Diff for /imach/src/imach.c between versions 1.50 and 1.117

version 1.50, 2002/06/26 23:25:02 version 1.117, 2006/03/14 17:16:22
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.117  2006/03/14 17:16:22  brouard
      (Module): varevsij Comments added explaining the second
   This program computes Healthy Life Expectancies from    table of variances if popbased=1 .
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   first survey ("cross") where individuals from different ages are    (Module): Function pstamp added
   interviewed on their health status or degree of disability (in the    (Module): Version 0.98d
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.116  2006/03/06 10:29:27  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Variance-covariance wrong links and
   computed from the time spent in each health state according to a    varian-covariance of ej. is needed (Saito).
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.115  2006/02/27 12:17:45  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): One freematrix added in mlikeli! 0.98c
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.114  2006/02/26 12:57:58  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): Some improvements in processing parameter
   'age' is age and 'sex' is a covariate. If you want to have a more    filename with strsep.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.113  2006/02/24 14:20:24  brouard
   you to do it.  More covariates you add, slower the    (Module): Memory leaks checks with valgrind and:
   convergence.    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.112  2006/01/30 09:55:26  brouard
   identical for each individual. Also, if a individual missed an    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
   hPijx is the probability to be observed in state i at age x+h    (Module): Comments can be added in data file. Missing date values
   conditional to the observed state i at age x. The delay 'h' can be    can be a simple dot '.'.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.110  2006/01/25 00:51:50  brouard
   semester or year) is model as a multinomial logistic.  The hPx    (Module): Lots of cleaning and bugs added (Gompertz)
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.109  2006/01/24 19:37:15  brouard
   hPijx.    (Module): Comments (lines starting with a #) are allowed in data.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.108  2006/01/19 18:05:42  lievre
   of the life expectancies. It also computes the prevalence limits.    Gnuplot problem appeared...
      To be fixed
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.107  2006/01/19 16:20:37  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Test existence of gnuplot in imach path
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.106  2006/01/19 13:24:36  brouard
   software can be distributed freely for non commercial use. Latest version    Some cleaning and links added in html output
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.105  2006/01/05 20:23:19  lievre
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.104  2005/09/30 16:11:43  lievre
 #include <stdlib.h>    (Module): sump fixed, loop imx fixed, and simplifications.
 #include <unistd.h>    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 #define MAXLINE 256    (instead of missing=-1 in earlier versions) and his/her
 #define GNUPLOTPROGRAM "gnuplot"    contributions to the likelihood is 1 - Prob of dying from last
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define FILENAMELENGTH 80    the healthy state at last known wave). Version is 0.98
 /*#define DEBUG*/  
 #define windows    Revision 1.103  2005/09/30 15:54:49  lievre
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): sump fixed, loop imx fixed, and simplifications.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.102  2004/09/15 17:31:30  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Add the possibility to read data file including tab characters.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.101  2004/09/15 10:38:38  brouard
 #define NINTERVMAX 8    Fix on curr_time
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.100  2004/07/12 18:29:06  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Add version for Mac OS X. Just define UNIX in Makefile
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.99  2004/06/05 08:57:40  brouard
 #define AGESUP 130    *** empty log message ***
 #define AGEBASE 40  
 #ifdef windows    Revision 1.98  2004/05/16 15:05:56  brouard
 #define DIRSEPARATOR '\\'    New version 0.97 . First attempt to estimate force of mortality
 #define ODIRSEPARATOR '/'    directly from the data i.e. without the need of knowing the health
 #else    state at each age, but using a Gompertz model: log u =a + b*age .
 #define DIRSEPARATOR '/'    This is the basic analysis of mortality and should be done before any
 #define ODIRSEPARATOR '\\'    other analysis, in order to test if the mortality estimated from the
 #endif    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    The same imach parameter file can be used but the option for mle should be -3.
 int nvar;  
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    Agnès, who wrote this part of the code, tried to keep most of the
 int npar=NPARMAX;    former routines in order to include the new code within the former code.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    The output is very simple: only an estimate of the intercept and of
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    the slope with 95% confident intervals.
 int popbased=0;  
     Current limitations:
 int *wav; /* Number of waves for this individuual 0 is possible */    A) Even if you enter covariates, i.e. with the
 int maxwav; /* Maxim number of waves */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int jmin, jmax; /* min, max spacing between 2 waves */    B) There is no computation of Life Expectancy nor Life Table.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.97  2004/02/20 13:25:42  lievre
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Version 0.96d. Population forecasting command line is (temporarily)
 double jmean; /* Mean space between 2 waves */    suppressed.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.96  2003/07/15 15:38:55  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 FILE *ficlog;    rewritten within the same printf. Workaround: many printfs.
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    Revision 1.95  2003/07/08 07:54:34  brouard
 FILE *fichtm; /* Html File */    * imach.c (Repository):
 FILE *ficreseij;    (Repository): Using imachwizard code to output a more meaningful covariance
 char filerese[FILENAMELENGTH];    matrix (cov(a12,c31) instead of numbers.
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];    Revision 1.94  2003/06/27 13:00:02  brouard
 FILE  *ficresvpl;    Just cleaning
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];    Revision 1.93  2003/06/25 16:33:55  brouard
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    (Module): On windows (cygwin) function asctime_r doesn't
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    Revision 1.92  2003/06/25 16:30:45  brouard
 char filerest[FILENAMELENGTH];    (Module): On windows (cygwin) function asctime_r doesn't
 char fileregp[FILENAMELENGTH];    exist so I changed back to asctime which exists.
 char popfile[FILENAMELENGTH];  
     Revision 1.91  2003/06/25 15:30:29  brouard
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 #define NR_END 1    helps to forecast when convergence will be reached. Elapsed time
 #define FREE_ARG char*    is stamped in powell.  We created a new html file for the graphs
 #define FTOL 1.0e-10    concerning matrix of covariance. It has extension -cov.htm.
   
 #define NRANSI    Revision 1.90  2003/06/24 12:34:15  brouard
 #define ITMAX 200    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define TOL 2.0e-4    of the covariance matrix to be input.
   
 #define CGOLD 0.3819660    Revision 1.89  2003/06/24 12:30:52  brouard
 #define ZEPS 1.0e-10    (Module): Some bugs corrected for windows. Also, when
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.88  2003/06/23 17:54:56  brouard
 #define TINY 1.0e-20    * 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.
   
 static double maxarg1,maxarg2;    Revision 1.87  2003/06/18 12:26:01  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Version 0.96
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.86  2003/06/17 20:04:08  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Change position of html and gnuplot routines and added
 #define rint(a) floor(a+0.5)    routine fileappend.
   
 static double sqrarg;    Revision 1.85  2003/06/17 13:12:43  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * imach.c (Repository): Check when date of death was earlier that
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 int imx;    was wrong (infinity). We still send an "Error" but patch by
 int stepm;    assuming that the date of death was just one stepm after the
 /* Stepm, step in month: minimum step interpolation*/    interview.
     (Repository): Because some people have very long ID (first column)
 int estepm;    we changed int to long in num[] and we added a new lvector for
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    memory allocation. But we also truncated to 8 characters (left
     truncation)
 int m,nb;    (Repository): No more line truncation errors.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.84  2003/06/13 21:44:43  brouard
 double **pmmij, ***probs, ***mobaverage;    * imach.c (Repository): Replace "freqsummary" at a correct
 double dateintmean=0;    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 double *weight;    parcimony.
 int **s; /* Status */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  */
 {  /*
    char *s;                             /* pointer */     Interpolated Markov Chain
    int  l1, l2;                         /* length counters */  
     Short summary of the programme:
    l1 = strlen( path );                 /* length of path */    
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    This program computes Healthy Life Expectancies from
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    if ( s == NULL ) {                   /* no directory, so use current */    first survey ("cross") where individuals from different ages are
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    interviewed on their health status or degree of disability (in the
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    case of a health survey which is our main interest) -2- at least a
 #if     defined(__bsd__)                /* get current working directory */    second wave of interviews ("longitudinal") which measure each change
       extern char       *getwd( );    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
       if ( getwd( dirc ) == NULL ) {    model. More health states you consider, more time is necessary to reach the
 #else    Maximum Likelihood of the parameters involved in the model.  The
       extern char       *getcwd( );    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    conditional to be observed in state i at the first wave. Therefore
 #endif    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
          return( GLOCK_ERROR_GETCWD );    'age' is age and 'sex' is a covariate. If you want to have a more
       }    complex model than "constant and age", you should modify the program
       strcpy( name, path );             /* we've got it */    where the markup *Covariates have to be included here again* invites
    } else {                             /* strip direcotry from path */    you to do it.  More covariates you add, slower the
       s++;                              /* after this, the filename */    convergence.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    The advantage of this computer programme, compared to a simple
       strcpy( name, s );                /* save file name */    multinomial logistic model, is clear when the delay between waves is not
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    identical for each individual. Also, if a individual missed an
       dirc[l1-l2] = 0;                  /* add zero */    intermediate interview, the information is lost, but taken into
    }    account using an interpolation or extrapolation.  
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    hPijx is the probability to be observed in state i at age x+h
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    conditional to the observed state i at age x. The delay 'h' can be
 #else    split into an exact number (nh*stepm) of unobserved intermediate
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    states. This elementary transition (by month, quarter,
 #endif    semester or year) is modelled as a multinomial logistic.  The hPx
    s = strrchr( name, '.' );            /* find last / */    matrix is simply the matrix product of nh*stepm elementary matrices
    s++;    and the contribution of each individual to the likelihood is simply
    strcpy(ext,s);                       /* save extension */    hPijx.
    l1= strlen( name);  
    l2= strlen( s)+1;    Also this programme outputs the covariance matrix of the parameters but also
    strncpy( finame, name, l1-l2);    of the life expectancies. It also computes the period (stable) prevalence. 
    finame[l1-l2]= 0;    
    return( 0 );                         /* we're done */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 }             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 /******************************************/    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 void replace(char *s, char*t)    can be accessed at http://euroreves.ined.fr/imach .
 {  
   int i;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int lg=20;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   i=0;    
   lg=strlen(t);    **********************************************************************/
   for(i=0; i<= lg; i++) {  /*
     (s[i] = t[i]);    main
     if (t[i]== '\\') s[i]='/';    read parameterfile
   }    read datafile
 }    concatwav
     freqsummary
 int nbocc(char *s, char occ)    if (mle >= 1)
 {      mlikeli
   int i,j=0;    print results files
   int lg=20;    if mle==1 
   i=0;       computes hessian
   lg=strlen(s);    read end of parameter file: agemin, agemax, bage, fage, estepm
   for(i=0; i<= lg; i++) {        begin-prev-date,...
   if  (s[i] == occ ) j++;    open gnuplot file
   }    open html file
   return j;    period (stable) prevalence
 }     for age prevalim()
     h Pij x
 void cutv(char *u,char *v, char*t, char occ)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   /* cuts string t into u and v where u is ended by char occ excluding it    health expectancies
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    Variance-covariance of DFLE
      gives u="abcedf" and v="ghi2j" */    prevalence()
   int i,lg,j,p=0;     movingaverage()
   i=0;    varevsij() 
   for(j=0; j<=strlen(t)-1; j++) {    if popbased==1 varevsij(,popbased)
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    total life expectancies
   }    Variance of period (stable) prevalence
    end
   lg=strlen(t);  */
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  
   }  
      u[p]='\0';   
   #include <math.h>
    for(j=0; j<= lg; j++) {  #include <stdio.h>
     if (j>=(p+1))(v[j-p-1] = t[j]);  #include <stdlib.h>
   }  #include <string.h>
 }  #include <unistd.h>
   
 /********************** nrerror ********************/  #include <limits.h>
   #include <sys/types.h>
 void nrerror(char error_text[])  #include <sys/stat.h>
 {  #include <errno.h>
   fprintf(stderr,"ERREUR ...\n");  extern int errno;
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  /* #include <sys/time.h> */
 }  #include <time.h>
 /*********************** vector *******************/  #include "timeval.h"
 double *vector(int nl, int nh)  
 {  /* #include <libintl.h> */
   double *v;  /* #define _(String) gettext (String) */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define MAXLINE 256
   return v-nl+NR_END;  
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /************************ free vector ******************/  #define FILENAMELENGTH 132
 void free_vector(double*v, int nl, int nh)  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   free((FREE_ARG)(v+nl-NR_END));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 /************************ivector *******************************/  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 int *ivector(long nl,long nh)  
 {  #define NINTERVMAX 8
   int *v;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   if (!v) nrerror("allocation failure in ivector");  #define NCOVMAX 8 /* Maximum number of covariates */
   return v-nl+NR_END;  #define MAXN 20000
 }  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 /******************free ivector **************************/  #define AGEBASE 40
 void free_ivector(int *v, long nl, long nh)  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 {  #ifdef UNIX
   free((FREE_ARG)(v+nl-NR_END));  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /******************* imatrix *******************************/  #else
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define DIRSEPARATOR '\\'
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define CHARSEPARATOR "\\"
 {  #define ODIRSEPARATOR '/'
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #endif
   int **m;  
    /* $Id$ */
   /* allocate pointers to rows */  /* $State$ */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
   m += NR_END;  char fullversion[]="$Revision$ $Date$"; 
   m -= nrl;  char strstart[80];
    char optionfilext[10], optionfilefiname[FILENAMELENGTH];
    int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   /* allocate rows and set pointers to them */  int nvar;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int npar=NPARMAX;
   m[nrl] += NR_END;  int nlstate=2; /* Number of live states */
   m[nrl] -= ncl;  int ndeath=1; /* Number of dead states */
    int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int popbased=0;
    
   /* return pointer to array of pointers to rows */  int *wav; /* Number of waves for this individuual 0 is possible */
   return m;  int maxwav; /* Maxim number of waves */
 }  int jmin, jmax; /* min, max spacing between 2 waves */
   int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 /****************** free_imatrix *************************/  int gipmx, gsw; /* Global variables on the number of contributions 
 void free_imatrix(m,nrl,nrh,ncl,nch)                     to the likelihood and the sum of weights (done by funcone)*/
       int **m;  int mle, weightopt;
       long nch,ncl,nrh,nrl;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
      /* free an int matrix allocated by imatrix() */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   free((FREE_ARG) (m[nrl]+ncl-NR_END));             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   free((FREE_ARG) (m+nrl-NR_END));  double jmean; /* Mean space between 2 waves */
 }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 /******************* matrix *******************************/  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  double fretone; /* Only one call to likelihood */
   double **m;  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char filerespow[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   m += NR_END;  FILE *ficresilk;
   m -= nrl;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  FILE *fichtm, *fichtmcov; /* Html File */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *ficreseij;
   m[nrl] += NR_END;  char filerese[FILENAMELENGTH];
   m[nrl] -= ncl;  FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE *ficrescveij;
   return m;  char filerescve[FILENAMELENGTH];
 }  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 /*************************free matrix ************************/  FILE  *ficresvpl;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
 /******************* ma3x *******************************/  int  outcmd=0;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileregp[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char popfile[FILENAMELENGTH];
   m += NR_END;  
   m -= nrl;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  struct timezone tzp;
   m[nrl] += NR_END;  extern int gettimeofday();
   m[nrl] -= ncl;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  extern long time();
   char strcurr[80], strfor[80];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char *endptr;
   m[nrl][ncl] += NR_END;  long lval;
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  #define NR_END 1
     m[nrl][j]=m[nrl][j-1]+nlay;  #define FREE_ARG char*
    #define FTOL 1.0e-10
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define NRANSI 
     for (j=ncl+1; j<=nch; j++)  #define ITMAX 200 
       m[i][j]=m[i][j-1]+nlay;  
   }  #define TOL 2.0e-4 
   return m;  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /*************************free ma3x ************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #define GOLD 1.618034 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define GLIMIT 100.0 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define TINY 1.0e-20 
   free((FREE_ARG)(m+nrl-NR_END));  
 }  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /***************** f1dim *************************/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 extern int ncom;    
 extern double *pcom,*xicom;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 extern double (*nrfunc)(double []);  #define rint(a) floor(a+0.5)
    
 double f1dim(double x)  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   int j;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   double f;  int agegomp= AGEGOMP;
   double *xt;  
    int imx; 
   xt=vector(1,ncom);  int stepm=1;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /* Stepm, step in month: minimum step interpolation*/
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  int estepm;
   return f;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 }  
   int m,nb;
 /*****************brent *************************/  long *num;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   int iter;  double **pmmij, ***probs;
   double a,b,d,etemp;  double *ageexmed,*agecens;
   double fu,fv,fw,fx;  double dateintmean=0;
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double *weight;
   double e=0.0;  int **s; /* Status */
    double *agedc, **covar, idx;
   a=(ax < cx ? ax : cx);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   b=(ax > cx ? ax : cx);  double *lsurv, *lpop, *tpop;
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   for (iter=1;iter<=ITMAX;iter++) {  double ftolhess; /* Tolerance for computing hessian */
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /**************** split *************************/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     printf(".");fflush(stdout);  {
     fprintf(ficlog,".");fflush(ficlog);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 #ifdef DEBUG       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     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);    */ 
     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);    char  *ss;                            /* pointer */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    int   l1, l2;                         /* length counters */
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    l1 = strlen(path );                   /* length of path */
       *xmin=x;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       return fx;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     ftemp=fu;      strcpy( name, path );               /* we got the fullname name because no directory */
     if (fabs(e) > tol1) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       r=(x-w)*(fx-fv);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       q=(x-v)*(fx-fw);      /* get current working directory */
       p=(x-v)*q-(x-w)*r;      /*    extern  char* getcwd ( char *buf , int len);*/
       q=2.0*(q-r);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       if (q > 0.0) p = -p;        return( GLOCK_ERROR_GETCWD );
       q=fabs(q);      }
       etemp=e;      /* got dirc from getcwd*/
       e=d;      printf(" DIRC = %s \n",dirc);
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    } else {                              /* strip direcotry from path */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      ss++;                               /* after this, the filename */
       else {      l2 = strlen( ss );                  /* length of filename */
         d=p/q;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         u=x+d;      strcpy( name, ss );         /* save file name */
         if (u-a < tol2 || b-u < tol2)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
           d=SIGN(tol1,xm-x);      dirc[l1-l2] = 0;                    /* add zero */
       }      printf(" DIRC2 = %s \n",dirc);
     } else {    }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    /* We add a separator at the end of dirc if not exists */
     }    l1 = strlen( dirc );                  /* length of directory */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    if( dirc[l1-1] != DIRSEPARATOR ){
     fu=(*f)(u);      dirc[l1] =  DIRSEPARATOR;
     if (fu <= fx) {      dirc[l1+1] = 0; 
       if (u >= x) a=x; else b=x;      printf(" DIRC3 = %s \n",dirc);
       SHFT(v,w,x,u)    }
         SHFT(fv,fw,fx,fu)    ss = strrchr( name, '.' );            /* find last / */
         } else {    if (ss >0){
           if (u < x) a=u; else b=u;      ss++;
           if (fu <= fw || w == x) {      strcpy(ext,ss);                     /* save extension */
             v=w;      l1= strlen( name);
             w=u;      l2= strlen(ss)+1;
             fv=fw;      strncpy( finame, name, l1-l2);
             fw=fu;      finame[l1-l2]= 0;
           } else if (fu <= fv || v == x || v == w) {    }
             v=u;  
             fv=fu;    return( 0 );                          /* we're done */
           }  }
         }  
   }  
   nrerror("Too many iterations in brent");  /******************************************/
   *xmin=x;  
   return fx;  void replace_back_to_slash(char *s, char*t)
 }  {
     int i;
 /****************** mnbrak ***********************/    int lg=0;
     i=0;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    lg=strlen(t);
             double (*func)(double))    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   double ulim,u,r,q, dum;      if (t[i]== '\\') s[i]='/';
   double fu;    }
    }
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  int nbocc(char *s, char occ)
   if (*fb > *fa) {  {
     SHFT(dum,*ax,*bx,dum)    int i,j=0;
       SHFT(dum,*fb,*fa,dum)    int lg=20;
       }    i=0;
   *cx=(*bx)+GOLD*(*bx-*ax);    lg=strlen(s);
   *fc=(*func)(*cx);    for(i=0; i<= lg; i++) {
   while (*fb > *fc) {    if  (s[i] == occ ) j++;
     r=(*bx-*ax)*(*fb-*fc);    }
     q=(*bx-*cx)*(*fb-*fa);    return j;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  }
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  void cutv(char *u,char *v, char*t, char occ)
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     } else if ((*cx-u)*(u-ulim) > 0.0) {       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       fu=(*func)(u);       gives u="abcedf" and v="ghi2j" */
       if (fu < *fc) {    int i,lg,j,p=0;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    i=0;
           SHFT(*fb,*fc,fu,(*func)(u))    for(j=0; j<=strlen(t)-1; j++) {
           }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    }
       u=ulim;  
       fu=(*func)(u);    lg=strlen(t);
     } else {    for(j=0; j<p; j++) {
       u=(*cx)+GOLD*(*cx-*bx);      (u[j] = t[j]);
       fu=(*func)(u);    }
     }       u[p]='\0';
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)     for(j=0; j<= lg; j++) {
       }      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /*************** linmin ************************/  
   /********************** nrerror ********************/
 int ncom;  
 double *pcom,*xicom;  void nrerror(char error_text[])
 double (*nrfunc)(double []);  {
      fprintf(stderr,"ERREUR ...\n");
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    fprintf(stderr,"%s\n",error_text);
 {    exit(EXIT_FAILURE);
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  /*********************** vector *******************/
   double f1dim(double x);  double *vector(int nl, int nh)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  {
               double *fc, double (*func)(double));    double *v;
   int j;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double xx,xmin,bx,ax;    if (!v) nrerror("allocation failure in vector");
   double fx,fb,fa;    return v-nl+NR_END;
    }
   ncom=n;  
   pcom=vector(1,n);  /************************ free vector ******************/
   xicom=vector(1,n);  void free_vector(double*v, int nl, int nh)
   nrfunc=func;  {
   for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  
   }  /************************ivector *******************************/
   ax=0.0;  int *ivector(long nl,long nh)
   xx=1.0;  {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    int *v;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in ivector");
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    return v-nl+NR_END;
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  /******************free ivector **************************/
     xi[j] *= xmin;  void free_ivector(int *v, long nl, long nh)
     p[j] += xi[j];  {
   }    free((FREE_ARG)(v+nl-NR_END));
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 /*************** powell ************************/  {
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    long *v;
             double (*func)(double []))    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 {    if (!v) nrerror("allocation failure in ivector");
   void linmin(double p[], double xi[], int n, double *fret,    return v-nl+NR_END;
               double (*func)(double []));  }
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  /******************free lvector **************************/
   double fp,fptt;  void free_lvector(long *v, long nl, long nh)
   double *xits;  {
   pt=vector(1,n);    free((FREE_ARG)(v+nl-NR_END));
   ptt=vector(1,n);  }
   xit=vector(1,n);  
   xits=vector(1,n);  /******************* imatrix *******************************/
   *fret=(*func)(p);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for (j=1;j<=n;j++) pt[j]=p[j];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (*iter=1;;++(*iter)) {  { 
     fp=(*fret);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     ibig=0;    int **m; 
     del=0.0;    
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    /* allocate pointers to rows */ 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     for (i=1;i<=n;i++)    if (!m) nrerror("allocation failure 1 in matrix()"); 
       printf(" %d %.12f",i, p[i]);    m += NR_END; 
     fprintf(ficlog," %d %.12f",i, p[i]);    m -= nrl; 
     printf("\n");    
     fprintf(ficlog,"\n");    
     for (i=1;i<=n;i++) {    /* allocate rows and set pointers to them */ 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       fptt=(*fret);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 #ifdef DEBUG    m[nrl] += NR_END; 
       printf("fret=%lf \n",*fret);    m[nrl] -= ncl; 
       fprintf(ficlog,"fret=%lf \n",*fret);    
 #endif    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       printf("%d",i);fflush(stdout);    
       fprintf(ficlog,"%d",i);fflush(ficlog);    /* return pointer to array of pointers to rows */ 
       linmin(p,xit,n,fret,func);    return m; 
       if (fabs(fptt-(*fret)) > del) {  } 
         del=fabs(fptt-(*fret));  
         ibig=i;  /****************** free_imatrix *************************/
       }  void free_imatrix(m,nrl,nrh,ncl,nch)
 #ifdef DEBUG        int **m;
       printf("%d %.12e",i,(*fret));        long nch,ncl,nrh,nrl; 
       fprintf(ficlog,"%d %.12e",i,(*fret));       /* free an int matrix allocated by imatrix() */ 
       for (j=1;j<=n;j++) {  { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         printf(" x(%d)=%.12e",j,xit[j]);    free((FREE_ARG) (m+nrl-NR_END)); 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  } 
       }  
       for(j=1;j<=n;j++) {  /******************* matrix *******************************/
         printf(" p=%.12e",p[j]);  double **matrix(long nrl, long nrh, long ncl, long nch)
         fprintf(ficlog," p=%.12e",p[j]);  {
       }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       printf("\n");    double **m;
       fprintf(ficlog,"\n");  
 #endif    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m += NR_END;
 #ifdef DEBUG    m -= nrl;
       int k[2],l;  
       k[0]=1;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       k[1]=-1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       printf("Max: %.12e",(*func)(p));    m[nrl] += NR_END;
       fprintf(ficlog,"Max: %.12e",(*func)(p));    m[nrl] -= ncl;
       for (j=1;j<=n;j++) {  
         printf(" %.12e",p[j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         fprintf(ficlog," %.12e",p[j]);    return m;
       }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       printf("\n");     */
       fprintf(ficlog,"\n");  }
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /*************************free matrix ************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
           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]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         }    free((FREE_ARG)(m+nrl-NR_END));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  }
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /******************* ma3x *******************************/
 #endif  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       free_vector(xit,1,n);    double ***m;
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       free_vector(pt,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
       return;    m += NR_END;
     }    m -= nrl;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       ptt[j]=2.0*p[j]-pt[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       xit[j]=p[j]-pt[j];    m[nrl] += NR_END;
       pt[j]=p[j];    m[nrl] -= ncl;
     }  
     fptt=(*func)(ptt);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       if (t < 0.0) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         linmin(p,xit,n,fret,func);    m[nrl][ncl] += NR_END;
         for (j=1;j<=n;j++) {    m[nrl][ncl] -= nll;
           xi[j][ibig]=xi[j][n];    for (j=ncl+1; j<=nch; j++) 
           xi[j][n]=xit[j];      m[nrl][j]=m[nrl][j-1]+nlay;
         }    
 #ifdef DEBUG    for (i=nrl+1; i<=nrh; i++) {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      for (j=ncl+1; j<=nch; j++) 
         for(j=1;j<=n;j++){        m[i][j]=m[i][j-1]+nlay;
           printf(" %.12e",xit[j]);    }
           fprintf(ficlog," %.12e",xit[j]);    return m; 
         }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         printf("\n");             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         fprintf(ficlog,"\n");    */
 #endif  }
       }  
     }  /*************************free ma3x ************************/
   }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 /**** Prevalence limit ****************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  }
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /*************** function subdirf ***********/
      matrix by transitions matrix until convergence is reached */  char *subdirf(char fileres[])
   {
   int i, ii,j,k;    /* Caution optionfilefiname is hidden */
   double min, max, maxmin, maxmax,sumnew=0.;    strcpy(tmpout,optionfilefiname);
   double **matprod2();    strcat(tmpout,"/"); /* Add to the right */
   double **out, cov[NCOVMAX], **pmij();    strcat(tmpout,fileres);
   double **newm;    return tmpout;
   double agefin, delaymax=50 ; /* Max number of years to converge */  }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /*************** function subdirf2 ***********/
     for (j=1;j<=nlstate+ndeath;j++){  char *subdirf2(char fileres[], char *preop)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
     }    
     /* Caution optionfilefiname is hidden */
    cov[1]=1.;    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/");
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,preop);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    strcat(tmpout,fileres);
     newm=savm;    return tmpout;
     /* Covariates have to be included here again */  }
      cov[2]=agefin;  
    /*************** function subdirf3 ***********/
       for (k=1; k<=cptcovn;k++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
         /*      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]]);*/    
       }    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcpy(tmpout,optionfilefiname);
       for (k=1; k<=cptcovprod;k++)    strcat(tmpout,"/");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,preop);
     strcat(tmpout,preop2);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    strcat(tmpout,fileres);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    return tmpout;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   /***************** f1dim *************************/
     savm=oldm;  extern int ncom; 
     oldm=newm;  extern double *pcom,*xicom;
     maxmax=0.;  extern double (*nrfunc)(double []); 
     for(j=1;j<=nlstate;j++){   
       min=1.;  double f1dim(double x) 
       max=0.;  { 
       for(i=1; i<=nlstate; i++) {    int j; 
         sumnew=0;    double f;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double *xt; 
         prlim[i][j]= newm[i][j]/(1-sumnew);   
         max=FMAX(max,prlim[i][j]);    xt=vector(1,ncom); 
         min=FMIN(min,prlim[i][j]);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
       maxmin=max-min;    free_vector(xt,1,ncom); 
       maxmax=FMAX(maxmax,maxmin);    return f; 
     }  } 
     if(maxmax < ftolpl){  
       return prlim;  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   }  { 
 }    int iter; 
     double a,b,d,etemp;
 /*************** transition probabilities ***************/    double fu,fv,fw,fx;
     double ftemp;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 {    double e=0.0; 
   double s1, s2;   
   /*double t34;*/    a=(ax < cx ? ax : cx); 
   int i,j,j1, nc, ii, jj;    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
     for(i=1; i<= nlstate; i++){    fw=fv=fx=(*f)(x); 
     for(j=1; j<i;j++){    for (iter=1;iter<=ITMAX;iter++) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      xm=0.5*(a+b); 
         /*s2 += param[i][j][nc]*cov[nc];*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
       ps[i][j]=s2;  #ifdef DEBUG
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      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);
     }      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);
     for(j=i+1; j<=nlstate+ndeath;j++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #endif
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        *xmin=x; 
       }        return fx; 
       ps[i][j]=s2;      } 
     }      ftemp=fu;
   }      if (fabs(e) > tol1) { 
     /*ps[3][2]=1;*/        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
   for(i=1; i<= nlstate; i++){        p=(x-v)*q-(x-w)*r; 
      s1=0;        q=2.0*(q-r); 
     for(j=1; j<i; j++)        if (q > 0.0) p = -p; 
       s1+=exp(ps[i][j]);        q=fabs(q); 
     for(j=i+1; j<=nlstate+ndeath; j++)        etemp=e; 
       s1+=exp(ps[i][j]);        e=d; 
     ps[i][i]=1./(s1+1.);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for(j=1; j<i; j++)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        else { 
     for(j=i+1; j<=nlstate+ndeath; j++)          d=p/q; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          u=x+d; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          if (u-a < tol2 || b-u < tol2) 
   } /* end i */            d=SIGN(tol1,xm-x); 
         } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      } else { 
     for(jj=1; jj<= nlstate+ndeath; jj++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ps[ii][jj]=0;      } 
       ps[ii][ii]=1;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     }      fu=(*f)(u); 
   }      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          SHFT(fv,fw,fx,fu) 
     for(jj=1; jj<= nlstate+ndeath; jj++){          } else { 
      printf("%lf ",ps[ii][jj]);            if (u < x) a=u; else b=u; 
    }            if (fu <= fw || w == x) { 
     printf("\n ");              v=w; 
     }              w=u; 
     printf("\n ");printf("%lf ",cov[2]);*/              fv=fw; 
 /*              fw=fu; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);            } else if (fu <= fv || v == x || v == w) { 
   goto end;*/              v=u; 
     return ps;              fv=fu; 
 }            } 
           } 
 /**************** Product of 2 matrices ******************/    } 
     nrerror("Too many iterations in brent"); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    *xmin=x; 
 {    return fx; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  /****************** mnbrak ***********************/
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   long i, j, k;              double (*func)(double)) 
   for(i=nrl; i<= nrh; i++)  { 
     for(k=ncolol; k<=ncoloh; k++)    double ulim,u,r,q, dum;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    double fu; 
         out[i][k] +=in[i][j]*b[j][k];   
     *fa=(*func)(*ax); 
   return out;    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
 /************* Higher Matrix Product ***************/        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    *fc=(*func)(*cx); 
 {    while (*fb > *fc) { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      r=(*bx-*ax)*(*fb-*fc); 
      duration (i.e. until      q=(*bx-*cx)*(*fb-*fa); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
      (typically every 2 years instead of every month which is too big).      ulim=(*bx)+GLIMIT*(*cx-*bx); 
      Model is determined by parameters x and covariates have to be      if ((*bx-u)*(u-*cx) > 0.0) { 
      included manually here.        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
      */        fu=(*func)(u); 
         if (fu < *fc) { 
   int i, j, d, h, k;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double **out, cov[NCOVMAX];            SHFT(*fb,*fc,fu,(*func)(u)) 
   double **newm;            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   /* Hstepm could be zero and should return the unit matrix */        u=ulim; 
   for (i=1;i<=nlstate+ndeath;i++)        fu=(*func)(u); 
     for (j=1;j<=nlstate+ndeath;j++){      } else { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        u=(*cx)+GOLD*(*cx-*bx); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        fu=(*func)(u); 
     }      } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      SHFT(*ax,*bx,*cx,u) 
   for(h=1; h <=nhstepm; h++){        SHFT(*fa,*fb,*fc,fu) 
     for(d=1; d <=hstepm; d++){        } 
       newm=savm;  } 
       /* Covariates have to be included here again */  
       cov[1]=1.;  /*************** linmin ************************/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  int ncom; 
       for (k=1; k<=cptcovage;k++)  double *pcom,*xicom;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  double (*nrfunc)(double []); 
       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]]];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
     double brent(double ax, double bx, double cx, 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/                 double (*f)(double), double tol, double *xmin); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double f1dim(double x); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));                double *fc, double (*func)(double)); 
       savm=oldm;    int j; 
       oldm=newm;    double xx,xmin,bx,ax; 
     }    double fx,fb,fa;
     for(i=1; i<=nlstate+ndeath; i++)   
       for(j=1;j<=nlstate+ndeath;j++) {    ncom=n; 
         po[i][j][h]=newm[i][j];    pcom=vector(1,n); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    xicom=vector(1,n); 
          */    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
   } /* end h */      pcom[j]=p[j]; 
   return po;      xicom[j]=xi[j]; 
 }    } 
     ax=0.0; 
     xx=1.0; 
 /*************** log-likelihood *************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 double func( double *x)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 {  #ifdef DEBUG
   int i, ii, j, k, mi, d, kk;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double **out;  #endif
   double sw; /* Sum of weights */    for (j=1;j<=n;j++) { 
   double lli; /* Individual log likelihood */      xi[j] *= xmin; 
   long ipmx;      p[j] += xi[j]; 
   /*extern weight */    } 
   /* We are differentiating ll according to initial status */    free_vector(xicom,1,n); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    free_vector(pcom,1,n); 
   /*for(i=1;i<imx;i++)  } 
     printf(" %d\n",s[4][i]);  
   */  char *asc_diff_time(long time_sec, char ascdiff[])
   cov[1]=1.;  {
     long sec_left, days, hours, minutes;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    days = (time_sec) / (60*60*24);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    sec_left = (time_sec) % (60*60*24);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    hours = (sec_left) / (60*60) ;
     for(mi=1; mi<= wav[i]-1; mi++){    sec_left = (sec_left) %(60*60);
       for (ii=1;ii<=nlstate+ndeath;ii++)    minutes = (sec_left) /60;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    sec_left = (sec_left) % (60);
       for(d=0; d<dh[mi][i]; d++){    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         newm=savm;    return ascdiff;
         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];  /*************** powell ************************/
         }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                      double (*func)(double [])) 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    void linmin(double p[], double xi[], int n, double *fret, 
         savm=oldm;                double (*func)(double [])); 
         oldm=newm;    int i,ibig,j; 
            double del,t,*pt,*ptt,*xit;
            double fp,fptt;
       } /* end mult */    double *xits;
          int niterf, itmp;
       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]]);*/    pt=vector(1,n); 
       ipmx +=1;    ptt=vector(1,n); 
       sw += weight[i];    xit=vector(1,n); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    xits=vector(1,n); 
     } /* end of wave */    *fret=(*func)(p); 
   } /* end of individual */    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      fp=(*fret); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      ibig=0; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      del=0.0; 
   return -l;      last_time=curr_time;
 }      (void) gettimeofday(&curr_time,&tzp);
       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);
 /*********** Maximum Likelihood Estimation ***************/      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))     for (i=1;i<=n;i++) {
 {        printf(" %d %.12f",i, p[i]);
   int i,j, iter;        fprintf(ficlog," %d %.12lf",i, p[i]);
   double **xi,*delti;        fprintf(ficrespow," %.12lf", p[i]);
   double fret;      }
   xi=matrix(1,npar,1,npar);      printf("\n");
   for (i=1;i<=npar;i++)      fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++)      fprintf(ficrespow,"\n");fflush(ficrespow);
       xi[i][j]=(i==j ? 1.0 : 0.0);      if(*iter <=3){
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        tm = *localtime(&curr_time.tv_sec);
   powell(p,xi,npar,ftol,&iter,&fret,func);        strcpy(strcurr,asctime(&tm));
   /*       asctime_r(&tm,strcurr); */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        forecast_time=curr_time; 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        itmp = strlen(strcurr);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
 }        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);
 /**** Computes Hessian and covariance matrix ***/        for(niterf=10;niterf<=30;niterf+=10){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
 {          tmf = *localtime(&forecast_time.tv_sec);
   double  **a,**y,*x,pd;  /*      asctime_r(&tmf,strfor); */
   double **hess;          strcpy(strfor,asctime(&tmf));
   int i, j,jk;          itmp = strlen(strfor);
   int *indx;          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
   double hessii(double p[], double delta, int theta, double delti[]);          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);
   double hessij(double p[], double delti[], int i, int j);          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);
   void lubksb(double **a, int npar, int *indx, double b[]) ;        }
   void ludcmp(double **a, int npar, int *indx, double *d) ;      }
       for (i=1;i<=n;i++) { 
   hess=matrix(1,npar,1,npar);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   printf("\nCalculation of the hessian matrix. Wait...\n");  #ifdef DEBUG
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");        printf("fret=%lf \n",*fret);
   for (i=1;i<=npar;i++){        fprintf(ficlog,"fret=%lf \n",*fret);
     printf("%d",i);fflush(stdout);  #endif
     fprintf(ficlog,"%d",i);fflush(ficlog);        printf("%d",i);fflush(stdout);
     hess[i][i]=hessii(p,ftolhess,i,delti);        fprintf(ficlog,"%d",i);fflush(ficlog);
     /*printf(" %f ",p[i]);*/        linmin(p,xit,n,fret,func); 
     /*printf(" %lf ",hess[i][i]);*/        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
            ibig=i; 
   for (i=1;i<=npar;i++) {        } 
     for (j=1;j<=npar;j++)  {  #ifdef DEBUG
       if (j>i) {        printf("%d %.12e",i,(*fret));
         printf(".%d%d",i,j);fflush(stdout);        fprintf(ficlog,"%d %.12e",i,(*fret));
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);        for (j=1;j<=n;j++) {
         hess[i][j]=hessij(p,delti,i,j);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         hess[j][i]=hess[i][j];              printf(" x(%d)=%.12e",j,xit[j]);
         /*printf(" %lf ",hess[i][j]);*/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
     }        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
   printf("\n");          fprintf(ficlog," p=%.12e",p[j]);
   fprintf(ficlog,"\n");        }
         printf("\n");
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        fprintf(ficlog,"\n");
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");  #endif
        } 
   a=matrix(1,npar,1,npar);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   y=matrix(1,npar,1,npar);  #ifdef DEBUG
   x=vector(1,npar);        int k[2],l;
   indx=ivector(1,npar);        k[0]=1;
   for (i=1;i<=npar;i++)        k[1]=-1;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        printf("Max: %.12e",(*func)(p));
   ludcmp(a,npar,indx,&pd);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   for (j=1;j<=npar;j++) {          printf(" %.12e",p[j]);
     for (i=1;i<=npar;i++) x[i]=0;          fprintf(ficlog," %.12e",p[j]);
     x[j]=1;        }
     lubksb(a,npar,indx,x);        printf("\n");
     for (i=1;i<=npar;i++){        fprintf(ficlog,"\n");
       matcov[i][j]=x[i];        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
   }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   printf("\n#Hessian matrix#\n");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   fprintf(ficlog,"\n#Hessian matrix#\n");          }
   for (i=1;i<=npar;i++) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (j=1;j<=npar;j++) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       printf("%.3e ",hess[i][j]);        }
       fprintf(ficlog,"%.3e ",hess[i][j]);  #endif
     }  
     printf("\n");  
     fprintf(ficlog,"\n");        free_vector(xit,1,n); 
   }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   /* Recompute Inverse */        free_vector(pt,1,n); 
   for (i=1;i<=npar;i++)        return; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      } 
   ludcmp(a,npar,indx,&pd);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   /*  printf("\n#Hessian matrix recomputed#\n");        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
   for (j=1;j<=npar;j++) {        pt[j]=p[j]; 
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      fptt=(*func)(ptt); 
     lubksb(a,npar,indx,x);      if (fptt < fp) { 
     for (i=1;i<=npar;i++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       y[i][j]=x[i];        if (t < 0.0) { 
       printf("%.3e ",y[i][j]);          linmin(p,xit,n,fret,func); 
       fprintf(ficlog,"%.3e ",y[i][j]);          for (j=1;j<=n;j++) { 
     }            xi[j][ibig]=xi[j][n]; 
     printf("\n");            xi[j][n]=xit[j]; 
     fprintf(ficlog,"\n");          }
   }  #ifdef DEBUG
   */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   free_matrix(a,1,npar,1,npar);          for(j=1;j<=n;j++){
   free_matrix(y,1,npar,1,npar);            printf(" %.12e",xit[j]);
   free_vector(x,1,npar);            fprintf(ficlog," %.12e",xit[j]);
   free_ivector(indx,1,npar);          }
   free_matrix(hess,1,npar,1,npar);          printf("\n");
           fprintf(ficlog,"\n");
   #endif
 }        }
       } 
 /*************** hessian matrix ****************/    } 
 double hessii( double x[], double delta, int theta, double delti[])  } 
 {  
   int i;  /**** Prevalence limit (stable or period prevalence)  ****************/
   int l=1, lmax=20;  
   double k1,k2;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double p2[NPARMAX+1];  {
   double res;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;       matrix by transitions matrix until convergence is reached */
   double fx;  
   int k=0,kmax=10;    int i, ii,j,k;
   double l1;    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   fx=func(x);    double **out, cov[NCOVMAX], **pmij();
   for (i=1;i<=npar;i++) p2[i]=x[i];    double **newm;
   for(l=0 ; l <=lmax; l++){    double agefin, delaymax=50 ; /* Max number of years to converge */
     l1=pow(10,l);  
     delts=delt;    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(k=1 ; k <kmax; k=k+1){      for (j=1;j<=nlstate+ndeath;j++){
       delt = delta*(l1*k);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       p2[theta]=x[theta] +delt;      }
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;     cov[1]=1.;
       k2=func(p2)-fx;   
       /*res= (k1-2.0*fx+k2)/delt/delt; */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
            newm=savm;
 #ifdef DEBUG      /* Covariates have to be included here again */
       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);       cov[2]=agefin;
       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        for (k=1; k<=cptcovn;k++) {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*      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]]);*/
         k=kmax;        }
       }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        for (k=1; k<=cptcovprod;k++)
         k=kmax; l=lmax*10.;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         delts=delt;        /*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]);*/
     }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
   delti[theta]=delts;      savm=oldm;
   return res;      oldm=newm;
        maxmax=0.;
 }      for(j=1;j<=nlstate;j++){
         min=1.;
 double hessij( double x[], double delti[], int thetai,int thetaj)        max=0.;
 {        for(i=1; i<=nlstate; i++) {
   int i;          sumnew=0;
   int l=1, l1, lmax=20;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   double k1,k2,k3,k4,res,fx;          prlim[i][j]= newm[i][j]/(1-sumnew);
   double p2[NPARMAX+1];          max=FMAX(max,prlim[i][j]);
   int k;          min=FMIN(min,prlim[i][j]);
         }
   fx=func(x);        maxmin=max-min;
   for (k=1; k<=2; k++) {        maxmax=FMAX(maxmax,maxmin);
     for (i=1;i<=npar;i++) p2[i]=x[i];      }
     p2[thetai]=x[thetai]+delti[thetai]/k;      if(maxmax < ftolpl){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        return prlim;
     k1=func(p2)-fx;      }
      }
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  /*************** transition probabilities ***************/ 
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  {
     k3=func(p2)-fx;    double s1, s2;
      /*double t34;*/
     p2[thetai]=x[thetai]-delti[thetai]/k;    int i,j,j1, nc, ii, jj;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;      for(i=1; i<= nlstate; i++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for(j=1; j<i;j++){
 #ifdef DEBUG          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     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);            /*s2 += param[i][j][nc]*cov[nc];*/
     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);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 #endif  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   }          }
   return res;          ps[i][j]=s2;
 }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         }
 /************** Inverse of matrix **************/        for(j=i+1; j<=nlstate+ndeath;j++){
 void ludcmp(double **a, int n, int *indx, double *d)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int i,imax,j,k;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   double big,dum,sum,temp;          }
   double *vv;          ps[i][j]=s2;
          }
   vv=vector(1,n);      }
   *d=1.0;      /*ps[3][2]=1;*/
   for (i=1;i<=n;i++) {      
     big=0.0;      for(i=1; i<= nlstate; i++){
     for (j=1;j<=n;j++)        s1=0;
       if ((temp=fabs(a[i][j])) > big) big=temp;        for(j=1; j<i; j++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          s1+=exp(ps[i][j]);
     vv[i]=1.0/big;        for(j=i+1; j<=nlstate+ndeath; j++)
   }          s1+=exp(ps[i][j]);
   for (j=1;j<=n;j++) {        ps[i][i]=1./(s1+1.);
     for (i=1;i<j;i++) {        for(j=1; j<i; j++)
       sum=a[i][j];          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        for(j=i+1; j<=nlstate+ndeath; j++)
       a[i][j]=sum;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     big=0.0;      } /* end i */
     for (i=j;i<=n;i++) {      
       sum=a[i][j];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for (k=1;k<j;k++)        for(jj=1; jj<= nlstate+ndeath; jj++){
         sum -= a[i][k]*a[k][j];          ps[ii][jj]=0;
       a[i][j]=sum;          ps[ii][ii]=1;
       if ( (dum=vv[i]*fabs(sum)) >= big) {        }
         big=dum;      }
         imax=i;      
       }  
     }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     if (j != imax) {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       for (k=1;k<=n;k++) {  /*         printf("ddd %lf ",ps[ii][jj]); */
         dum=a[imax][k];  /*       } */
         a[imax][k]=a[j][k];  /*       printf("\n "); */
         a[j][k]=dum;  /*        } */
       }  /*        printf("\n ");printf("%lf ",cov[2]); */
       *d = -(*d);         /*
       vv[imax]=vv[j];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     }        goto end;*/
     indx[j]=imax;      return ps;
     if (a[j][j] == 0.0) a[j][j]=TINY;  }
     if (j != n) {  
       dum=1.0/(a[j][j]);  /**************** Product of 2 matrices ******************/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   }  {
   free_vector(vv,1,n);  /* Doesn't work */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 ;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 }    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
 void lubksb(double **a, int n, int *indx, double b[])       a pointer to pointers identical to out */
 {    long i, j, k;
   int i,ii=0,ip,j;    for(i=nrl; i<= nrh; i++)
   double sum;      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
   for (i=1;i<=n;i++) {          out[i][k] +=in[i][j]*b[j][k];
     ip=indx[i];  
     sum=b[ip];    return out;
     b[ip]=b[i];  }
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  /************* Higher Matrix Product ***************/
     b[i]=sum;  
   }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   for (i=n;i>=1;i--) {  {
     sum=b[i];    /* Computes the transition matrix starting at age 'age' over 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];       'nhstepm*hstepm*stepm' months (i.e. until
     b[i]=sum/a[i][i];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   }       nhstepm*hstepm matrices. 
 }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
 /************ Frequencies ********************/       for the memory).
 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)       Model is determined by parameters x and covariates have to be 
 {  /* Some frequencies */       included manually here. 
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;       */
   int first;  
   double ***freq; /* Frequencies */    int i, j, d, h, k;
   double *pp;    double **out, cov[NCOVMAX];
   double pos, k2, dateintsum=0,k2cpt=0;    double **newm;
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
   pp=vector(1,nlstate);      for (j=1;j<=nlstate+ndeath;j++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   strcpy(fileresp,"p");        po[i][j][0]=(i==j ? 1.0 : 0.0);
   strcat(fileresp,fileres);      }
   if((ficresp=fopen(fileresp,"w"))==NULL) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     printf("Problem with prevalence resultfile: %s\n", fileresp);    for(h=1; h <=nhstepm; h++){
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      for(d=1; d <=hstepm; d++){
     exit(0);        newm=savm;
   }        /* Covariates have to be included here again */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        cov[1]=1.;
   j1=0;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   j=cptcoveff;        for (k=1; k<=cptcovage;k++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   first=1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       j1++;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         scanf("%d", i);*/                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (i=-1; i<=nlstate+ndeath; i++)          savm=oldm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)          oldm=newm;
           for(m=agemin; m <= agemax+3; m++)      }
             freq[i][jk][m]=0;      for(i=1; i<=nlstate+ndeath; i++)
              for(j=1;j<=nlstate+ndeath;j++) {
       dateintsum=0;          po[i][j][h]=newm[i][j];
       k2cpt=0;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       for (i=1; i<=imx; i++) {           */
         bool=1;        }
         if  (cptcovn>0) {    } /* end h */
           for (z1=1; z1<=cptcoveff; z1++)    return po;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  }
               bool=0;  
         }  
         if (bool==1) {  /*************** log-likelihood *************/
           for(m=firstpass; m<=lastpass; m++){  double func( double *x)
             k2=anint[m][i]+(mint[m][i]/12.);  {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    int i, ii, j, k, mi, d, kk;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double **out;
               if (m<lastpass) {    double sw; /* Sum of weights */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double lli; /* Individual log likelihood */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    int s1, s2;
               }    double bbh, survp;
                  long ipmx;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    /*extern weight */
                 dateintsum=dateintsum+k2;    /* We are differentiating ll according to initial status */
                 k2cpt++;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
               }    /*for(i=1;i<imx;i++) 
             }      printf(" %d\n",s[4][i]);
           }    */
         }    cov[1]=1.;
       }  
            for(k=1; k<=nlstate; k++) ll[k]=0.;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
     if(mle==1){
       if  (cptcovn>0) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficresp, "\n#********** Variable ");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(mi=1; mi<= wav[i]-1; mi++){
         fprintf(ficresp, "**********\n#");          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresp, "\n");            }
                for(d=0; d<dh[mi][i]; d++){
       for(i=(int)agemin; i <= (int)agemax+3; i++){            newm=savm;
         if(i==(int)agemax+3){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           fprintf(ficlog,"Total");            for (kk=1; kk<=cptcovage;kk++) {
         }else{              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if(first==1){            }
             first=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             printf("See log file for details...\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }            savm=oldm;
           fprintf(ficlog,"Age %d", i);            oldm=newm;
         }          } /* end mult */
         for(jk=1; jk <=nlstate ; jk++){        
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             pp[jk] += freq[jk][m][i];          /* 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 
         for(jk=1; jk <=nlstate ; jk++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
           for(m=-1, pos=0; m <=0 ; m++)           * the nearest (and in case of equal distance, to the lowest) interval but now
             pos += freq[jk][m][i];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           if(pp[jk]>=1.e-10){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
             if(first==1){           * probability in order to take into account the bias as a fraction of the way
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
             }           * -stepm/2 to stepm/2 .
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);           * For stepm=1 the results are the same as for previous versions of Imach.
           }else{           * For stepm > 1 the results are less biased than in previous versions. 
             if(first==1)           */
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          s1=s[mw[mi][i]][i];
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          s2=s[mw[mi+1][i]][i];
           }          bbh=(double)bh[mi][i]/(double)stepm; 
         }          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
         for(jk=1; jk <=nlstate ; jk++){           */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
             pp[jk] += freq[jk][m][i];          if( s2 > nlstate){ 
         }            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
         for(jk=1,pos=0; jk <=nlstate ; jk++)               die between last step unit time and current  step unit time, 
           pos += pp[jk];               which is also equal to probability to die before dh 
         for(jk=1; jk <=nlstate ; jk++){               minus probability to die before dh-stepm . 
           if(pos>=1.e-5){               In version up to 0.92 likelihood was computed
             if(first==1)          as if date of death was unknown. Death was treated as any other
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          health state: the date of the interview describes the actual state
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          and not the date of a change in health state. The former idea was
           }else{          to consider that at each interview the state was recorded
             if(first==1)          (healthy, disable or death) and IMaCh was corrected; but when we
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          introduced the exact date of death then we should have modified
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          the contribution of an exact death to the likelihood. This new
           }          contribution is smaller and very dependent of the step unit
           if( i <= (int) agemax){          stepm. It is no more the probability to die between last interview
             if(pos>=1.e-5){          and month of death but the probability to survive from last
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          interview up to one month before death multiplied by the
               probs[i][jk][j1]= pp[jk]/pos;          probability to die within a month. Thanks to Chris
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          Jackson for correcting this bug.  Former versions increased
             }          mortality artificially. The bad side is that we add another loop
             else          which slows down the processing. The difference can be up to 10%
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          lower mortality.
           }            */
         }            lli=log(out[s1][s2] - savm[s1][s2]);
          
         for(jk=-1; jk <=nlstate+ndeath; jk++)  
           for(m=-1; m <=nlstate+ndeath; m++)          } else if  (s2==-2) {
             if(freq[jk][m][i] !=0 ) {            for (j=1,survp=0. ; j<=nlstate; j++) 
             if(first==1)              survp += out[s1][j];
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            lli= survp;
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          }
             }          
         if(i <= (int) agemax)          else if  (s2==-4) {
           fprintf(ficresp,"\n");            for (j=3,survp=0. ; j<=nlstate; j++) 
         if(first==1)              survp += out[s1][j];
           printf("Others in log...\n");            lli= survp;
         fprintf(ficlog,"\n");          }
       }          
     }          else if  (s2==-5) {
   }            for (j=1,survp=0. ; j<=2; j++) 
   dateintmean=dateintsum/k2cpt;              survp += out[s1][j];
              lli= survp;
   fclose(ficresp);          }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  
            else{
   /* End of Freq */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 }            /*  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 */
           } 
 /************ Prevalence ********************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 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)          /*if(lli ==000.0)*/
 {  /* Some frequencies */          /*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;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          sw += weight[i];
   double ***freq; /* Frequencies */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *pp;        } /* end of wave */
   double pos, k2;      } /* end of individual */
     }  else if(mle==2){
   pp=vector(1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          for (ii=1;ii<=nlstate+ndeath;ii++)
   j1=0;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j=cptcoveff;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            }
            for(d=0; d<=dh[mi][i]; d++){
   for(k1=1; k1<=j;k1++){            newm=savm;
     for(i1=1; i1<=ncodemax[k1];i1++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       j1++;            for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (i=-1; i<=nlstate+ndeath; i++)              }
         for (jk=-1; jk<=nlstate+ndeath; jk++)              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(m=agemin; m <= agemax+3; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             freq[i][jk][m]=0;            savm=oldm;
                  oldm=newm;
       for (i=1; i<=imx; i++) {          } /* end mult */
         bool=1;        
         if  (cptcovn>0) {          s1=s[mw[mi][i]][i];
           for (z1=1; z1<=cptcoveff; z1++)          s2=s[mw[mi+1][i]][i];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          bbh=(double)bh[mi][i]/(double)stepm; 
               bool=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 */
         }          ipmx +=1;
         if (bool==1) {          sw += weight[i];
           for(m=firstpass; m<=lastpass; m++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             k2=anint[m][i]+(mint[m][i]/12.);        } /* end of wave */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      } /* end of individual */
               if(agev[m][i]==0) agev[m][i]=agemax+1;    }  else if(mle==3){  /* exponential inter-extrapolation */
               if(agev[m][i]==1) agev[m][i]=agemax+2;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               if (m<lastpass) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                 if (calagedate>0)        for(mi=1; mi<= wav[i]-1; mi++){
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
                 else            for (j=1;j<=nlstate+ndeath;j++){
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               }            }
             }          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){            }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
         for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
           for(m=-1, pos=0; m <=0 ; m++)          } /* end mult */
             pos += freq[jk][m][i];        
         }          s1=s[mw[mi][i]][i];
                  s2=s[mw[mi+1][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          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 */
             pp[jk] += freq[jk][m][i];          ipmx +=1;
         }          sw += weight[i];
                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        } /* end of wave */
              } /* end of individual */
         for(jk=1; jk <=nlstate ; jk++){        }else if (mle==4){  /* ml=4 no inter-extrapolation */
           if( i <= (int) agemax){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             if(pos>=1.e-5){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               probs[i][jk][j1]= pp[jk]/pos;        for(mi=1; mi<= wav[i]-1; mi++){
             }          for (ii=1;ii<=nlstate+ndeath;ii++)
           }            for (j=1;j<=nlstate+ndeath;j++){
         }/* end jk */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }/* end i */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     } /* end i1 */            }
   } /* end k1 */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            for (kk=1; kk<=cptcovage;kk++) {
   free_vector(pp,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
 }  /* End of Freq */          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************* Waves Concatenation ***************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            oldm=newm;
 {          } /* end mult */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        
      Death is a valid wave (if date is known).          s1=s[mw[mi][i]][i];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          s2=s[mw[mi+1][i]][i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          if( s2 > nlstate){ 
      and mw[mi+1][i]. dh depends on stepm.            lli=log(out[s1][s2] - savm[s1][s2]);
      */          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   int i, mi, m;          }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          ipmx +=1;
      double sum=0., jmean=0.;*/          sw += weight[i];
   int first;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int j, k=0,jk, ju, jl;  /*      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]); */
   double sum=0.;        } /* end of wave */
   first=0;      } /* end of individual */
   jmin=1e+5;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   jmax=-1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   jmean=0.;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(i=1; i<=imx; i++){        for(mi=1; mi<= wav[i]-1; mi++){
     mi=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
     m=firstpass;            for (j=1;j<=nlstate+ndeath;j++){
     while(s[m][i] <= nlstate){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(s[m][i]>=1)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         mw[++mi][i]=m;            }
       if(m >=lastpass)          for(d=0; d<dh[mi][i]; d++){
         break;            newm=savm;
       else            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         m++;            for (kk=1; kk<=cptcovage;kk++) {
     }/* end while */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (s[m][i] > nlstate){            }
       mi++;     /* Death is another wave */          
       /* if(mi==0)  never been interviewed correctly before death */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          /* Only death is a correct wave */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       mw[mi][i]=m;            savm=oldm;
     }            oldm=newm;
           } /* end mult */
     wav[i]=mi;        
     if(mi==0){          s1=s[mw[mi][i]][i];
       if(first==0){          s2=s[mw[mi+1][i]][i];
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         first=1;          ipmx +=1;
       }          sw += weight[i];
       if(first==1){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],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]);*/
       }        } /* end of wave */
     } /* end mi==0 */      } /* end of individual */
   }    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for(i=1; i<=imx; i++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for(mi=1; mi<wav[i];mi++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       if (stepm <=0)    return -l;
         dh[mi][i]=1;  }
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {  /*************** log-likelihood *************/
           if (agedc[i] < 2*AGESUP) {  double funcone( double *x)
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  {
           if(j==0) j=1;  /* Survives at least one month after exam */    /* Same as likeli but slower because of a lot of printf and if */
           k=k+1;    int i, ii, j, k, mi, d, kk;
           if (j >= jmax) jmax=j;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           if (j <= jmin) jmin=j;    double **out;
           sum=sum+j;    double lli; /* Individual log likelihood */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    double llt;
           }    int s1, s2;
         }    double bbh, survp;
         else{    /*extern weight */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    /* We are differentiating ll according to initial status */
           k=k+1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           if (j >= jmax) jmax=j;    /*for(i=1;i<imx;i++) 
           else if (j <= jmin)jmin=j;      printf(" %d\n",s[4][i]);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    */
           sum=sum+j;    cov[1]=1.;
         }  
         jk= j/stepm;    for(k=1; k<=nlstate; k++) ll[k]=0.;
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if(jl <= -ju)      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           dh[mi][i]=jk;      for(mi=1; mi<= wav[i]-1; mi++){
         else        for (ii=1;ii<=nlstate+ndeath;ii++)
           dh[mi][i]=jk+1;          for (j=1;j<=nlstate+ndeath;j++){
         if(dh[mi][i]==0)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=1; /* At least one step */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }          }
     }        for(d=0; d<dh[mi][i]; d++){
   }          newm=savm;
   jmean=sum/k;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
  }          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /*********** Tricode ****************************/                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void tricode(int *Tvar, int **nbcode, int imx)          savm=oldm;
 {          oldm=newm;
   int Ndum[20],ij=1, k, j, i;        } /* end mult */
   int cptcode=0;        
   cptcoveff=0;        s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
   for (k=0; k<19; k++) Ndum[k]=0;        bbh=(double)bh[mi][i]/(double)stepm; 
   for (k=1; k<=7; k++) ncodemax[k]=0;        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {         */
     for (i=1; i<=imx; i++) {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       ij=(int)(covar[Tvar[j]][i]);          lli=log(out[s1][s2] - savm[s1][s2]);
       Ndum[ij]++;        } else if (mle==1){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       if (ij > cptcode) cptcode=ij;        } else if(mle==2){
     }          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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
     for (i=0; i<=cptcode; i++) {          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 */
       if(Ndum[i]!=0) ncodemax[j]++;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     }          lli=log(out[s1][s2]); /* Original formula */
     ij=1;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
     for (i=1; i<=ncodemax[j]; i++) {        ipmx +=1;
       for (k=0; k<=19; k++) {        sw += weight[i];
         if (Ndum[k] != 0) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           nbcode[Tvar[j]][ij]=k;  /*       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]); */
                  if(globpr){
           ij++;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
         if (ij > ncodemax[j]) break;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       }                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   }              llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
  for (k=0; k<19; k++) Ndum[k]=0;          }
           fprintf(ficresilk," %10.6f\n", -llt);
  for (i=1; i<=ncovmodel-2; i++) {        }
    ij=Tvar[i];      } /* end of wave */
    Ndum[ij]++;    } /* end of individual */
  }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  ij=1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  for (i=1; i<=10; i++) {    if(globpr==0){ /* First time we count the contributions and weights */
    if((Ndum[i]!=0) && (i<=ncovcol)){      gipmx=ipmx;
      Tvaraff[ij]=i;      gsw=sw;
      ij++;    }
    }    return -l;
  }  }
    
  cptcoveff=ij-1;  
 }  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 /*********** Health Expectancies ****************/  {
     /* This routine should help understanding what is done with 
 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 )       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
 {       Plotting could be done.
   /* Health expectancies */     */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    int k;
   double age, agelim, hf;  
   double ***p3mat,***varhe;    if(*globpri !=0){ /* Just counts and sums, no printings */
   double **dnewm,**doldm;      strcpy(fileresilk,"ilk"); 
   double *xp;      strcat(fileresilk,fileres);
   double **gp, **gm;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double ***gradg, ***trgradg;        printf("Problem with resultfile: %s\n", fileresilk);
   int theta;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);      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");
   xp=vector(1,npar);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   dnewm=matrix(1,nlstate*2,1,npar);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   doldm=matrix(1,nlstate*2,1,nlstate*2);      for(k=1; k<=nlstate; k++) 
          fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficreseij,"# Health expectancies\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   fprintf(ficreseij,"# Age");    }
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    *fretone=(*funcone)(p);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    if(*globpri !=0){
   fprintf(ficreseij,"\n");      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   if(estepm < stepm){      fflush(fichtm); 
     printf ("Problem %d lower than %d\n",estepm, stepm);    } 
   }    return;
   else  hstepm=estepm;    }
   /* We compute the life expectancy from trapezoids spaced every estepm months  
    * 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  /*********** Maximum Likelihood Estimation ***************/
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    * to the curvature of the survival function. If, for the same date, we  {
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    int i,j, iter;
    * to compare the new estimate of Life expectancy with the same linear    double **xi;
    * hypothesis. A more precise result, taking into account a more precise    double fret;
    * curvature will be obtained if estepm is as small as stepm. */    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   /* For example we decided to compute the life expectancy with the smallest unit */    xi=matrix(1,npar,1,npar);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    for (i=1;i<=npar;i++)
      nhstepm is the number of hstepm from age to agelim      for (j=1;j<=npar;j++)
      nstepm is the number of stepm from age to agelin.        xi[i][j]=(i==j ? 1.0 : 0.0);
      Look at hpijx to understand the reason of that which relies in memory size    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      and note for a fixed period like estepm months */    strcpy(filerespow,"pow"); 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    strcat(filerespow,fileres);
      survival function given by stepm (the optimization length). Unfortunately it    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      means that if the survival funtion is printed only each two years of age and if      printf("Problem with resultfile: %s\n", filerespow);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      results. So we changed our mind and took the option of the best precision.    }
   */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
   agelim=AGESUP;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fprintf(ficrespow,"\n");
     /* nhstepm age range expressed in number of stepm */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    powell(p,xi,npar,ftol,&iter,&fret,func);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  
     /* if (stepm >= YEARM) hstepm=1;*/    free_matrix(xi,1,npar,1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fclose(ficrespow);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     gp=matrix(0,nhstepm,1,nlstate*2);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     gm=matrix(0,nhstepm,1,nlstate*2);  
   }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  /**** Computes Hessian and covariance matrix ***/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
     double  **a,**y,*x,pd;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double **hess;
     int i, j,jk;
     /* Computing Variances of health expectancies */    int *indx;
   
      for(theta=1; theta <=npar; theta++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(i=1; i<=npar; i++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    void lubksb(double **a, int npar, int *indx, double b[]) ;
       }    void ludcmp(double **a, int npar, int *indx, double *d) ;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double gompertz(double p[]);
      hess=matrix(1,npar,1,npar);
       cptj=0;  
       for(j=1; j<= nlstate; j++){    printf("\nCalculation of the hessian matrix. Wait...\n");
         for(i=1; i<=nlstate; i++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           cptj=cptj+1;    for (i=1;i<=npar;i++){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      printf("%d",i);fflush(stdout);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      fprintf(ficlog,"%d",i);fflush(ficlog);
           }     
         }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       }      
            /*  printf(" %f ",p[i]);
                printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       for(i=1; i<=npar; i++)    }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (i=1;i<=npar;i++) {
            for (j=1;j<=npar;j++)  {
       cptj=0;        if (j>i) { 
       for(j=1; j<= nlstate; j++){          printf(".%d%d",i,j);fflush(stdout);
         for(i=1;i<=nlstate;i++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           cptj=cptj+1;          hess[i][j]=hessij(p,delti,i,j,func,npar);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          hess[j][i]=hess[i][j];    
           }          /*printf(" %lf ",hess[i][j]);*/
         }        }
       }      }
       for(j=1; j<= nlstate*2; j++)    }
         for(h=0; h<=nhstepm-1; h++){    printf("\n");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fprintf(ficlog,"\n");
         }  
      }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 /* End theta */    
     a=matrix(1,npar,1,npar);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
      for(h=0; h<=nhstepm-1; h++)    indx=ivector(1,npar);
       for(j=1; j<=nlstate*2;j++)    for (i=1;i<=npar;i++)
         for(theta=1; theta <=npar; theta++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           trgradg[h][j][theta]=gradg[h][theta][j];    ludcmp(a,npar,indx,&pd);
        
     for (j=1;j<=npar;j++) {
      for(i=1;i<=nlstate*2;i++)      for (i=1;i<=npar;i++) x[i]=0;
       for(j=1;j<=nlstate*2;j++)      x[j]=1;
         varhe[i][j][(int)age] =0.;      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
      printf("%d|",(int)age);fflush(stdout);        matcov[i][j]=x[i];
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      }
      for(h=0;h<=nhstepm-1;h++){    }
       for(k=0;k<=nhstepm-1;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    printf("\n#Hessian matrix#\n");
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    fprintf(ficlog,"\n#Hessian matrix#\n");
         for(i=1;i<=nlstate*2;i++)    for (i=1;i<=npar;i++) { 
           for(j=1;j<=nlstate*2;j++)      for (j=1;j<=npar;j++) { 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        printf("%.3e ",hess[i][j]);
       }        fprintf(ficlog,"%.3e ",hess[i][j]);
     }      }
     /* Computing expectancies */      printf("\n");
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
       for(j=1; j<=nlstate;j++)    }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    /* Recompute Inverse */
              for (i=1;i<=npar;i++)
 /* 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]);*/      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
         }  
     /*  printf("\n#Hessian matrix recomputed#\n");
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;    for (j=1;j<=npar;j++) {
     for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++) x[i]=0;
       for(j=1; j<=nlstate;j++){      x[j]=1;
         cptj++;      lubksb(a,npar,indx,x);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      for (i=1;i<=npar;i++){ 
       }        y[i][j]=x[i];
     fprintf(ficreseij,"\n");        printf("%.3e ",y[i][j]);
            fprintf(ficlog,"%.3e ",y[i][j]);
     free_matrix(gm,0,nhstepm,1,nlstate*2);      }
     free_matrix(gp,0,nhstepm,1,nlstate*2);      printf("\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      fprintf(ficlog,"\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    */
   }  
   printf("\n");    free_matrix(a,1,npar,1,npar);
   fprintf(ficlog,"\n");    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   free_vector(xp,1,npar);    free_ivector(indx,1,npar);
   free_matrix(dnewm,1,nlstate*2,1,npar);    free_matrix(hess,1,npar,1,npar);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  
 }  }
   
 /************ Variance ******************/  /*************** hessian matrix ****************/
 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)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  {
   /* Variance of health expectancies */    int i;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int l=1, lmax=20;
   /* double **newm;*/    double k1,k2;
   double **dnewm,**doldm;    double p2[NPARMAX+1];
   double **dnewmp,**doldmp;    double res;
   int i, j, nhstepm, hstepm, h, nstepm ;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   int k, cptcode;    double fx;
   double *xp;    int k=0,kmax=10;
   double **gp, **gm;  /* for var eij */    double l1;
   double ***gradg, ***trgradg; /*for var eij */  
   double **gradgp, **trgradgp; /* for var p point j */    fx=func(x);
   double *gpp, *gmp; /* for var p point j */    for (i=1;i<=npar;i++) p2[i]=x[i];
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    for(l=0 ; l <=lmax; l++){
   double ***p3mat;      l1=pow(10,l);
   double age,agelim, hf;      delts=delt;
   int theta;      for(k=1 ; k <kmax; k=k+1){
   char digit[4];        delt = delta*(l1*k);
   char digitp[16];        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
   char fileresprobmorprev[FILENAMELENGTH];        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
   if(popbased==1)        /*res= (k1-2.0*fx+k2)/delt/delt; */
     strcpy(digitp,"-populbased-");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   else        
     strcpy(digitp,"-stablbased-");  #ifdef DEBUG
         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);
   strcpy(fileresprobmorprev,"prmorprev");        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);
   sprintf(digit,"%-d",ij);  #endif
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   strcat(fileresprobmorprev,digit); /* Tvar to be done */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   strcat(fileresprobmorprev,digitp); /* Popbased or not */          k=kmax;
   strcat(fileresprobmorprev,fileres);        }
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     printf("Problem with resultfile: %s\n", fileresprobmorprev);          k=kmax; l=lmax*10.;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);        }
   }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          delts=delt;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);        }
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");      }
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    }
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    delti[theta]=delts;
     fprintf(ficresprobmorprev," p.%-d SE",j);    return res; 
     for(i=1; i<=nlstate;i++)    
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);  }
   }    
   fprintf(ficresprobmorprev,"\n");  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  {
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    int i;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    int l=1, l1, lmax=20;
     exit(0);    double k1,k2,k3,k4,res,fx;
   }    double p2[NPARMAX+1];
   else{    int k;
     fprintf(ficgp,"\n# Routine varevsij");  
   }    fx=func(x);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    for (k=1; k<=2; k++) {
     printf("Problem with html file: %s\n", optionfilehtm);      for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      p2[thetai]=x[thetai]+delti[thetai]/k;
     exit(0);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   }      k1=func(p2)-fx;
   else{    
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      k2=func(p2)-fx;
     
   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");      p2[thetai]=x[thetai]-delti[thetai]/k;
   fprintf(ficresvij,"# Age");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for(i=1; i<=nlstate;i++)      k3=func(p2)-fx;
     for(j=1; j<=nlstate;j++)    
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      p2[thetai]=x[thetai]-delti[thetai]/k;
   fprintf(ficresvij,"\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
   xp=vector(1,npar);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   dnewm=matrix(1,nlstate,1,npar);  #ifdef DEBUG
   doldm=matrix(1,nlstate,1,nlstate);      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);
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      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);
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  #endif
     }
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    return res;
   gpp=vector(nlstate+1,nlstate+ndeath);  }
   gmp=vector(nlstate+1,nlstate+ndeath);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
   if(estepm < stepm){  { 
     printf ("Problem %d lower than %d\n",estepm, stepm);    int i,imax,j,k; 
   }    double big,dum,sum,temp; 
   else  hstepm=estepm;      double *vv; 
   /* For example we decided to compute the life expectancy with the smallest unit */   
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    vv=vector(1,n); 
      nhstepm is the number of hstepm from age to agelim    *d=1.0; 
      nstepm is the number of stepm from age to agelin.    for (i=1;i<=n;i++) { 
      Look at hpijx to understand the reason of that which relies in memory size      big=0.0; 
      and note for a fixed period like k years */      for (j=1;j<=n;j++) 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        if ((temp=fabs(a[i][j])) > big) big=temp; 
      survival function given by stepm (the optimization length). Unfortunately it      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      means that if the survival funtion is printed only each two years of age and if      vv[i]=1.0/big; 
      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.    for (j=1;j<=n;j++) { 
   */      for (i=1;i<j;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        sum=a[i][j]; 
   agelim = AGESUP;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        a[i][j]=sum; 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      big=0.0; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=j;i<=n;i++) { 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        sum=a[i][j]; 
     gp=matrix(0,nhstepm,1,nlstate);        for (k=1;k<j;k++) 
     gm=matrix(0,nhstepm,1,nlstate);          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(theta=1; theta <=npar; theta++){          big=dum; 
       for(i=1; i<=npar; i++){ /* Computes gradient */          imax=i; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } 
       }      } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        if (j != imax) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
       if (popbased==1) {          a[imax][k]=a[j][k]; 
         for(i=1; i<=nlstate;i++)          a[j][k]=dum; 
           prlim[i][i]=probs[(int)age][i][ij];        } 
       }        *d = -(*d); 
          vv[imax]=vv[j]; 
       for(j=1; j<= nlstate; j++){      } 
         for(h=0; h<=nhstepm; h++){      indx[j]=imax; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      if (j != n) { 
         }        dum=1.0/(a[j][j]); 
       }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       /* This for computing forces of mortality (h=1)as a weighted average */      } 
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    } 
         for(i=1; i<= nlstate; i++)    free_vector(vv,1,n);  /* Doesn't work */
           gpp[j] += prlim[i][i]*p3mat[i][j][1];  ;
       }      } 
       /* end force of mortality */  
   void lubksb(double **a, int n, int *indx, double b[]) 
       for(i=1; i<=npar; i++) /* Computes gradient */  { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i,ii=0,ip,j; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double sum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   
      for (i=1;i<=n;i++) { 
       if (popbased==1) {      ip=indx[i]; 
         for(i=1; i<=nlstate;i++)      sum=b[ip]; 
           prlim[i][i]=probs[(int)age][i][ij];      b[ip]=b[i]; 
       }      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for(j=1; j<= nlstate; j++){      else if (sum) ii=i; 
         for(h=0; h<=nhstepm; h++){      b[i]=sum; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    } 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    for (i=n;i>=1;i--) { 
         }      sum=b[i]; 
       }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       /* This for computing force of mortality (h=1)as a weighted average */      b[i]=sum/a[i][i]; 
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    } 
         for(i=1; i<= nlstate; i++)  } 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];  
       }      void pstamp(FILE *fichier)
       /* end force of mortality */  {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       for(j=1; j<= nlstate; j++) /* vareij */  }
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  /************ Frequencies ********************/
         }  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[])
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */  {  /* Some frequencies */
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];    
       }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
     } /* End theta */    double ***freq; /* Frequencies */
     double *pp, **prop;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
     for(h=0; h<=nhstepm; h++) /* veij */    
       for(j=1; j<=nlstate;j++)    pp=vector(1,nlstate);
         for(theta=1; theta <=npar; theta++)    prop=matrix(1,nlstate,iagemin,iagemax+3);
           trgradg[h][j][theta]=gradg[h][theta][j];    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    if((ficresp=fopen(fileresp,"w"))==NULL) {
       for(theta=1; theta <=npar; theta++)      printf("Problem with prevalence resultfile: %s\n", fileresp);
         trgradgp[j][theta]=gradgp[theta][j];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    }
     for(i=1;i<=nlstate;i++)    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       for(j=1;j<=nlstate;j++)    j1=0;
         vareij[i][j][(int)age] =0.;    
     j=cptcoveff;
     for(h=0;h<=nhstepm;h++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    first=1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)    for(k1=1; k1<=j;k1++){
           for(j=1;j<=nlstate;j++)      for(i1=1; i1<=ncodemax[k1];i1++){
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        j1++;
       }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
     /* pptj */          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);            for(m=iagemin; m <= iagemax+3; m++)
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);              freq[i][jk][m]=0;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)  
       for(i=nlstate+1;i<=nlstate+ndeath;i++)      for (i=1; i<=nlstate; i++)  
         varppt[j][i]=doldmp[j][i];        for(m=iagemin; m <= iagemax+3; m++)
     /* end ppptj */          prop[i][m]=0;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);          
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        dateintsum=0;
          k2cpt=0;
     if (popbased==1) {        for (i=1; i<=imx; i++) {
       for(i=1; i<=nlstate;i++)          bool=1;
         prlim[i][i]=probs[(int)age][i][ij];          if  (cptcovn>0) {
     }            for (z1=1; z1<=cptcoveff; z1++) 
                  if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     /* This for computing force of mortality (h=1)as a weighted average */                bool=0;
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          }
       for(i=1; i<= nlstate; i++)          if (bool==1){
         gmp[j] += prlim[i][i]*p3mat[i][j][1];            for(m=firstpass; m<=lastpass; m++){
     }                  k2=anint[m][i]+(mint[m][i]/12.);
     /* end force of mortality */              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));                if (m<lastpass) {
       for(i=1; i<=nlstate;i++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       }                }
     }                
     fprintf(ficresprobmorprev,"\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
     fprintf(ficresvij,"%.0f ",age );                  k2cpt++;
     for(i=1; i<=nlstate;i++)                }
       for(j=1; j<=nlstate;j++){                /*}*/
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            }
       }          }
     fprintf(ficresvij,"\n");        }
     free_matrix(gp,0,nhstepm,1,nlstate);         
     free_matrix(gm,0,nhstepm,1,nlstate);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        pstamp(ficresp);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        if  (cptcovn>0) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresp, "\n#********** Variable "); 
   } /* End age */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   free_vector(gpp,nlstate+1,nlstate+ndeath);          fprintf(ficresp, "**********\n#");
   free_vector(gmp,nlstate+1,nlstate+ndeath);        }
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        for(i=1; i<=nlstate;i++) 
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");        fprintf(ficresp, "\n");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */        
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");        for(i=iagemin; i <= iagemax+3; i++){
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);          if(i==iagemax+3){
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);            fprintf(ficlog,"Total");
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);          }else{
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);            if(first==1){
   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);              first=0;
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);              printf("See log file for details...\n");
             }
   free_vector(xp,1,npar);            fprintf(ficlog,"Age %d", i);
   free_matrix(doldm,1,nlstate,1,nlstate);          }
   free_matrix(dnewm,1,nlstate,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);              pp[jk] += freq[jk][m][i]; 
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          }
   fclose(ficresprobmorprev);          for(jk=1; jk <=nlstate ; jk++){
   fclose(ficgp);            for(m=-1, pos=0; m <=0 ; m++)
   fclose(fichtm);              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
 }              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 /************ Variance of prevlim ******************/              }
 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)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 {            }else{
   /* Variance of prevalence limit */              if(first==1)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double **newm;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double **dnewm,**doldm;            }
   int i, j, nhstepm, hstepm;          }
   int k, cptcode;  
   double *xp;          for(jk=1; jk <=nlstate ; jk++){
   double *gp, *gm;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double **gradg, **trgradg;              pp[jk] += freq[jk][m][i];
   double age,agelim;          }       
   int theta;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                pos += pp[jk];
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");            posprop += prop[jk][i];
   fprintf(ficresvpl,"# Age");          }
   for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficresvpl," %1d-%1d",i,i);            if(pos>=1.e-5){
   fprintf(ficresvpl,"\n");              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   xp=vector(1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   dnewm=matrix(1,nlstate,1,npar);            }else{
   doldm=matrix(1,nlstate,1,nlstate);              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   hstepm=1*YEARM; /* Every year of age */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }
   agelim = AGESUP;            if( i <= iagemax){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(pos>=1.e-5){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     if (stepm >= YEARM) hstepm=1;                /*probs[i][jk][j1]= pp[jk]/pos;*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     gradg=matrix(1,npar,1,nlstate);              }
     gp=vector(1,nlstate);              else
     gm=vector(1,nlstate);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */          
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(jk=-1; jk <=nlstate+ndeath; jk++)
       }            for(m=-1; m <=nlstate+ndeath; m++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              if(freq[jk][m][i] !=0 ) {
       for(i=1;i<=nlstate;i++)              if(first==1)
         gp[i] = prlim[i][i];                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                    fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       for(i=1; i<=npar; i++) /* Computes gradient */              }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          if(i <= iagemax)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            fprintf(ficresp,"\n");
       for(i=1;i<=nlstate;i++)          if(first==1)
         gm[i] = prlim[i][i];            printf("Others in log...\n");
           fprintf(ficlog,"\n");
       for(i=1;i<=nlstate;i++)        }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      }
     } /* End theta */    }
     dateintmean=dateintsum/k2cpt; 
     trgradg =matrix(1,nlstate,1,npar);   
     fclose(ficresp);
     for(j=1; j<=nlstate;j++)    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       for(theta=1; theta <=npar; theta++)    free_vector(pp,1,nlstate);
         trgradg[j][theta]=gradg[theta][j];    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     for(i=1;i<=nlstate;i++)  }
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  /************ Prevalence ********************/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  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)
     for(i=1;i<=nlstate;i++)  {  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
     fprintf(ficresvpl,"%.0f ",age );       We still use firstpass and lastpass as another selection.
     for(i=1; i<=nlstate;i++)    */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));   
     fprintf(ficresvpl,"\n");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     free_vector(gp,1,nlstate);    double ***freq; /* Frequencies */
     free_vector(gm,1,nlstate);    double *pp, **prop;
     free_matrix(gradg,1,npar,1,nlstate);    double pos,posprop; 
     free_matrix(trgradg,1,nlstate,1,npar);    double  y2; /* in fractional years */
   } /* End age */    int iagemin, iagemax;
   
   free_vector(xp,1,npar);    iagemin= (int) agemin;
   free_matrix(doldm,1,nlstate,1,npar);    iagemax= (int) agemax;
   free_matrix(dnewm,1,nlstate,1,nlstate);    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
 }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
 /************ 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)    j=cptcoveff;
 {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int i, j=0,  i1, k1, l1, t, tj;    
   int k2, l2, j1,  z1;    for(k1=1; k1<=j;k1++){
   int k=0,l, cptcode;      for(i1=1; i1<=ncodemax[k1];i1++){
   int first=1, first1;        j1++;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;        
   double **dnewm,**doldm;        for (i=1; i<=nlstate; i++)  
   double *xp;          for(m=iagemin; m <= iagemax+3; m++)
   double *gp, *gm;            prop[i][m]=0.0;
   double **gradg, **trgradg;       
   double **mu;        for (i=1; i<=imx; i++) { /* Each individual */
   double age,agelim, cov[NCOVMAX];          bool=1;
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */          if  (cptcovn>0) {
   int theta;            for (z1=1; z1<=cptcoveff; z1++) 
   char fileresprob[FILENAMELENGTH];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   char fileresprobcov[FILENAMELENGTH];                bool=0;
   char fileresprobcor[FILENAMELENGTH];          } 
           if (bool==1) { 
   double ***varpij;            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 */
   strcpy(fileresprob,"prob");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   strcat(fileresprob,fileres);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     printf("Problem with resultfile: %s\n", fileresprob);                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); 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);                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]]);*/
   strcpy(fileresprobcov,"probcov");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   strcat(fileresprobcov,fileres);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {                } 
     printf("Problem with resultfile: %s\n", fileresprobcov);              }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);            } /* end selection of waves */
   }          }
   strcpy(fileresprobcor,"probcor");        }
   strcat(fileresprobcor,fileres);        for(i=iagemin; i <= iagemax+3; i++){  
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {          
     printf("Problem with resultfile: %s\n", fileresprobcor);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);            posprop += prop[jk][i]; 
   }          } 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          for(jk=1; jk <=nlstate ; jk++){     
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);            if( i <=  iagemax){ 
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              if(posprop>=1.e-5){ 
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);                probs[i][jk][j1]= prop[jk][i]/posprop;
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);              } 
              } 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");          }/* end jk */ 
   fprintf(ficresprob,"# Age");        }/* end i */ 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      } /* end i1 */
   fprintf(ficresprobcov,"# Age");    } /* end k1 */
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    
   fprintf(ficresprobcov,"# Age");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   for(i=1; i<=nlstate;i++)  }  /* End of prevalence */
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  /************* Waves Concatenation ***************/
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  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)
     }    {
   fprintf(ficresprob,"\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   fprintf(ficresprobcov,"\n");       Death is a valid wave (if date is known).
   fprintf(ficresprobcor,"\n");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   xp=vector(1,npar);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       and mw[mi+1][i]. dh depends on stepm.
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));       */
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    int i, mi, m;
   first=1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       double sum=0., jmean=0.;*/
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    int first;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    int j, k=0,jk, ju, jl;
     exit(0);    double sum=0.;
   }    first=0;
   else{    jmin=1e+5;
     fprintf(ficgp,"\n# Routine varprob");    jmax=-1;
   }    jmean=0.;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    for(i=1; i<=imx; i++){
     printf("Problem with html file: %s\n", optionfilehtm);      mi=0;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      m=firstpass;
     exit(0);      while(s[m][i] <= nlstate){
   }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   else{          mw[++mi][i]=m;
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");        if(m >=lastpass)
     fprintf(fichtm,"\n");          break;
         else
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");          m++;
     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");      }/* end while */
     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");      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
          mw[mi][i]=m;
   cov[1]=1;      }
   tj=cptcoveff;  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}      wav[i]=mi;
   j1=0;      if(mi==0){
   for(t=1; t<=tj;t++){        nbwarn++;
     for(i1=1; i1<=ncodemax[t];i1++){        if(first==0){
       j1++;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                first=1;
       if  (cptcovn>0) {        }
         fprintf(ficresprob, "\n#********** Variable ");        if(first==1){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         fprintf(ficresprob, "**********\n#");        }
         fprintf(ficresprobcov, "\n#********** Variable ");      } /* end mi==0 */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    } /* End individuals */
         fprintf(ficresprobcov, "**********\n#");  
            for(i=1; i<=imx; i++){
         fprintf(ficgp, "\n#********** Variable ");      for(mi=1; mi<wav[i];mi++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        if (stepm <=0)
         fprintf(ficgp, "**********\n#");          dh[mi][i]=1;
                else{
                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");            if (agedc[i] < 2*AGESUP) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");              if(j==0) j=1;  /* Survives at least one month after exam */
                      else if(j<0){
         fprintf(ficresprobcor, "\n#********** Variable ");                    nberr++;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                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]);
         fprintf(ficgp, "**********\n#");                    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]);
       for (age=bage; age<=fage; age ++){                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);
         cov[2]=age;              }
         for (k=1; k<=cptcovn;k++) {              k=k+1;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];              if (j >= jmax){
         }                jmax=j;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                ijmax=i;
         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]]];              if (j <= jmin){
                        jmin=j;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));                ijmin=i;
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              }
         gp=vector(1,(nlstate)*(nlstate+ndeath));              sum=sum+j;
         gm=vector(1,(nlstate)*(nlstate+ndeath));              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                  /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for(theta=1; theta <=npar; theta++){            }
           for(i=1; i<=npar; i++)          }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          else{
                      j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  /*        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]); */
            
           k=0;            k=k+1;
           for(i=1; i<= (nlstate); i++){            if (j >= jmax) {
             for(j=1; j<=(nlstate+ndeath);j++){              jmax=j;
               k=k+1;              ijmax=i;
               gp[k]=pmmij[i][j];            }
             }            else if (j <= jmin){
           }              jmin=j;
                        ijmin=i;
           for(i=1; i<=npar; i++)            }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                /*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]);*/
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            if(j<0){
           k=0;              nberr++;
           for(i=1; i<=(nlstate); i++){              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]);
             for(j=1; j<=(nlstate+ndeath);j++){              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]);
               k=k+1;            }
               gm[k]=pmmij[i][j];            sum=sum+j;
             }          }
           }          jk= j/stepm;
                jl= j -jk*stepm;
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)          ju= j -(jk+1)*stepm;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         }            if(jl==0){
               dh[mi][i]=jk;
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)              bh[mi][i]=0;
           for(theta=1; theta <=npar; theta++)            }else{ /* We want a negative bias in order to only have interpolation ie
             trgradg[j][theta]=gradg[theta][j];                    * at the price of an extra matrix product in likelihood */
                      dh[mi][i]=jk+1;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);              bh[mi][i]=ju;
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);            }
                  }else{
         pmij(pmmij,cov,ncovmodel,x,nlstate);            if(jl <= -ju){
                      dh[mi][i]=jk;
         k=0;              bh[mi][i]=jl;       /* bias is positive if real duration
         for(i=1; i<=(nlstate); i++){                                   * is higher than the multiple of stepm and negative otherwise.
           for(j=1; j<=(nlstate+ndeath);j++){                                   */
             k=k+1;            }
             mu[k][(int) age]=pmmij[i][j];            else{
           }              dh[mi][i]=jk+1;
         }              bh[mi][i]=ju;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            }
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)            if(dh[mi][i]==0){
             varpij[i][j][(int)age] = doldm[i][j];              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
         /*printf("\n%d ",(int)age);              /*  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 (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]));          } /* end if mle */
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        }
      }*/      } /* end wave */
     }
         fprintf(ficresprob,"\n%d ",(int)age);    jmean=sum/k;
         fprintf(ficresprobcov,"\n%d ",(int)age);    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(ficresprobcor,"\n%d ",(int)age);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
    }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)  
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  /*********** Tricode ****************************/
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  void tricode(int *Tvar, int **nbcode, int imx)
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  {
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    
         }    int Ndum[20],ij=1, k, j, i, maxncov=19;
         i=0;    int cptcode=0;
         for (k=1; k<=(nlstate);k++){    cptcoveff=0; 
           for (l=1; l<=(nlstate+ndeath);l++){   
             i=i++;    for (k=0; k<maxncov; k++) Ndum[k]=0;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    for (k=1; k<=7; k++) ncodemax[k]=0;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);  
             for (j=1; j<=i;j++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));                                 modality*/ 
             }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           }        Ndum[ij]++; /*store the modality */
         }/* end of loop for state */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       } /* end of loop for age */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
       /* Confidence intervalle of pij  */                                         female is 1, then  cptcode=1.*/
       /*      }
       fprintf(ficgp,"\nset noparametric;unset label");  
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      for (i=0; i<=cptcode; i++) {
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       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);      }
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);  
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      ij=1; 
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);      for (i=1; i<=ncodemax[j]; i++) {
       */        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/            nbcode[Tvar[j]][ij]=k; 
       first1=1;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       for (k1=1; k1<=(nlstate);k1++){            
         for (l1=1; l1<=(nlstate+ndeath);l1++){            ij++;
           if(l1==k1) continue;          }
           i=(k1-1)*(nlstate+ndeath)+l1;          if (ij > ncodemax[j]) break; 
           for (k2=1; k2<=(nlstate);k2++){        }  
             for (l2=1; l2<=(nlstate+ndeath);l2++){      } 
               if(l2==k2) continue;    }  
               j=(k2-1)*(nlstate+ndeath)+l2;  
               if(j<=i) continue;   for (k=0; k< maxncov; k++) Ndum[k]=0;
               for (age=bage; age<=fage; age ++){  
                 if ((int)age %5==0){   for (i=1; i<=ncovmodel-2; i++) { 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;     ij=Tvar[i];
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;     Ndum[ij]++;
                   mu1=mu[i][(int) age]/stepm*YEARM ;   }
                   mu2=mu[j][(int) age]/stepm*YEARM;  
                   /* Computing eigen value of matrix of covariance */   ij=1;
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));   for (i=1; i<= maxncov; i++) {
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));     if((Ndum[i]!=0) && (i<=ncovcol)){
                   if(first1==1){       Tvaraff[ij]=i; /*For printing */
                     first1=0;       ij++;
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);     }
                   }   }
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);   
                   /* Eigen vectors */   cptcoveff=ij-1; /*Number of simple covariates*/
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  }
                   v21=sqrt(1.-v11*v11);  
                   v12=-v21;  /*********** Health Expectancies ****************/
                   v22=v11;  
                   /*printf(fignu*/  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */  
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */  {
                   if(first==1){    /* Health expectancies, no variances */
                     first=0;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
                     fprintf(ficgp,"\nset parametric;set nolabel");    double age, agelim, hf;
                     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);    double ***p3mat;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    double eip;
                     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);  
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    pstamp(ficreseij);
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    fprintf(ficreseij,"# Age");
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    for(i=1; i<=nlstate;i++){
                     /*              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\"",\      for(j=1; j<=nlstate;j++){
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \        fprintf(ficreseij," e%1d%1d ",i,j);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      }
                     */      fprintf(ficreseij," e%1d. ",i);
                     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",\    }
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    fprintf(ficreseij,"\n");
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));  
                   }else{    
                     first=0;    if(estepm < stepm){
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      printf ("Problem %d lower than %d\n",estepm, stepm);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    }
                     /*    else  hstepm=estepm;   
                     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\"",\    /* We compute the life expectancy from trapezoids spaced every estepm months
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \     * This is mainly to measure the difference between two models: for example
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);     * 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 
                     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",\     * progression in between and thus overestimating or underestimating according
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \     * to the curvature of the survival function. If, for the same date, we 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));     * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   }/* if first */     * to compare the new estimate of Life expectancy with the same linear 
                 } /* age mod 5 */     * hypothesis. A more precise result, taking into account a more precise
               } /* end loop age */     * curvature will be obtained if estepm is as small as stepm. */
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);  
               first=1;    /* For example we decided to compute the life expectancy with the smallest unit */
             } /*l12 */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           } /* k12 */       nhstepm is the number of hstepm from age to agelim 
         } /*l1 */       nstepm is the number of stepm from age to agelin. 
       }/* k1 */       Look at hpijx to understand the reason of that which relies in memory size
     } /* loop covariates */       and note for a fixed period like estepm months */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       survival function given by stepm (the optimization length). Unfortunately it
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));       means that if the survival funtion is printed only each two years of age and if
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       results. So we changed our mind and took the option of the best precision.
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   free_vector(xp,1,npar);  
   fclose(ficresprob);    agelim=AGESUP;
   fclose(ficresprobcov);    /* nhstepm age range expressed in number of stepm */
   fclose(ficresprobcor);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   fclose(ficgp);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(fichtm);    /* if (stepm >= YEARM) hstepm=1;*/
 }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
 /******************* Printing html file ***********/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   int lastpass, int stepm, int weightopt, char model[],\         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\  
                   int popforecast, int estepm ,\      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
                   double jprev1, double mprev1,double anprev1, \   
                   double jprev2, double mprev2,double anprev2){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   int jj1, k1, i1, cpt;  
   /*char optionfilehtm[FILENAMELENGTH];*/      /* Computing  Variances of health expectancies */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     printf("Problem with %s \n",optionfilehtm), exit(0);         decrease memory allocation */
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       /* Computing expectancies */
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      for(i=1; i<=nlstate;i++)
  - 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        for(j=1; j<=nlstate;j++)
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
  - Life expectancies by age and initial health status (estepm=%2d months):            
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  /* 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]);*/
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  
           }
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  
       fprintf(ficreseij,"%3.0f",age );
  m=cptcoveff;      for(i=1; i<=nlstate;i++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        eip=0;
         for(j=1; j<=nlstate;j++){
  jj1=0;          eip +=eij[i][j][(int)age];
  for(k1=1; k1<=m;k1++){          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
    for(i1=1; i1<=ncodemax[k1];i1++){        }
      jj1++;        fprintf(ficreseij,"%9.4f", eip );
      if (cptcovn > 0) {      }
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      fprintf(ficreseij,"\n");
        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\">");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }    printf("\n");
      /* Pij */    fprintf(ficlog,"\n");
      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 */  
      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 cvevsij(char fileres[], 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[] )
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
        /* Stable prevalence in each health state */  {
        for(cpt=1; cpt<nlstate;cpt++){    /* Covariances of health expectancies eij and of total life expectancies according
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>     to initial status i, ei. .
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    */
        }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      for(cpt=1; cpt<=nlstate;cpt++) {    double age, agelim, hf;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    double ***p3matp, ***p3matm, ***varhe;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double **dnewm,**doldm;
      }    double *xp, *xm;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    double **gp, **gm;
 health expectancies in states (1) and (2): e%s%d.png<br>    double ***gradg, ***trgradg;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    int theta;
    } /* end i1 */  
  }/* End k1 */    double eip, vip;
  fprintf(fichtm,"</ul>");  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    xm=vector(1,npar);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    dnewm=matrix(1,nlstate*nlstate,1,npar);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    pstamp(ficresstdeij);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    fprintf(ficresstdeij,"# Age");
  - 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);    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
  if(popforecast==1) fprintf(fichtm,"\n        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      fprintf(ficresstdeij," e%1d. ",i);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    }
         <br>",fileres,fileres,fileres,fileres);    fprintf(ficresstdeij,"\n");
  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);    pstamp(ficrescveij);
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
  m=cptcoveff;    for(i=1; i<=nlstate;i++)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
  jj1=0;        for(i2=1; i2<=nlstate;i2++)
  for(k1=1; k1<=m;k1++){          for(j2=1; j2<=nlstate;j2++){
    for(i1=1; i1<=ncodemax[k1];i1++){            cptj2= (j2-1)*nlstate+i2;
      jj1++;            if(cptj2 <= cptj)
      if (cptcovn > 0) {              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
        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(ficrescveij,"\n");
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    
      }    if(estepm < stepm){
      for(cpt=1; cpt<=nlstate;cpt++) {      printf ("Problem %d lower than %d\n",estepm, stepm);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    }
 interval) in state (%d): v%s%d%d.png <br>    else  hstepm=estepm;   
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      /* We compute the life expectancy from trapezoids spaced every estepm months
      }     * This is mainly to measure the difference between two models: for example
    } /* end i1 */     * if stepm=24 months pijx are given only every 2 years and by summing them
  }/* End k1 */     * we are calculating an estimate of the Life Expectancy assuming a linear 
  fprintf(fichtm,"</ul>");     * progression in between and thus overestimating or underestimating according
 fclose(fichtm);     * to the curvature of the survival function. If, for the same date, we 
 }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
 /******************* Gnuplot file **************/     * hypothesis. A more precise result, taking into account a more precise
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){     * curvature will be obtained if estepm is as small as stepm. */
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    /* For example we decided to compute the life expectancy with the smallest unit */
   int ng;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       nhstepm is the number of hstepm from age to agelim 
     printf("Problem with file %s",optionfilegnuplot);       nstepm is the number of stepm from age to agelin. 
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 #ifdef windows       survival function given by stepm (the optimization length). Unfortunately it
     fprintf(ficgp,"cd \"%s\" \n",pathc);       means that if the survival funtion is printed only each two years of age and if
 #endif       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 m=pow(2,cptcoveff);       results. So we changed our mind and took the option of the best precision.
      */
  /* 1eme*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
 #ifdef windows    agelim=AGESUP;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
      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);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 #endif    /* if (stepm >= YEARM) hstepm=1;*/
 #ifdef unix    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 for (i=1; i<= nlstate ; i ++) {    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    gm=matrix(0,nhstepm,1,nlstate*nlstate);
 }  
     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 (age=bage; age<=fage; age ++){ 
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   else fprintf(ficgp," \%%*lf (\%%*lf)");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 }   
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /* Computing  Variances of health expectancies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
 }           decrease memory allocation */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      for(theta=1; theta <=npar; theta++){
 #ifdef unix        for(i=1; i<=npar; i++){ 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #endif          xm[i] = x[i] - (i==theta ?delti[theta]:0);
    }        }
   }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   /*2 eme*/        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          for(i=1; i<=nlstate; i++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            for(h=0; h<=nhstepm-1; h++){
                  gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     for (i=1; i<= nlstate+1 ; i ++) {              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       k=2*i;            }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(ij=1; ij<= nlstate*nlstate; ij++)
 }            for(h=0; h<=nhstepm-1; h++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      }/* End theta */
       for (j=1; j<= nlstate+1 ; j ++) {      
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      
         else fprintf(ficgp," \%%*lf (\%%*lf)");      for(h=0; h<=nhstepm-1; h++)
 }          for(j=1; j<=nlstate*nlstate;j++)
       fprintf(ficgp,"\" t\"\" w l 0,");          for(theta=1; theta <=npar; theta++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            trgradg[h][j][theta]=gradg[h][theta][j];
       for (j=1; j<= nlstate+1 ; j ++) {      
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");       for(ij=1;ij<=nlstate*nlstate;ij++)
 }          for(ji=1;ji<=nlstate*nlstate;ji++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          varhe[ij][ji][(int)age] =0.;
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
   /*3eme*/        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   for (k1=1; k1<= m ; k1 ++) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(ij=1;ij<=nlstate*nlstate;ij++)
       k=2+nlstate*(2*cpt-2);            for(ji=1;ji<=nlstate*nlstate;ji++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        }
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      /* Computing expectancies */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      for(i=1; i<=nlstate;i++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        for(j=1; j<=nlstate;j++)
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
 */            
       for (i=1; i< nlstate ; i ++) {            /* 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]);*/
         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);  
           }
       }  
     }      fprintf(ficresstdeij,"%3.0f",age );
   }      for(i=1; i<=nlstate;i++){
          eip=0.;
   /* CV preval stat */        vip=0.;
     for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<=nlstate;j++){
     for (cpt=1; cpt<nlstate ; cpt ++) {          eip += eij[i][j][(int)age];
       k=3;          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
       for (i=1; i< nlstate ; i ++)        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         fprintf(ficgp,"+$%d",k+i+1);      }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      fprintf(ficresstdeij,"\n");
        
       l=3+(nlstate+ndeath)*cpt;      fprintf(ficrescveij,"%3.0f",age );
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {        for(j=1; j<=nlstate;j++){
         l=3+(nlstate+ndeath)*cpt;          cptj= (j-1)*nlstate+i;
         fprintf(ficgp,"+$%d",l+i+1);          for(i2=1; i2<=nlstate;i2++)
       }            for(j2=1; j2<=nlstate;j2++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                cptj2= (j2-1)*nlstate+i2;
     }              if(cptj2 <= cptj)
   }                  fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
              }
   /* proba elementaires */        }
    for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficrescveij,"\n");
     for(k=1; k <=(nlstate+ndeath); k++){     
       if (k != i) {    }
         for(j=1; j <=ncovmodel; j++){    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           jk++;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           fprintf(ficgp,"\n");    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    printf("\n");
    }    fprintf(ficlog,"\n");
   
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    free_vector(xm,1,npar);
      for(jk=1; jk <=m; jk++) {    free_vector(xp,1,npar);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
        if (ng==2)    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
        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);  /************ Variance ******************/
        i=1;  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[])
        for(k2=1; k2<=nlstate; k2++) {  {
          k3=i;    /* Variance of health expectancies */
          for(k=1; k<=(nlstate+ndeath); k++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
            if (k != k2){    /* double **newm;*/
              if(ng==2)    double **dnewm,**doldm;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    double **dnewmp,**doldmp;
              else    int i, j, nhstepm, hstepm, h, nstepm ;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    int k, cptcode;
              ij=1;    double *xp;
              for(j=3; j <=ncovmodel; j++) {    double **gp, **gm;  /* for var eij */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double ***gradg, ***trgradg; /*for var eij */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double **gradgp, **trgradgp; /* for var p point j */
                  ij++;    double *gpp, *gmp; /* for var p point j */
                }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                else    double ***p3mat;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double age,agelim, hf;
              }    double ***mobaverage;
              fprintf(ficgp,")/(1");    int theta;
                  char digit[4];
              for(k1=1; k1 <=nlstate; k1++){      char digitp[25];
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
                ij=1;    char fileresprobmorprev[FILENAMELENGTH];
                for(j=3; j <=ncovmodel; j++){  
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    if(popbased==1){
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      if(mobilav!=0)
                    ij++;        strcpy(digitp,"-populbased-mobilav-");
                  }      else strcpy(digitp,"-populbased-nomobil-");
                  else    }
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    else 
                }      strcpy(digitp,"-stablbased-");
                fprintf(ficgp,")");  
              }    if (mobilav!=0) {
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
              i=i+ncovmodel;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          } /* end k */      }
        } /* end k2 */    }
      } /* end jk */  
    } /* end ng */    strcpy(fileresprobmorprev,"prmorprev"); 
    fclose(ficgp);    sprintf(digit,"%-d",ij);
 }  /* end gnuplot */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 /*************** Moving average **************/    strcat(fileresprobmorprev,fileres);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   int i, cpt, cptcod;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    }
       for (i=1; i<=nlstate;i++)    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   
           mobaverage[(int)agedeb][i][cptcod]=0.;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        pstamp(ficresprobmorprev);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    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);
       for (i=1; i<=nlstate;i++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           for (cpt=0;cpt<=4;cpt++){      fprintf(ficresprobmorprev," p.%-d SE",j);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      for(i=1; i<=nlstate;i++)
           }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    }  
         }    fprintf(ficresprobmorprev,"\n");
       }    fprintf(ficgp,"\n# Routine varevsij");
     }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
        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);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 /************** Forecasting ******************/    pstamp(ficresvij);
 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){    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
   int *popage;    else
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   double *popeffectif,*popcount;    fprintf(ficresvij,"# Age");
   double ***p3mat;    for(i=1; i<=nlstate;i++)
   char fileresf[FILENAMELENGTH];      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
  agelim=AGESUP;    fprintf(ficresvij,"\n");
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
     xp=vector(1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   strcpy(fileresf,"f");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     printf("Problem with forecast resultfile: %s\n", fileresf);    gpp=vector(nlstate+1,nlstate+ndeath);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    gmp=vector(nlstate+1,nlstate+ndeath);
   }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   printf("Computing forecasting: result on file '%s' \n", fileresf);    
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    }
     else  hstepm=estepm;   
   if (mobilav==1) {    /* For example we decided to compute the life expectancy with the smallest unit */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     movingaverage(agedeb, fage, ageminpar, mobaverage);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   stepsize=(int) (stepm+YEARM-1)/YEARM;       and note for a fixed period like k years */
   if (stepm<=12) stepsize=1;    /* 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
   agelim=AGESUP;       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 
   hstepm=1;       results. So we changed our mind and took the option of the best precision.
   hstepm=hstepm/stepm;    */
   yp1=modf(dateintmean,&yp);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   anprojmean=yp;    agelim = AGESUP;
   yp2=modf((yp1*12),&yp);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   mprojmean=yp;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   yp1=modf((yp2*30.5),&yp);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   jprojmean=yp;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if(jprojmean==0) jprojmean=1;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   if(mprojmean==0) jprojmean=1;      gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
    
   for(cptcov=1;cptcov<=i2;cptcov++){      for(theta=1; theta <=npar; theta++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       k=k+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficresf,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }  
       fprintf(ficresf,"******\n");        if (popbased==1) {
       fprintf(ficresf,"# StartingAge FinalAge");          if(mobilav ==0){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
                }else{ /* mobilav */ 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            for(i=1; i<=nlstate;i++)
         fprintf(ficresf,"\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
         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--){    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(j=1; j<= nlstate; j++){
           nhstepm = nhstepm/hstepm;          for(h=0; h<=nhstepm; h++){
                      for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           oldm=oldms;savm=savms;          }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
                /* This for computing probability of death (h=1 means
           for (h=0; h<=nhstepm; h++){           computed over hstepm matrices product = hstepm*stepm months) 
             if (h==(int) (calagedate+YEARM*cpt)) {           as a weighted average of prlim.
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        */
             }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             for(j=1; j<=nlstate+ndeath;j++) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
               kk1=0.;kk2=0;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
               for(i=1; i<=nlstate;i++) {                      }    
                 if (mobilav==1)        /* end probability of death */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                 }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               }   
               if (h==(int)(calagedate+12*cpt)){        if (popbased==1) {
                 fprintf(ficresf," %.3f", kk1);          if(mobilav ==0){
                                    for(i=1; i<=nlstate;i++)
               }              prlim[i][i]=probs[(int)age][i][ij];
             }          }else{ /* mobilav */ 
           }            for(i=1; i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              prlim[i][i]=mobaverage[(int)age][i][ij];
         }          }
       }        }
     }  
   }        for(j=1; j<= nlstate; j++){
                  for(h=0; h<=nhstepm; h++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   fclose(ficresf);          }
 }        }
 /************** Forecasting ******************/        /* This for computing probability of death (h=1 means
 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){           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        */
   int *popage;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   double *popeffectif,*popcount;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   double ***p3mat,***tabpop,***tabpopprev;        }    
   char filerespop[FILENAMELENGTH];        /* end probability of death */
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<= nlstate; j++) /* vareij */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(h=0; h<=nhstepm; h++){
   agelim=AGESUP;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          }
    
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);      } /* End theta */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", filerespop);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  
   }      for(h=0; h<=nhstepm; h++) /* veij */
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for(j=1; j<=nlstate;j++)
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   if (mobilav==1) {        for(theta=1; theta <=npar; theta++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          trgradgp[j][theta]=gradgp[theta][j];
     movingaverage(agedeb, fage, ageminpar, mobaverage);    
   }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for(i=1;i<=nlstate;i++)
   if (stepm<=12) stepsize=1;        for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
   agelim=AGESUP;  
        for(h=0;h<=nhstepm;h++){
   hstepm=1;        for(k=0;k<=nhstepm;k++){
   hstepm=hstepm/stepm;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   if (popforecast==1) {          for(i=1;i<=nlstate;i++)
     if((ficpop=fopen(popfile,"r"))==NULL) {            for(j=1;j<=nlstate;j++)
       printf("Problem with population file : %s\n",popfile);exit(0);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);        }
     }      }
     popage=ivector(0,AGESUP);    
     popeffectif=vector(0,AGESUP);      /* pptj */
     popcount=vector(0,AGESUP);      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);
     i=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
              varppt[j][i]=doldmp[j][i];
     imx=i;      /* end ppptj */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   for(cptcov=1;cptcov<=i2;cptcov++){   
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if (popbased==1) {
       k=k+1;        if(mobilav ==0){
       fprintf(ficrespop,"\n#******");          for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {            prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }else{ /* mobilav */ 
       }          for(i=1; i<=nlstate;i++)
       fprintf(ficrespop,"******\n");            prlim[i][i]=mobaverage[(int)age][i][ij];
       fprintf(ficrespop,"# Age");        }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      }
       if (popforecast==1)  fprintf(ficrespop," [Population]");               
            /* This for computing probability of death (h=1 means
       for (cpt=0; cpt<=0;cpt++) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);           as a weighted average of prlim.
              */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           nhstepm = nhstepm/hstepm;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                }    
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* end probability of death */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
              for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           for (h=0; h<=nhstepm; h++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
             if (h==(int) (calagedate+YEARM*cpt)) {        for(i=1; i<=nlstate;i++){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             }        }
             for(j=1; j<=nlstate+ndeath;j++) {      } 
               kk1=0.;kk2=0;      fprintf(ficresprobmorprev,"\n");
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)      fprintf(ficresvij,"%.0f ",age );
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for(i=1; i<=nlstate;i++)
                 else {        for(j=1; j<=nlstate;j++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                 }        }
               }      fprintf(ficresvij,"\n");
               if (h==(int)(calagedate+12*cpt)){      free_matrix(gp,0,nhstepm,1,nlstate);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      free_matrix(gm,0,nhstepm,1,nlstate);
                   /*fprintf(ficrespop," %.3f", kk1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
               }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }    } /* End age */
             for(i=1; i<=nlstate;i++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
               kk1=0.;    free_vector(gmp,nlstate+1,nlstate+ndeath);
                 for(j=1; j<=nlstate;j++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                 }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
             }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  /*   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 1 ",subdirf(fileresprobmorprev));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      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);
   /******/    /*  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);
   */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_vector(xp,1,npar);
           nhstepm = nhstepm/hstepm;    free_matrix(doldm,1,nlstate,1,nlstate);
              free_matrix(dnewm,1,nlstate,1,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           oldm=oldms;savm=savms;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for (h=0; h<=nhstepm; h++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             if (h==(int) (calagedate+YEARM*cpt)) {    fclose(ficresprobmorprev);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fflush(ficgp);
             }    fflush(fichtm); 
             for(j=1; j<=nlstate+ndeath;j++) {  }  /* end varevsij */
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                /************ Variance of prevlim ******************/
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      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[])
               }  {
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    /* Variance of prevalence limit */
             }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           }    double **newm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
       }    int k, cptcode;
    }    double *xp;
   }    double *gp, *gm;
      double **gradg, **trgradg;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double age,agelim;
     int theta;
   if (popforecast==1) {    
     free_ivector(popage,0,AGESUP);    pstamp(ficresvpl);
     free_vector(popeffectif,0,AGESUP);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     free_vector(popcount,0,AGESUP);    fprintf(ficresvpl,"# Age");
   }    for(i=1; i<=nlstate;i++)
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresvpl," %1d-%1d",i,i);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresvpl,"\n");
   fclose(ficrespop);  
 }    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
 /***********************************************/    doldm=matrix(1,nlstate,1,nlstate);
 /**************** Main Program *****************/    
 /***********************************************/    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 int main(int argc, char *argv[])    agelim = AGESUP;
 {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      if (stepm >= YEARM) hstepm=1;
   double agedeb, agefin,hf;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   double fret;      gm=vector(1,nlstate);
   double **xi,tmp,delta;  
       for(theta=1; theta <=npar; theta++){
   double dum; /* Dummy variable */        for(i=1; i<=npar; i++){ /* Computes gradient */
   double ***p3mat;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int *indx;        }
   char line[MAXLINE], linepar[MAXLINE];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];        for(i=1;i<=nlstate;i++)
   int firstobs=1, lastobs=10;          gp[i] = prlim[i][i];
   int sdeb, sfin; /* Status at beginning and end */      
   int c,  h , cpt,l;        for(i=1; i<=npar; i++) /* Computes gradient */
   int ju,jl, mi;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for(i=1;i<=nlstate;i++)
   int mobilav=0,popforecast=0;          gm[i] = prlim[i][i];
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   double bage, fage, age, agelim, agebase;      } /* End theta */
   double ftolpl=FTOL;  
   double **prlim;      trgradg =matrix(1,nlstate,1,npar);
   double *severity;  
   double ***param; /* Matrix of parameters */      for(j=1; j<=nlstate;j++)
   double  *p;        for(theta=1; theta <=npar; theta++)
   double **matcov; /* Matrix of covariance */          trgradg[j][theta]=gradg[theta][j];
   double ***delti3; /* Scale */  
   double *delti; /* Scale */      for(i=1;i<=nlstate;i++)
   double ***eij, ***vareij;        varpl[i][(int)age] =0.;
   double **varpl; /* Variances of prevalence limits by age */      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   double *epj, vepp;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   double kk1, kk2;      for(i=1;i<=nlstate;i++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
       fprintf(ficresvpl,"%.0f ",age );
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   char z[1]="c", occ;      free_vector(gp,1,nlstate);
 #include <sys/time.h>      free_vector(gm,1,nlstate);
 #include <time.h>      free_matrix(gradg,1,npar,1,nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
   /* long total_usecs;  
   struct timeval start_time, end_time;    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,npar);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    free_matrix(dnewm,1,nlstate,1,nlstate);
   getcwd(pathcd, size);  
   }
   printf("\n%s",version);  
   if(argc <=1){  /************ Variance of one-step probabilities  ******************/
     printf("\nEnter the parameter file name: ");  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[])
     scanf("%s",pathtot);  {
   }    int i, j=0,  i1, k1, l1, t, tj;
   else{    int k2, l2, j1,  z1;
     strcpy(pathtot,argv[1]);    int k=0,l, cptcode;
   }    int first=1, first1;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   /*cygwin_split_path(pathtot,path,optionfile);    double **dnewm,**doldm;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double *xp;
   /* cutv(path,optionfile,pathtot,'\\');*/    double *gp, *gm;
     double **gradg, **trgradg;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    double **mu;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    double age,agelim, cov[NCOVMAX];
   chdir(path);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   replace(pathc,path);    int theta;
     char fileresprob[FILENAMELENGTH];
 /*-------- arguments in the command line --------*/    char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   /* Log file */  
   strcat(filelog, optionfilefiname);    double ***varpij;
   strcat(filelog,".log");    /* */  
   if((ficlog=fopen(filelog,"w"))==NULL)    {    strcpy(fileresprob,"prob"); 
     printf("Problem with logfile %s\n",filelog);    strcat(fileresprob,fileres);
     goto end;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprob);
   fprintf(ficlog,"Log filename:%s\n",filelog);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   fprintf(ficlog,"\n%s",version);    }
   fprintf(ficlog,"\nEnter the parameter file name: ");    strcpy(fileresprobcov,"probcov"); 
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    strcat(fileresprobcov,fileres);
   fflush(ficlog);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
   /* */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   strcpy(fileres,"r");    }
   strcat(fileres, optionfilefiname);    strcpy(fileresprobcor,"probcor"); 
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   /*---------arguments file --------*/      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }
     printf("Problem with optionfile %s\n",optionfile);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     goto end;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   }    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);
   strcpy(filereso,"o");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   strcat(filereso,fileres);    pstamp(ficresprob);
   if((ficparo=fopen(filereso,"w"))==NULL) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     printf("Problem with Output resultfile: %s\n", filereso);    fprintf(ficresprob,"# Age");
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    pstamp(ficresprobcov);
     goto end;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   }    fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobcor,"# Age");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   ungetc(c,ficpar);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   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);      }  
   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(ficresprob,"\n");
   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(ficresprobcov,"\n");
 while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobcor,"\n");
     ungetc(c,ficpar);   */
     fgets(line, MAXLINE, ficpar);   xp=vector(1,npar);
     puts(line);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fputs(line,ficparo);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   ungetc(c,ficpar);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
        fprintf(ficgp,"\n# Routine varprob");
   covar=matrix(0,NCOVMAX,1,n);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   cptcovn=0;    fprintf(fichtm,"\n");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   ncovmodel=2+cptcovn;    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    file %s<br>\n",optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   /* Read guess parameters */  and drawn. It helps understanding how is the covariance between two incidences.\
   /* Reads comments: lines beginning with '#' */   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    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. \
     ungetc(c,ficpar);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     fgets(line, MAXLINE, ficpar);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     puts(line);  standard deviations wide on each axis. <br>\
     fputs(line,ficparo);   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>\
   ungetc(c,ficpar);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    cov[1]=1;
     for(i=1; i <=nlstate; i++)    tj=cptcoveff;
     for(j=1; j <=nlstate+ndeath-1; j++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       fscanf(ficpar,"%1d%1d",&i1,&j1);    j1=0;
       fprintf(ficparo,"%1d%1d",i1,j1);    for(t=1; t<=tj;t++){
       if(mle==1)      for(i1=1; i1<=ncodemax[t];i1++){ 
         printf("%1d%1d",i,j);        j1++;
       fprintf(ficlog,"%1d%1d",i,j);        if  (cptcovn>0) {
       for(k=1; k<=ncovmodel;k++){          fprintf(ficresprob, "\n#********** Variable "); 
         fscanf(ficpar," %lf",&param[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if(mle==1){          fprintf(ficresprob, "**********\n#\n");
           printf(" %lf",param[i][j][k]);          fprintf(ficresprobcov, "\n#********** Variable "); 
           fprintf(ficlog," %lf",param[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprobcov, "**********\n#\n");
         else          
           fprintf(ficlog," %lf",param[i][j][k]);          fprintf(ficgp, "\n#********** Variable "); 
         fprintf(ficparo," %lf",param[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficgp, "**********\n#\n");
       fscanf(ficpar,"\n");          
       if(mle==1)          
         printf("\n");          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       fprintf(ficlog,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficparo,"\n");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     }          
            fprintf(ficresprobcor, "\n#********** Variable ");    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
   p=param[1][1];        }
          
   /* Reads comments: lines beginning with '#' */        for (age=bage; age<=fage; age ++){ 
   while((c=getc(ficpar))=='#' && c!= EOF){          cov[2]=age;
     ungetc(c,ficpar);          for (k=1; k<=cptcovn;k++) {
     fgets(line, MAXLINE, ficpar);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     puts(line);          }
     fputs(line,ficparo);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }          for (k=1; k<=cptcovprod;k++)
   ungetc(c,ficpar);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   for(i=1; i <=nlstate; i++){          gp=vector(1,(nlstate)*(nlstate+ndeath));
     for(j=1; j <=nlstate+ndeath-1; j++){          gm=vector(1,(nlstate)*(nlstate+ndeath));
       fscanf(ficpar,"%1d%1d",&i1,&j1);      
       printf("%1d%1d",i,j);          for(theta=1; theta <=npar; theta++){
       fprintf(ficparo,"%1d%1d",i1,j1);            for(i=1; i<=npar; i++)
       for(k=1; k<=ncovmodel;k++){              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
         fscanf(ficpar,"%le",&delti3[i][j][k]);            
         printf(" %le",delti3[i][j][k]);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         fprintf(ficparo," %le",delti3[i][j][k]);            
       }            k=0;
       fscanf(ficpar,"\n");            for(i=1; i<= (nlstate); i++){
       printf("\n");              for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo,"\n");                k=k+1;
     }                gp[k]=pmmij[i][j];
   }              }
   delti=delti3[1][1];            }
              
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=npar; i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     puts(line);            k=0;
     fputs(line,ficparo);            for(i=1; i<=(nlstate); i++){
   }              for(j=1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);                k=k+1;
                  gm[k]=pmmij[i][j];
   matcov=matrix(1,npar,1,npar);              }
   for(i=1; i <=npar; i++){            }
     fscanf(ficpar,"%s",&str);       
     if(mle==1)            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       printf("%s",str);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fprintf(ficlog,"%s",str);          }
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       fscanf(ficpar," %le",&matcov[i][j]);            for(theta=1; theta <=npar; theta++)
       if(mle==1){              trgradg[j][theta]=gradg[theta][j];
         printf(" %.5le",matcov[i][j]);          
         fprintf(ficlog," %.5le",matcov[i][j]);          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);
       else          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficlog," %.5le",matcov[i][j]);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       fprintf(ficparo," %.5le",matcov[i][j]);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     fscanf(ficpar,"\n");  
     if(mle==1)          pmij(pmmij,cov,ncovmodel,x,nlstate);
       printf("\n");          
     fprintf(ficlog,"\n");          k=0;
     fprintf(ficparo,"\n");          for(i=1; i<=(nlstate); i++){
   }            for(j=1; j<=(nlstate+ndeath);j++){
   for(i=1; i <=npar; i++)              k=k+1;
     for(j=i+1;j<=npar;j++)              mu[k][(int) age]=pmmij[i][j];
       matcov[i][j]=matcov[j][i];            }
              }
   if(mle==1)          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     printf("\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   fprintf(ficlog,"\n");              varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
     /*-------- Rewriting paramater file ----------*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      strcpy(rfileres,"r");    /* "Rparameterfile */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      strcat(rfileres,".");    /* */            }*/
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {          fprintf(ficresprob,"\n%d ",(int)age);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficresprobcov,"\n%d ",(int)age);
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficresprobcor,"\n%d ",(int)age);
     }  
     fprintf(ficres,"#%s\n",version);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     /*-------- data file ----------*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     if((fic=fopen(datafile,"r"))==NULL)    {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       printf("Problem with datafile: %s\n", datafile);goto end;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;          }
     }          i=0;
           for (k=1; k<=(nlstate);k++){
     n= lastobs;            for (l=1; l<=(nlstate+ndeath);l++){ 
     severity = vector(1,maxwav);              i=i++;
     outcome=imatrix(1,maxwav+1,1,n);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     num=ivector(1,n);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     moisnais=vector(1,n);              for (j=1; j<=i;j++){
     annais=vector(1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     moisdc=vector(1,n);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     andc=vector(1,n);              }
     agedc=vector(1,n);            }
     cod=ivector(1,n);          }/* end of loop for state */
     weight=vector(1,n);        } /* end of loop for age */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  
     mint=matrix(1,maxwav,1,n);        /* Confidence intervalle of pij  */
     anint=matrix(1,maxwav,1,n);        /*
     s=imatrix(1,maxwav+1,1,n);          fprintf(ficgp,"\nset noparametric;unset label");
     adl=imatrix(1,maxwav+1,1,n);              fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     tab=ivector(1,NCOVMAX);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     ncodemax=ivector(1,8);          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);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     i=1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     while (fgets(line, MAXLINE, fic) != NULL)    {          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       if ((i >= firstobs) && (i <=lastobs)) {        */
          
         for (j=maxwav;j>=1;j--){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        first1=1;
           strcpy(line,stra);        for (k2=1; k2<=(nlstate);k2++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            if(l2==k2) continue;
         }            j=(k2-1)*(nlstate+ndeath)+l2;
                    for (k1=1; k1<=(nlstate);k1++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                if(i<=j) continue;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         for (j=ncovcol;j>=1;j--){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    mu1=mu[i][(int) age]/stepm*YEARM ;
         num[i]=atol(stra);                    mu2=mu[j][(int) age]/stepm*YEARM;
                            c12=cv12/sqrt(v1*v2);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    /* Computing eigen value of matrix of covariance */
           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;}*/                    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.;
         i=i+1;                    /* Eigen vectors */
       }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     }                    /*v21=sqrt(1.-v11*v11); *//* error */
     /* printf("ii=%d", ij);                    v21=(lc1-v1)/cv12*v11;
        scanf("%d",i);*/                    v12=-v21;
   imx=i-1; /* Number of individuals */                    v22=v11;
                     tnalp=v21/v11;
   /* for (i=1; i<=imx; i++){                    if(first1==1){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                      first1=0;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                      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);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                    }
     }*/                    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);
    /*  for (i=1; i<=imx; i++){                    /*printf(fignu*/
      if (s[4][i]==9)  s[4][i]=-1;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
      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]));}*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                      if(first==1){
                        first=0;
   /* Calculation of the number of parameter from char model*/                      fprintf(ficgp,"\nset parametric;unset label");
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */                      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);
   Tprod=ivector(1,15);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   Tvaraff=ivector(1,15);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   Tvard=imatrix(1,15,1,2);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   Tage=ivector(1,15);        %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                  subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   if (strlen(model) >1){                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     j=0, j1=0, k1=1, k2=1;                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     j=nbocc(model,'+');                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     j1=nbocc(model,'*');                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     cptcovn=j+1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     cptcovprod=j1;                      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",\
     strcpy(modelsav,model);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       printf("Error. Non available option model=%s ",model);                    }else{
       fprintf(ficlog,"Error. Non available option model=%s ",model);                      first=0;
       goto end;                      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);
     for(i=(j+1); i>=1;i--){                      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",\
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                    }/* if first */
       /*scanf("%d",i);*/                  } /* age mod 5 */
       if (strchr(strb,'*')) {  /* Model includes a product */                } /* end loop age */
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         if (strcmp(strc,"age")==0) { /* Vn*age */                first=1;
           cptcovprod--;              } /*l12 */
           cutv(strb,stre,strd,'V');            } /* k12 */
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/          } /*l1 */
           cptcovage++;        }/* k1 */
             Tage[cptcovage]=i;      } /* loop covariates */
             /*printf("stre=%s ", stre);*/    }
         }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
           cptcovprod--;    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           cutv(strb,stre,strc,'V');    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
           Tvar[i]=atoi(stre);    free_vector(xp,1,npar);
           cptcovage++;    fclose(ficresprob);
           Tage[cptcovage]=i;    fclose(ficresprobcov);
         }    fclose(ficresprobcor);
         else {  /* Age is not in the model */    fflush(ficgp);
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    fflush(fichtmcov);
           Tvar[i]=ncovcol+k1;  }
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */  
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc); /* m*/  /******************* Printing html file ***********/
           Tvard[k1][2]=atoi(stre); /* n */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           Tvar[cptcovn+k2]=Tvard[k1][1];                    int lastpass, int stepm, int weightopt, char model[],\
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           for (k=1; k<=lastobs;k++)                    int popforecast, int estepm ,\
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                    double jprev1, double mprev1,double anprev1, \
           k1++;                    double jprev2, double mprev2,double anprev2){
           k2=k2+2;    int jj1, k1, i1, cpt;
         }  
       }     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
       else { /* no more sum */     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  </ul>");
        /*  scanf("%d",i);*/     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
       cutv(strd,strc,strb,'V');   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
       Tvar[i]=atoi(strc);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
       }     fprintf(fichtm,"\
       strcpy(modelsav,stra);     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
         scanf("%d",i);*/     fprintf(fichtm,"\
     } /* end of loop + */   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
   } /* end model */             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       fprintf(fichtm,"\
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij (estepm=%2d months): \
   printf("cptcovprod=%d ", cptcovprod);     <a href=\"%s\">%s</a> <br>\n</li>",
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   scanf("%d ",i);*/  
     fclose(fic);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/   m=cptcoveff;
       for(i=1;i<=n;i++) weight[i]=1.0;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     }  
     /*-calculation of age at interview from date of interview and age at death -*/   jj1=0;
     agev=matrix(1,maxwav,1,imx);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
     for (i=1; i<=imx; i++) {       jj1++;
       for(m=2; (m<= maxwav); m++) {       if (cptcovn > 0) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          anint[m][i]=9999;         for (cpt=1; cpt<=cptcoveff;cpt++) 
          s[m][i]=-1;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
        }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;       }
       }       /* 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%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     for (i=1; i<=imx; i++)  {       /* Quasi-incidences */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       for(m=1; (m<= maxwav); m++){   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
         if(s[m][i] >0){  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           if (s[m][i] >= nlstate+1) {         /* Period (stable) prevalence in each health state */
             if(agedc[i]>0)         for(cpt=1; cpt<nlstate;cpt++){
               if(moisdc[i]!=99 && andc[i]!=9999)           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
                 agev[m][i]=agedc[i];  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/         }
            else {       for(cpt=1; cpt<=nlstate;cpt++) {
               if (andc[i]!=9999){          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> \
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);       }
               agev[m][i]=-1;     } /* end i1 */
               }   }/* End k1 */
             }   fprintf(fichtm,"</ul>");
           }  
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   fprintf(fichtm,"\
             if(mint[m][i]==99 || anint[m][i]==9999)  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
               agev[m][i]=1;   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
             }   fprintf(fichtm,"\
             else if(agev[m][i] >agemax){   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
               agemax=agev[m][i];           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }   fprintf(fichtm,"\
             /*agev[m][i]=anint[m][i]-annais[i];*/   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             /*   agev[m][i] = age[i]+2*m;*/           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
           }   fprintf(fichtm,"\
           else { /* =9 */   - 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): \
             agev[m][i]=1;     <a href=\"%s\">%s</a> <br>\n</li>",
             s[m][i]=-1;             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): \
         else /*= 0 Unknown */     <a href=\"%s\">%s</a> <br>\n</li>",
           agev[m][i]=1;             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), eij 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"));
     for (i=1; i<=imx; i++)  {   fprintf(fichtm,"\
       for(m=1; (m<= maxwav); m++){   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
         if (s[m][i] > (nlstate+ndeath)) {           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
           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(fichtm,"\
           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);     - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
           goto end;           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 */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  /*      <br>",fileres,fileres,fileres,fileres); */
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  /*  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); */
     free_vector(severity,1,maxwav);   fflush(fichtm);
     free_imatrix(outcome,1,maxwav+1,1,n);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);   m=cptcoveff;
     /* free_matrix(mint,1,maxwav,1,n);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);   jj1=0;
     free_vector(andc,1,n);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
           jj1++;
     wav=ivector(1,imx);       if (cptcovn > 0) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     /* Concatenates waves */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
       Tcode=ivector(1,100);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
       ncodemax[1]=1;       }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
        health expectancies in states (1) and (2): %s%d.png<br>\
    codtab=imatrix(1,100,1,10);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    h=0;     } /* end i1 */
    m=pow(2,cptcoveff);   }/* End k1 */
     fprintf(fichtm,"</ul>");
    for(k=1;k<=cptcoveff; k++){   fflush(fichtm);
      for(i=1; i <=(m/pow(2,k));i++){  }
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /******************* Gnuplot file **************/
            h++;  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;  
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    char dirfileres[132],optfileres[132];
          }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
        }    int ng;
      }  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
    }  /*     printf("Problem with file %s",optionfilegnuplot); */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
       codtab[1][2]=1;codtab[2][2]=2; */  /*   } */
    /* for(i=1; i <=m ;i++){  
       for(k=1; k <=cptcovn; k++){    /*#ifdef windows */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    fprintf(ficgp,"cd \"%s\" \n",pathc);
       }      /*#endif */
       printf("\n");    m=pow(2,cptcoveff);
       }  
       scanf("%d",i);*/    strcpy(dirfileres,optionfilefiname);
        strcpy(optfileres,"vpl");
    /* Calculates basic frequencies. Computes observed prevalence at single age   /* 1eme*/
        and prints on file fileres'p'. */    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
           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);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       fprintf(ficgp,"set xlabel \"Age\" \n\
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  set ylabel \"Probability\" \n\
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  set ter png small\n\
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  set size 0.65,0.65\n\
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
        
     /* For Powell, parameters are in a vector p[] starting at p[1]       for (i=1; i<= nlstate ; i ++) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
     if(mle==1){       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       for (i=1; i<= nlstate ; i ++) {
     }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
     /*--------- 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(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    jk=1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       }  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    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++){    /*2 eme*/
        if (k != i)    
          {    for (k1=1; k1<= m ; k1 ++) { 
            printf("%d%d ",i,k);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
            fprintf(ficlog,"%d%d ",i,k);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
            fprintf(ficres,"%1d%1d ",i,k);      
            for(j=1; j <=ncovmodel; j++){      for (i=1; i<= nlstate+1 ; i ++) {
              printf("%f ",p[jk]);        k=2*i;
              fprintf(ficlog,"%f ",p[jk]);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
              fprintf(ficres,"%f ",p[jk]);        for (j=1; j<= nlstate+1 ; j ++) {
              jk++;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            }          else fprintf(ficgp," \%%*lf (\%%*lf)");
            printf("\n");        }   
            fprintf(ficlog,"\n");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
            fprintf(ficres,"\n");        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)");
    if(mle==1){          else fprintf(ficgp," \%%*lf (\%%*lf)");
      /* Computing hessian and covariance matrix */        }   
      ftolhess=ftol; /* Usually correct */        fprintf(ficgp,"\" t\"\" w l 0,");
      hesscov(matcov, p, npar, delti, ftolhess, func);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    }        for (j=1; j<= nlstate+1 ; j ++) {
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    printf("# Scales (for hessian or gradient estimation)\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");        }   
    for(i=1,jk=1; i <=nlstate; i++){        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
      for(j=1; j <=nlstate+ndeath; j++){        else fprintf(ficgp,"\" t\"\" w l 0,");
        if (j!=i) {      }
          fprintf(ficres,"%1d%1d",i,j);    }
          printf("%1d%1d",i,j);    
          fprintf(ficlog,"%1d%1d",i,j);    /*3eme*/
          for(k=1; k<=ncovmodel;k++){    
            printf(" %.5e",delti[jk]);    for (k1=1; k1<= m ; k1 ++) { 
            fprintf(ficlog," %.5e",delti[jk]);      for (cpt=1; cpt<= nlstate ; cpt ++) {
            fprintf(ficres," %.5e",delti[jk]);        /*       k=2+nlstate*(2*cpt-2); */
            jk++;        k=2+(nlstate+1)*(cpt-1);
          }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
          printf("\n");        fprintf(ficgp,"set ter png small\n\
          fprintf(ficlog,"\n");  set size 0.65,0.65\n\
          fprintf(ficres,"\n");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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);
    k=1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    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");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
    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");        for (i=1; i< nlstate ; i ++) {
    for(i=1;i<=npar;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);
      /*  if (k>nlstate) k=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);*/
          i1=(i-1)/(ncovmodel*nlstate)+1;          
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        } 
          printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
      fprintf(ficres,"%3d",i);      }
      if(mle==1)    }
        printf("%3d",i);    
      fprintf(ficlog,"%3d",i);    /* CV preval stable (period) */
      for(j=1; j<=i;j++){    for (k1=1; k1<= m ; k1 ++) { 
        fprintf(ficres," %.5e",matcov[i][j]);      for (cpt=1; cpt<=nlstate ; cpt ++) {
        if(mle==1)        k=3;
          printf(" %.5e",matcov[i][j]);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
        fprintf(ficlog," %.5e",matcov[i][j]);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
      }  set ter png small\nset size 0.65,0.65\n\
      fprintf(ficres,"\n");  unset log y\n\
      if(mle==1)  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
        printf("\n");        
      fprintf(ficlog,"\n");        for (i=1; i< nlstate ; i ++)
      k++;          fprintf(ficgp,"+$%d",k+i+1);
    }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
            
    while((c=getc(ficpar))=='#' && c!= EOF){        l=3+(nlstate+ndeath)*cpt;
      ungetc(c,ficpar);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
      fgets(line, MAXLINE, ficpar);        for (i=1; i< nlstate ; i ++) {
      puts(line);          l=3+(nlstate+ndeath)*cpt;
      fputs(line,ficparo);          fprintf(ficgp,"+$%d",l+i+1);
    }        }
    ungetc(c,ficpar);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
    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) {    /* proba elementaires */
      bage = ageminpar;    for(i=1,jk=1; i <=nlstate; i++){
      fage = agemaxpar;      for(k=1; k <=(nlstate+ndeath); k++){
    }        if (k != i) {
              for(j=1; j <=ncovmodel; j++){
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            jk++; 
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            fprintf(ficgp,"\n");
              }
    while((c=getc(ficpar))=='#' && c!= EOF){        }
      ungetc(c,ficpar);      }
      fgets(line, MAXLINE, ficpar);     }
      puts(line);  
      fputs(line,ficparo);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
    }       for(jk=1; jk <=m; jk++) {
    ungetc(c,ficpar);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
           if (ng==2)
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         else
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           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);
    while((c=getc(ficpar))=='#' && c!= EOF){         i=1;
      ungetc(c,ficpar);         for(k2=1; k2<=nlstate; k2++) {
      fgets(line, MAXLINE, ficpar);           k3=i;
      puts(line);           for(k=1; k<=(nlstate+ndeath); k++) {
      fputs(line,ficparo);             if (k != k2){
    }               if(ng==2)
    ungetc(c,ficpar);                 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);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;               ij=1;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;               for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fscanf(ficpar,"pop_based=%d\n",&popbased);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   fprintf(ficparo,"pop_based=%d\n",popbased);                     ij++;
   fprintf(ficres,"pop_based=%d\n",popbased);                   }
                   else
   while((c=getc(ficpar))=='#' && c!= EOF){                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     ungetc(c,ficpar);               }
     fgets(line, MAXLINE, ficpar);               fprintf(ficgp,")/(1");
     puts(line);               
     fputs(line,ficparo);               for(k1=1; k1 <=nlstate; k1++){   
   }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   ungetc(c,ficpar);                 ij=1;
                  for(j=3; j <=ncovmodel; j++){
   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);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
 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,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 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);                     ij++;
                    }
                    else
 while((c=getc(ficpar))=='#' && c!= EOF){                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     ungetc(c,ficpar);                 }
     fgets(line, MAXLINE, ficpar);                 fprintf(ficgp,")");
     puts(line);               }
     fputs(line,ficparo);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   ungetc(c,ficpar);               i=i+ncovmodel;
              }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);           } /* end k */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);         } /* end k2 */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);       } /* end jk */
      } /* end ng */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     fflush(ficgp); 
   }  /* end gnuplot */
 /*------------ gnuplot -------------*/  
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp");  /*************** Moving average **************/
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     printf("Problem with file %s",optionfilegnuplot);  
   }    int i, cpt, cptcod;
   fclose(ficgp);    int modcovmax =1;
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    int mobilavrange, mob;
 /*--------- index.htm --------*/    double age;
   
   strcpy(optionfilehtm,optionfile);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   strcat(optionfilehtm,".htm");                             a covariate has 2 modalities */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      else mobilavrange=mobilav;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      for (age=bage; age<=fage; age++)
 \n        for (i=1; i<=nlstate;i++)
 Total number of observations=%d <br>\n          for (cptcod=1;cptcod<=modcovmax;cptcod++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
 <hr  size=\"2\" color=\"#EC5E5E\">      /* We keep the original values on the extreme ages bage, fage and for 
  <ul><li><h4>Parameter files</h4>\n         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n         we use a 5 terms etc. until the borders are no more concerned. 
  - Log file of the run: <a href=\"%s\">%s</a><br>\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,filelog,filelog,optionfilegnuplot,optionfilegnuplot);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   fclose(fichtm);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
 /*------------ free_vector  -------------*/                for (cpt=1;cpt<=(mob-1)/2;cpt++){
  chdir(path);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                    mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
  free_ivector(wav,1,imx);                }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              }
  free_ivector(num,1,n);          }
  free_vector(agedc,1,n);        }/* end age */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      }/* end mob */
  fclose(ficparo);    }else return -1;
  fclose(ficres);    return 0;
   }/* End movingaverage */
   
   /*--------------- Prevalence limit --------------*/  
    /************** Forecasting ******************/
   strcpy(filerespl,"pl");  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){
   strcat(filerespl,fileres);    /* proj1, year, month, day of starting projection 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       agemin, agemax range of age
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       dateprev1 dateprev2 range of dates during which prevalence is computed
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;       anproj2 year of en of projection (same day and month as proj1).
   }    */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    int *popage;
   fprintf(ficrespl,"#Prevalence limit\n");    double agec; /* generic age */
   fprintf(ficrespl,"#Age ");    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double *popeffectif,*popcount;
   fprintf(ficrespl,"\n");    double ***p3mat;
      double ***mobaverage;
   prlim=matrix(1,nlstate,1,nlstate);    char fileresf[FILENAMELENGTH];
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    agelim=AGESUP;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    strcpy(fileresf,"f"); 
   k=0;    strcat(fileresf,fileres);
   agebase=ageminpar;    if((ficresf=fopen(fileresf,"w"))==NULL) {
   agelim=agemaxpar;      printf("Problem with forecast resultfile: %s\n", fileresf);
   ftolpl=1.e-10;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}    printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    if (mobilav!=0) {
         fprintf(ficrespl,"\n#******");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         printf("\n#******");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog,"\n#******");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         for(j=1;j<=cptcoveff;j++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         }    stepsize=(int) (stepm+YEARM-1)/YEARM;
         fprintf(ficrespl,"******\n");    if (stepm<=12) stepsize=1;
         printf("******\n");    if(estepm < stepm){
         fprintf(ficlog,"******\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
            }
         for (age=agebase; age<=agelim; age++){    else  hstepm=estepm;   
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );    hstepm=hstepm/stepm; 
           for(i=1; i<=nlstate;i++)    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
           fprintf(ficrespl," %.5f", prlim[i][i]);                                 fractional in yp1 */
           fprintf(ficrespl,"\n");    anprojmean=yp;
         }    yp2=modf((yp1*12),&yp);
       }    mprojmean=yp;
     }    yp1=modf((yp2*30.5),&yp);
   fclose(ficrespl);    jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
   /*------------- h Pij x at various ages ------------*/    if(mprojmean==0) jprojmean=1;
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    i1=cptcoveff;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    if (cptcovn < 1){i1=1;}
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   }    
   printf("Computing pij: result on file '%s' \n", filerespij);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);  
    /*            if (h==(int)(YEARM*yearp)){ */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   /*if (stepm<=24) stepsize=2;*/      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
   agelim=AGESUP;        fprintf(ficresf,"\n#******");
   hstepm=stepsize*YEARM; /* Every year of age */        for(j=1;j<=cptcoveff;j++) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          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]]);
         }
   /* hstepm=1;   aff par mois*/        fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   k=0;        for(j=1; j<=nlstate+ndeath;j++){ 
   for(cptcov=1;cptcov<=i1;cptcov++){          for(i=1; i<=nlstate;i++)              
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            fprintf(ficresf," p%d%d",i,j);
       k=k+1;          fprintf(ficresf," p.%d",j);
         fprintf(ficrespij,"\n#****** ");        }
         for(j=1;j<=cptcoveff;j++)        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresf,"\n");
         fprintf(ficrespij,"******\n");          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (agec=fage; agec>=(ageminpar-1); agec--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
           oldm=oldms;savm=savms;            for (h=0; h<=nhstepm; h++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                if (h*hstepm/YEARM*stepm ==yearp) {
           fprintf(ficrespij,"# Age");                fprintf(ficresf,"\n");
           for(i=1; i<=nlstate;i++)                for(j=1;j<=cptcoveff;j++) 
             for(j=1; j<=nlstate+ndeath;j++)                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
               fprintf(ficrespij," %1d-%1d",i,j);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           fprintf(ficrespij,"\n");              } 
            for (h=0; h<=nhstepm; h++){              for(j=1; j<=nlstate+ndeath;j++) {
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                ppij=0.;
             for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++) {
               for(j=1; j<=nlstate+ndeath;j++)                  if (mobilav==1) 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
             fprintf(ficrespij,"\n");                  else {
              }                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  }
           fprintf(ficrespij,"\n");                  if (h*hstepm/YEARM*stepm== yearp) {
         }                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
     }                  }
   }                } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);                  fprintf(ficresf," %.3f", ppij);
                 }
   fclose(ficrespij);              }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*---------- Forecasting ------------------*/          } /* end agec */
   if((stepm == 1) && (strcmp(model,".")==0)){        } /* end yearp */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      } /* end cptcod */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    } /* end  cptcov */
   }         
   else{    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     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);    fclose(ficresf);
     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);  }
   }  
    /************** 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){
   /*---------- Health expectancies and variances ------------*/    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   strcpy(filerest,"t");    int *popage;
   strcat(filerest,fileres);    double calagedatem, agelim, kk1, kk2;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double *popeffectif,*popcount;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double ***p3mat,***tabpop,***tabpopprev;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    double ***mobaverage;
   }    char filerespop[FILENAMELENGTH];
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
   strcpy(filerese,"e");    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   strcat(filerese,fileres);    
   if((ficreseij=fopen(filerese,"w"))==NULL) {    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    
   }    strcpy(filerespop,"pop"); 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    strcat(filerespop,fileres);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
   strcpy(fileresv,"v");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   strcat(fileresv,fileres);    }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    printf("Computing forecasting: result on file '%s' \n", filerespop);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    if (mobilav!=0) {
   calagedate=-1;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   k=0;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   for(cptcov=1;cptcov<=i1;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;  
       fprintf(ficrest,"\n#****** ");    stepsize=(int) (stepm+YEARM-1)/YEARM;
       for(j=1;j<=cptcoveff;j++)    if (stepm<=12) stepsize=1;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficrest,"******\n");    agelim=AGESUP;
     
       fprintf(ficreseij,"\n#****** ");    hstepm=1;
       for(j=1;j<=cptcoveff;j++)    hstepm=hstepm/stepm; 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");    if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
       fprintf(ficresvij,"\n#****** ");        printf("Problem with population file : %s\n",popfile);exit(0);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } 
       fprintf(ficresvij,"******\n");      popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      popcount=vector(0,AGESUP);
       oldm=oldms;savm=savms;      
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        i=1;   
        while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     
       oldm=oldms;savm=savms;      imx=i;
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
       if(popbased==1){    }
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  
        }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
          k=k+1;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        fprintf(ficrespop,"\n#******");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficrest,"\n");          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
       epj=vector(1,nlstate+1);        fprintf(ficrespop,"******\n");
       for(age=bage; age <=fage ;age++){        fprintf(ficrespop,"# Age");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popbased==1) {        if (popforecast==1)  fprintf(ficrespop," [Population]");
           for(i=1; i<=nlstate;i++)        
             prlim[i][i]=probs[(int)age][i][k];        for (cpt=0; cpt<=0;cpt++) { 
         }          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                  
         fprintf(ficrest," %4.0f",age);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            nhstepm = nhstepm/hstepm; 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];            
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }            oldm=oldms;savm=savms;
           epj[nlstate+1] +=epj[j];            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         }          
             for (h=0; h<=nhstepm; h++){
         for(i=1, vepp=0.;i <=nlstate;i++)              if (h==(int) (calagedatem+YEARM*cpt)) {
           for(j=1;j <=nlstate;j++)                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
             vepp += vareij[i][j][(int)age];              } 
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));              for(j=1; j<=nlstate+ndeath;j++) {
         for(j=1;j <=nlstate;j++){                kk1=0.;kk2=0;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                for(i=1; i<=nlstate;i++) {              
         }                  if (mobilav==1) 
         fprintf(ficrest,"\n");                    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];
   }                  }
 free_matrix(mint,1,maxwav,1,n);                }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                if (h==(int)(calagedatem+12*cpt)){
     free_vector(weight,1,n);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   fclose(ficreseij);                    /*fprintf(ficrespop," %.3f", kk1);
   fclose(ficresvij);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   fclose(ficrest);                }
   fclose(ficpar);              }
   free_vector(epj,1,nlstate+1);              for(i=1; i<=nlstate;i++){
                  kk1=0.;
   /*------- Variance limit prevalence------*/                    for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   strcpy(fileresvpl,"vpl");                  }
   strcat(fileresvpl,fileres);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   }                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   
       k=k+1;    /******/
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       fprintf(ficresvpl,"******\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
                  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            nhstepm = nhstepm/hstepm; 
       oldm=oldms;savm=savms;            
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            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++){
   fclose(ficresvpl);              if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   /*---------- End : free ----------------*/              } 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              for(j=1; j<=nlstate+ndeath;j++) {
                  kk1=0.;kk2=0;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                for(i=1; i<=nlstate;i++) {              
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                  }
                  if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   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_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          }
          }
   free_matrix(matcov,1,npar,1,npar);     } 
   free_vector(delti,1,npar);    }
   free_matrix(agev,1,maxwav,1,imx);   
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   fprintf(fichtm,"\n</body>");    if (popforecast==1) {
   fclose(fichtm);      free_ivector(popage,0,AGESUP);
   fclose(ficgp);      free_vector(popeffectif,0,AGESUP);
        free_vector(popcount,0,AGESUP);
     }
   if(erreur >0){    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("End of Imach with error or warning %d\n",erreur);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    fclose(ficrespop);
   }else{  } /* End of popforecast */
    printf("End of Imach\n");  
    fprintf(ficlog,"End of Imach\n");  int fileappend(FILE *fichier, char *optionfich)
   }  {
   printf("See log file on %s\n",filelog);    if((fichier=fopen(optionfich,"a"))==NULL) {
   fclose(ficlog);      printf("Problem with file: %s\n", optionfich);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      fprintf(ficlog,"Problem with file: %s\n", optionfich);
        return (0);
   /* 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);*/    fflush(fichier);
   /*------ End -----------*/    return (1);
   }
   
  end:  
 #ifdef windows  /**************** function prwizard **********************/
   /* chdir(pathcd);*/  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
 #endif  {
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    /* Wizard to print covariance matrix template */
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    char ca[32], cb[32], cc[32];
  strcpy(plotcmd,GNUPLOTPROGRAM);    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
  strcat(plotcmd," ");    int numlinepar;
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 #ifdef windows    for(i=1; i <=nlstate; i++){
   while (z[0] != 'q') {      jj=0;
     /* chdir(path); */      for(j=1; j <=nlstate+ndeath; j++){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        if(j==i) continue;
     scanf("%s",z);        jj++;
     if (z[0] == 'c') system("./imach");        /*ca[0]= k+'a'-1;ca[1]='\0';*/
     else if (z[0] == 'e') system(optionfilehtm);        printf("%1d%1d",i,j);
     else if (z[0] == 'g') system(plotcmd);        fprintf(ficparo,"%1d%1d",i,j);
     else if (z[0] == 'q') exit(0);        for(k=1; k<=ncovmodel;k++){
   }          /*        printf(" %lf",param[i][j][k]); */
 #endif          /*        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;
   }
   
   /******************* 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\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);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     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;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  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, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*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 *severity;
     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];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     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; /* Un peu sale */
       }
     }
     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);
     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++;
       puts(line);
       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++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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);
       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 guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         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",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);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         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);
   
       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++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       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 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     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);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     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;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         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 '%d' at line number %d %s 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);
           exit(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.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(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 %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(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.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(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 */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        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]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         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 */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             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];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*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);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     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(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\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);     
           goto end;
         }
       }
     }
   
     /*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); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     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 */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],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);*/
       
     /*------------ 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");
     }
     /*  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,"<body>\n<title>IMaCh Cov %s</title>\n <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",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <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",\
             fileres,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);
       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]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       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);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  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");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       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,path); /* 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);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       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("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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,path); /* 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) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             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);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       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); */
         /*      } */
       }
     
   
       /*---------- 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(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);
   
       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);
   
       /* 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);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           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(ficreseij,"\n#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficreseij,"******\n");
           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;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
           cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state ( 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 (popbased==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,1,15,1,2);
       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(ficreseij);
       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++){
           k=k+1;
           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 */
     free_matrix(prlim,1,nlstate,1,nlstate);
       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,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       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 %d 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 %d 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>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     /*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.1.50  
changed lines
  Added in v.1.117


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