(ficres,"\n");      }
       printf("\n");    
       k++;      /* pptj */
     }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
          matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     while((c=getc(ficpar))=='#' && c!= EOF){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       ungetc(c,ficpar);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       fgets(line, MAXLINE, ficpar);          varppt[j][i]=doldmp[j][i];
       puts(line);      /* end ppptj */
       fputs(line,ficparo);      /*  x centered again */
     }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     ungetc(c,ficpar);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     estepm=0;   
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      if (popbased==1) {
     if (estepm==0 || estepm < stepm) estepm=stepm;        if(mobilav ==0){
     if (fage <= 2) {          for(i=1; i<=nlstate;i++)
       bage = ageminpar;            prlim[i][i]=probs[(int)age][i][ij];
       fage = agemaxpar;        }else{ /* mobilav */ 
     }          for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        }
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);               
        /* This for computing probability of death (h=1 means
     while((c=getc(ficpar))=='#' && c!= EOF){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     ungetc(c,ficpar);         as a weighted average of prlim.
     fgets(line, MAXLINE, ficpar);      */
     puts(line);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   ungetc(c,ficpar);      }    
        /* end probability of death */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      } 
     fputs(line,ficparo);      fprintf(ficresprobmorprev,"\n");
   }  
   ungetc(c,ficpar);      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        }
       fprintf(ficresvij,"\n");
   fscanf(ficpar,"pop_based=%d\n",&popbased);      free_matrix(gp,0,nhstepm,1,nlstate);
   fprintf(ficparo,"pop_based=%d\n",popbased);        free_matrix(gm,0,nhstepm,1,nlstate);
   fprintf(ficres,"pop_based=%d\n",popbased);        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);    } /* End age */
     fgets(line, MAXLINE, ficpar);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     puts(line);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   ungetc(c,ficpar);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
 while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     ungetc(c,ficpar);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fgets(line, MAXLINE, ficpar);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     puts(line);    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);
     fputs(line,ficparo);    /*  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);
   }  */
   ungetc(c,ficpar);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    free_vector(xp,1,npar);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 /*------------ gnuplot -------------*/    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcpy(optionfilegnuplot,optionfilefiname);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(optionfilegnuplot,".gp");    fclose(ficresprobmorprev);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    fflush(ficgp);
     printf("Problem with file %s",optionfilegnuplot);    fflush(fichtm); 
   }  }  /* end varevsij */
   fclose(ficgp);  
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  /************ Variance of prevlim ******************/
 /*--------- index.htm --------*/  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[])
   {
   strcpy(optionfilehtm,optionfile);    /* Variance of prevalence limit */
   strcat(optionfilehtm,".htm");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    double **newm;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double **dnewm,**doldm;
   }    int i, j, nhstepm, hstepm;
     int k, cptcode;
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    double *xp;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    double *gp, *gm;
 \n    double **gradg, **trgradg;
 Total number of observations=%d <br>\n    double age,agelim;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    int theta;
 <hr  size=\"2\" color=\"#EC5E5E\">    
  <ul><li><h4>Parameter files</h4>\n    pstamp(ficresvpl);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);    fprintf(ficresvpl,"# Age");
   fclose(fichtm);    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    fprintf(ficresvpl,"\n");
    
 /*------------ free_vector  -------------*/    xp=vector(1,npar);
  chdir(path);    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
  free_ivector(wav,1,imx);    
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    hstepm=1*YEARM; /* Every year of age */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
  free_ivector(num,1,n);    agelim = AGESUP;
  free_vector(agedc,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  fclose(ficparo);      if (stepm >= YEARM) hstepm=1;
  fclose(ficres);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   /*--------------- Prevalence limit --------------*/      gm=vector(1,nlstate);
    
   strcpy(filerespl,"pl");      for(theta=1; theta <=npar; theta++){
   strcat(filerespl,fileres);        for(i=1; i<=npar; i++){ /* Computes gradient */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        }
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        for(i=1;i<=nlstate;i++)
   fprintf(ficrespl,"#Prevalence limit\n");          gp[i] = prlim[i][i];
   fprintf(ficrespl,"#Age ");      
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(i=1; i<=npar; i++) /* Computes gradient */
   fprintf(ficrespl,"\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   prlim=matrix(1,nlstate,1,nlstate);        for(i=1;i<=nlstate;i++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          gm[i] = prlim[i][i];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=1;i<=nlstate;i++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      } /* End theta */
   k=0;  
   agebase=ageminpar;      trgradg =matrix(1,nlstate,1,npar);
   agelim=agemaxpar;  
   ftolpl=1.e-10;      for(j=1; j<=nlstate;j++)
   i1=cptcoveff;        for(theta=1; theta <=npar; theta++)
   if (cptcovn < 1){i1=1;}          trgradg[j][theta]=gradg[theta][j];
   
   for(cptcov=1;cptcov<=i1;cptcov++){      for(i=1;i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        varpl[i][(int)age] =0.;
         k=k+1;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         fprintf(ficrespl,"\n#******");      for(i=1;i<=nlstate;i++)
         for(j=1;j<=cptcoveff;j++)        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");      fprintf(ficresvpl,"%.0f ",age );
              for(i=1; i<=nlstate;i++)
         for (age=agebase; age<=agelim; age++){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficresvpl,"\n");
           fprintf(ficrespl,"%.0f",age );      free_vector(gp,1,nlstate);
           for(i=1; i<=nlstate;i++)      free_vector(gm,1,nlstate);
           fprintf(ficrespl," %.5f", prlim[i][i]);      free_matrix(gradg,1,npar,1,nlstate);
           fprintf(ficrespl,"\n");      free_matrix(trgradg,1,nlstate,1,npar);
         }    } /* End age */
       }  
     }    free_vector(xp,1,npar);
   fclose(ficrespl);    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   /*------------- h Pij x at various ages ------------*/  
    }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /************ Variance of one-step probabilities  ******************/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  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[])
   }  {
   printf("Computing pij: result on file '%s' \n", filerespij);    int i, j=0,  i1, k1, l1, t, tj;
      int k2, l2, j1,  z1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int k=0,l, cptcode;
   /*if (stepm<=24) stepsize=2;*/    int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   agelim=AGESUP;    double **dnewm,**doldm;
   hstepm=stepsize*YEARM; /* Every year of age */    double *xp;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double *gp, *gm;
     double **gradg, **trgradg;
   /* hstepm=1;   aff par mois*/    double **mu;
     double age,agelim, cov[NCOVMAX+1];
   k=0;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   for(cptcov=1;cptcov<=i1;cptcov++){    int theta;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char fileresprob[FILENAMELENGTH];
       k=k+1;    char fileresprobcov[FILENAMELENGTH];
         fprintf(ficrespij,"\n#****** ");    char fileresprobcor[FILENAMELENGTH];
         for(j=1;j<=cptcoveff;j++)    double ***varpij;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    strcpy(fileresprob,"prob"); 
            strcat(fileresprob,fileres);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("Problem with resultfile: %s\n", fileresprob);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
           /*      nhstepm=nhstepm*YEARM; aff par mois*/    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
           oldm=oldms;savm=savms;      printf("Problem with resultfile: %s\n", fileresprobcov);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           fprintf(ficrespij,"# Age");    }
           for(i=1; i<=nlstate;i++)    strcpy(fileresprobcor,"probcor"); 
             for(j=1; j<=nlstate+ndeath;j++)    strcat(fileresprobcor,fileres);
               fprintf(ficrespij," %1d-%1d",i,j);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           fprintf(ficrespij,"\n");      printf("Problem with resultfile: %s\n", fileresprobcor);
            for (h=0; h<=nhstepm; h++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    }
             for(i=1; i<=nlstate;i++)    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             fprintf(ficrespij,"\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
              }    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           fprintf(ficrespij,"\n");    pstamp(ficresprob);
         }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     }    fprintf(ficresprob,"# Age");
   }    pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
   fclose(ficrespij);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){    for(i=1; i<=nlstate;i++)
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      for(j=1; j<=(nlstate+ndeath);j++){
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   else{        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     erreur=108;      }  
     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);   /* fprintf(ficresprob,"\n");
   }    fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
    */
   /*---------- Health expectancies and variances ------------*/    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   strcpy(filerest,"t");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   strcat(filerest,fileres);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   if((ficrest=fopen(filerest,"w"))==NULL) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    first=1;
   }    fprintf(ficgp,"\n# Routine varprob");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
   strcpy(filerese,"e");    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   strcat(filerese,fileres);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   if((ficreseij=fopen(filerese,"w"))==NULL) {    file %s<br>\n",optionfilehtmcov);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   }  and drawn. It helps understanding how is the covariance between two incidences.\
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     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. \
  strcpy(fileresv,"v");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   strcat(fileresv,fileres);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  standard deviations wide on each axis. <br>\
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   calagedate=-1;  
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    cov[1]=1;
     /* tj=cptcoveff; */
   k=0;    tj = (int) pow(2,cptcoveff);
   for(cptcov=1;cptcov<=i1;cptcov++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    j1=0;
       k=k+1;    for(j1=1; j1<=tj;j1++){
       fprintf(ficrest,"\n#****** ");      /*for(i1=1; i1<=ncodemax[t];i1++){ */
       for(j=1;j<=cptcoveff;j++)      /*j1++;*/
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if  (cptcovn>0) {
       fprintf(ficrest,"******\n");          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficreseij,"\n#****** ");          fprintf(ficresprob, "**********\n#\n");
       for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficreseij,"******\n");          fprintf(ficresprobcov, "**********\n#\n");
           
       fprintf(ficresvij,"\n#****** ");          fprintf(ficgp, "\n#********** Variable "); 
       for(j=1;j<=cptcoveff;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp, "**********\n#\n");
       fprintf(ficresvij,"******\n");          
           
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       oldm=oldms;savm=savms;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);            fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
            
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          fprintf(ficresprobcor, "\n#********** Variable ");    
       oldm=oldms;savm=savms;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);          fprintf(ficresprobcor, "**********\n#");    
            }
         
          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficrest,"\n");        gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
       epj=vector(1,nlstate+1);          cov[2]=age;
       for(age=bage; age <=fage ;age++){          for (k=1; k<=cptcovn;k++) {
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
         if (popbased==1) {                                                           * 1  1 1 1 1
           for(i=1; i<=nlstate;i++)                                                           * 2  2 1 1 1
             prlim[i][i]=probs[(int)age][i][k];                                                           * 3  1 2 1 1
         }                                                           */
                    /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         fprintf(ficrest," %4.0f",age);          }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          for (k=1; k<=cptcovprod;k++)
             epj[j] += prlim[i][i]*eij[i][j][(int)age];            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/          
           }      
           epj[nlstate+1] +=epj[j];          for(theta=1; theta <=npar; theta++){
         }            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
         for(i=1, vepp=0.;i <=nlstate;i++)            
           for(j=1;j <=nlstate;j++)            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             vepp += vareij[i][j][(int)age];            
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            k=0;
         for(j=1;j <=nlstate;j++){            for(i=1; i<= (nlstate); i++){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              for(j=1; j<=(nlstate+ndeath);j++){
         }                k=k+1;
         fprintf(ficrest,"\n");                gp[k]=pmmij[i][j];
       }              }
     }            }
   }            
 free_matrix(mint,1,maxwav,1,n);            for(i=1; i<=npar; i++)
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     free_vector(weight,1,n);      
   fclose(ficreseij);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   fclose(ficresvij);            k=0;
   fclose(ficrest);            for(i=1; i<=(nlstate); i++){
   fclose(ficpar);              for(j=1; j<=(nlstate+ndeath);j++){
   free_vector(epj,1,nlstate+1);                k=k+1;
                  gm[k]=pmmij[i][j];
   /*------- Variance limit prevalence------*/                }
             }
   strcpy(fileresvpl,"vpl");       
   strcat(fileresvpl,fileres);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          }
     exit(0);  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   k=0;          
   for(cptcov=1;cptcov<=i1;cptcov++){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");          pmij(pmmij,cov,ncovmodel,x,nlstate);
       for(j=1;j<=cptcoveff;j++)          
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          k=0;
       fprintf(ficresvpl,"******\n");          for(i=1; i<=(nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);              k=k+1;
       oldm=oldms;savm=savms;              mu[k][(int) age]=pmmij[i][j];
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            }
     }          }
  }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   fclose(ficresvpl);              varpij[i][j][(int)age] = doldm[i][j];
   
   /*---------- End : free ----------------*/          /*printf("\n%d ",(int)age);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
              printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }*/
    
            fprintf(ficresprob,"\n%d ",(int)age);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficresprobcov,"\n%d ",(int)age);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficresprobcor,"\n%d ",(int)age);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   free_matrix(matcov,1,npar,1,npar);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   free_vector(delti,1,npar);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   free_matrix(agev,1,maxwav,1,imx);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          }
           i=0;
   fprintf(fichtm,"\n</body>");          for (k=1; k<=(nlstate);k++){
   fclose(fichtm);            for (l=1; l<=(nlstate+ndeath);l++){ 
   fclose(ficgp);              i++;
                fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   if(erreur >0)              for (j=1; j<=i;j++){
     printf("End of Imach with error or warning %d\n",erreur);                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
   else   printf("End of Imach\n");                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/            }
   /*printf("Total time was %d uSec.\n", total_usecs);*/          }/* end of loop for state */
   /*------ End -----------*/        } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
  end:        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 #ifdef windows        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   /* chdir(pathcd);*/        
 #endif        /* Confidence intervalle of pij  */
  /*system("wgnuplot graph.plt");*/        /*
  /*system("../gp37mgw/wgnuplot graph.plt");*/          fprintf(ficgp,"\nunset parametric;unset label");
  /*system("cd ../gp37mgw");*/          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
  strcpy(plotcmd,GNUPLOTPROGRAM);          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);
  strcat(plotcmd," ");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
  strcat(plotcmd,optionfilegnuplot);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
  system(plotcmd);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
 #ifdef windows  
   while (z[0] != 'q') {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     /* chdir(path); */        first1=1;first2=2;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        for (k2=1; k2<=(nlstate);k2++){
     scanf("%s",z);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     if (z[0] == 'c') system("./imach");            if(l2==k2) continue;
     else if (z[0] == 'e') system(optionfilehtm);            j=(k2-1)*(nlstate+ndeath)+l2;
     else if (z[0] == 'g') system(plotcmd);            for (k1=1; k1<=(nlstate);k1++){
     else if (z[0] == 'q') exit(0);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   }                if(l1==k1) continue;
 #endif                i=(k1-1)*(nlstate+ndeath)+l1;
 }                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       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);
                       }
                       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);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       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);
                     }
                     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);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       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);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (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): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        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> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    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> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           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> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - 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): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (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): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - 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",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - 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",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    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); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        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);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   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);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           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);
           /*      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);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   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){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           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]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   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){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# 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" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        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]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      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]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        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]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      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]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       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]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    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>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      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]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             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);
             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);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           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);
           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);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         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);
           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);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         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);
         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);
           return 1;
       }
       if (year==9999) {
         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);
         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);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         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);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             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);
             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);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         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;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - 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
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  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
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           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);
           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);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           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]); 
           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]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           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);     
           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);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     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);
     numlinepar++;
     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);
     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);
     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);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       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*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       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);
       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);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     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
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       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); 
       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); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       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 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             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]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         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]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       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);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       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");
       if(mle>=1)
         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");
       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");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       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);
       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);
       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);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       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);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       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);
       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);
       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);
       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);
       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);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        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); */
         /*        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); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  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",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             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 ");
             if(vpopbased==1)
               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);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.49  
changed lines
  Added in v.1.148


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