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Diff for /imach/src/imach.c between versions 1.56 and 1.94

version 1.56, 2002/07/24 17:28:25 version 1.94, 2003/06/27 13:00:02
Line 1 Line 1
 /* $Id$  /* $Id$
     $State$
     $Log$
     Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
   
     Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
     (Module): Version 0.96b
   
     Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
   
     Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
   
     Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   
     Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   
     Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
     Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
   
     Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
     routine fileappend.
   
     Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
     interview.
     (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
     truncation)
     (Repository): No more line truncation errors.
   
     Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
     parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
     Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
   
     Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   
   */
   /*
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
Line 32 Line 101
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
Line 48 Line 117
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
   **********************************************************************/    **********************************************************************/
   /*
     main
     read parameterfile
     read datafile
     concatwav
     freqsummary
     if (mle >= 1)
       mlikeli
     print results files
     if mle==1 
        computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
     open gnuplot file
     open html file
     stable prevalence
      for age prevalim()
     h Pij x
     variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
     Variance-covariance of DFLE
     prevalence()
      movingaverage()
     varevsij() 
     if popbased==1 varevsij(,popbased)
     total life expectancies
     Variance of stable prevalence
    end
   */
   
   
   
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
   #include <sys/time.h>
   #include <time.h>
   #include "timeval.h"
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 132
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  /*#define windows*/
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
Line 75 Line 185
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
 #ifdef windows  #ifdef unix
 #define DIRSEPARATOR '\\'  
 #define ODIRSEPARATOR '/'  
 #else  
 #define DIRSEPARATOR '/'  #define DIRSEPARATOR '/'
 #define ODIRSEPARATOR '\\'  #define ODIRSEPARATOR '\\'
   #else
   #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #endif  #endif
   
 char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";  /* $Id$ */
 int erreur; /* Error number */  /* $State$ */
   
   char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;  int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;  int npar=NPARMAX;
Line 96  int popbased=0; Line 210  int popbased=0;
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav; /* Maxim number of waves */
 int jmin, jmax; /* min, max spacing between 2 waves */  int jmin, jmax; /* min, max spacing between 2 waves */
   int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 int mle, weightopt;  int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  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
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double jmean; /* Mean space between 2 waves */  double jmean; /* Mean space between 2 waves */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficlog;  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE *ficresprobmorprev;  FILE *ficresprobmorprev;
 FILE *fichtm; /* Html File */  FILE *fichtm, *fichtmcov; /* Html File */
 FILE *ficreseij;  FILE *ficreseij;
 char filerese[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
 FILE  *ficresvij;  FILE  *ficresvij;
Line 116  char fileresvpl[FILENAMELENGTH]; Line 240  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
   int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char fileregp[FILENAMELENGTH];
 char popfile[FILENAMELENGTH];  char popfile[FILENAMELENGTH];
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
   extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
   extern long time();
   char strcurr[80], strfor[80];
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
Line 161  int estepm; Line 297  int estepm;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 int m,nb;  int m,nb;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs;
 double dateintmean=0;  double dateintmean=0;
Line 177  double ftolhess; /* Tolerance for comput Line 314  double ftolhess; /* Tolerance for comput
 /**************** split *************************/  /**************** split *************************/
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
    char *s;                             /* pointer */    char  *ss;                            /* pointer */
    int  l1, l2;                         /* length counters */    int   l1, l2;                         /* length counters */
   
    l1 = strlen( path );                 /* length of path */    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
    if ( s == NULL ) {                   /* no directory, so use current */    if ( ss == NULL ) {                   /* no directory, so use current */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #if     defined(__bsd__)                /* get current working directory */      /* get current working directory */
       extern char       *getwd( );      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       if ( getwd( dirc ) == NULL ) {        return( GLOCK_ERROR_GETCWD );
 #else      }
       extern char       *getcwd( );      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {      ss++;                               /* after this, the filename */
 #endif      l2 = strlen( ss );                  /* length of filename */
          return( GLOCK_ERROR_GETCWD );      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       }      strcpy( name, ss );         /* save file name */
       strcpy( name, path );             /* we've got it */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
    } else {                             /* strip direcotry from path */      dirc[l1-l2] = 0;                    /* add zero */
       s++;                              /* after this, the filename */    }
       l2 = strlen( s );                 /* length of filename */    l1 = strlen( dirc );                  /* length of directory */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    /*#ifdef windows
       strcpy( name, s );                /* save file name */    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  
    }  
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  #else
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 #endif  #endif
    s = strrchr( name, '.' );            /* find last / */    */
    s++;    ss = strrchr( name, '.' );            /* find last / */
    strcpy(ext,s);                       /* save extension */    ss++;
    l1= strlen( name);    strcpy(ext,ss);                       /* save extension */
    l2= strlen( s)+1;    l1= strlen( name);
    strncpy( finame, name, l1-l2);    l2= strlen(ss)+1;
    finame[l1-l2]= 0;    strncpy( finame, name, l1-l2);
    return( 0 );                         /* we're done */    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
 }  }
   
   
 /******************************************/  /******************************************/
   
 void replace(char *s, char*t)  void replace_back_to_slash(char *s, char*t)
 {  {
   int i;    int i;
   int lg=20;    int lg=0;
   i=0;    i=0;
   lg=strlen(t);    lg=strlen(t);
   for(i=0; i<= lg; i++) {    for(i=0; i<= lg; i++) {
Line 277  void nrerror(char error_text[]) Line 409  void nrerror(char error_text[])
 {  {
   fprintf(stderr,"ERREUR ...\n");    fprintf(stderr,"ERREUR ...\n");
   fprintf(stderr,"%s\n",error_text);    fprintf(stderr,"%s\n",error_text);
   exit(1);    exit(EXIT_FAILURE);
 }  }
 /*********************** vector *******************/  /*********************** vector *******************/
 double *vector(int nl, int nh)  double *vector(int nl, int nh)
Line 309  void free_ivector(int *v, long nl, long Line 441  void free_ivector(int *v, long nl, long
   free((FREE_ARG)(v+nl-NR_END));    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
   /************************lvector *******************************/
   long *lvector(long nl,long nh)
   {
     long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   }
   
   /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
   {
     free((FREE_ARG)(v+nl-NR_END));
   }
   
 /******************* imatrix *******************************/  /******************* imatrix *******************************/
 int **imatrix(long nrl, long nrh, long ncl, long nch)   int **imatrix(long nrl, long nrh, long ncl, long nch) 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
Line 363  double **matrix(long nrl, long nrh, long Line 510  double **matrix(long nrl, long nrh, long
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   return m;    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
 }  }
   
 /*************************free matrix ************************/  /*************************free matrix ************************/
Line 402  double ***ma3x(long nrl, long nrh, long Line 551  double ***ma3x(long nrl, long nrh, long
     for (j=ncl+1; j<=nch; j++)       for (j=ncl+1; j<=nch; j++) 
       m[i][j]=m[i][j-1]+nlay;        m[i][j]=m[i][j-1]+nlay;
   }    }
   return m;    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
 }  }
   
 /*************************free ma3x ************************/  /*************************free ma3x ************************/
Line 413  void free_ma3x(double ***m, long nrl, lo Line 565  void free_ma3x(double ***m, long nrl, lo
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
   /*************** function subdirf ***********/
   char *subdirf(char fileres[])
   {
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
     return tmpout;
   }
   
   /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
   {
     
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,fileres);
     return tmpout;
   }
   
   /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
   {
     
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,preop2);
     strcat(tmpout,fileres);
     return tmpout;
   }
   
 /***************** f1dim *************************/  /***************** f1dim *************************/
 extern int ncom;   extern int ncom; 
 extern double *pcom,*xicom;  extern double *pcom,*xicom;
Line 588  void linmin(double p[], double xi[], int Line 775  void linmin(double p[], double xi[], int
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
   
   char *asc_diff_time(long time_sec, char ascdiff[])
   {
     long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
   
 /*************** powell ************************/  /*************** powell ************************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             double (*func)(double []))               double (*func)(double [])) 
Line 598  void powell(double p[], double **xi, int Line 798  void powell(double p[], double **xi, int
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
     int niterf, itmp;
   
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
   xit=vector(1,n);     xit=vector(1,n); 
Line 608  void powell(double p[], double **xi, int Line 810  void powell(double p[], double **xi, int
     fp=(*fret);       fp=(*fret); 
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      last_time=curr_time;
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      (void) gettimeofday(&curr_time,&tzp);
     for (i=1;i<=n;i++)       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);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
     fprintf(ficlog," %d %.12f",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
       }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tmf));
   /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time;
         itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')
           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);
         for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
           fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         }
       }
     for (i=1;i<=n;i++) {       for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret);         fptt=(*fret); 
Line 854  double **matprod2(double **out, double * Line 1084  double **matprod2(double **out, double *
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month     /* Computes the transition matrix starting at age 'age' over 
      duration (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        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        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).       (typically every 2 years instead of every month which is too big 
        for the memory).
      Model is determined by parameters x and covariates have to be        Model is determined by parameters x and covariates have to be 
      included manually here.        included manually here. 
   
Line 914  double func( double *x) Line 1146  double func( double *x)
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
     int s1, s2;
     double bbh, survp;
   long ipmx;    long ipmx;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
Line 924  double func( double *x) Line 1158  double func( double *x)
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
     if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               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++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
            */
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
            */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           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 die between last step unit time and current 
                step unit time, which is also the differences between probability to die before dh 
                and probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
           lower mortality.
             */
             lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
             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 */
           } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
           /*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;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               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++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           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;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               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++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               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++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
             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 */
           }
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
       } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               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++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
       } /* end of individual */
     } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   }
   
   /*************** log-likelihood *************/
   double funcone( double *x)
   {
     /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
     double lli; /* Individual log likelihood */
     double llt;
     int s1, s2;
     double bbh, survp;
     /*extern weight */
     /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     */
     cov[1]=1.;
   
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(mi=1; mi<= wav[i]-1; mi++){      for(mi=1; mi<= wav[i]-1; mi++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
       for(d=0; d<dh[mi][i]; d++){        for(d=0; d<dh[mi][i]; d++){
         newm=savm;          newm=savm;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for (kk=1; kk<=cptcovage;kk++) {          for (kk=1; kk<=cptcovage;kk++) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }          }
           
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;          savm=oldm;
         oldm=newm;          oldm=newm;
           
           
       } /* end mult */        } /* end mult */
               
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        s1=s[mw[mi][i]][i];
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
          */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
         } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } 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 */
           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 */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
       ipmx +=1;        ipmx +=1;
       sw += weight[i];        sw += weight[i];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
                   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);
           }
           fprintf(ficresilk," %10.6f\n", -llt);
         }
     } /* end of wave */      } /* end of wave */
   } /* end of individual */    } /* end of individual */
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
       gsw=sw;
     }
   return -l;    return -l;
 }  }
   
   
   /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     /* This routine should help understanding what is done with 
        the selection of individuals/waves and
        to check the exact contribution to the likelihood.
        Plotting could be done.
      */
     int k;
   
     if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
       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");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  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; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   
     *fretone=(*funcone)(p);
     if(*globpri !=0){
       fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     } 
     return;
   }
   
   
 /*********** Maximum Likelihood Estimation ***************/  /*********** Maximum Likelihood Estimation ***************/
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j, iter;    int i,j, iter;
   double **xi,*delti;    double **xi;
   double fret;    double fret;
     double fretone; /* Only one call to likelihood */
     char filerespow[FILENAMELENGTH];
   xi=matrix(1,npar,1,npar);    xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     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,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    fclose(ficrespow);
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
 }  }
Line 1237  void lubksb(double **a, int n, int *indx Line 1785  void lubksb(double **a, int n, int *indx
 }   } 
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 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)  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)
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp;    double *pp, **prop;
   double pos, k2, dateintsum=0,k2cpt=0;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   FILE *ficresp;    FILE *ficresp;
   char fileresp[FILENAMELENGTH];    char fileresp[FILENAMELENGTH];
       
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   strcpy(fileresp,"p");    strcpy(fileresp,"p");
   strcat(fileresp,fileres);    strcat(fileresp,fileres);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
Line 1257  void  freqsummary(char fileres[], int ag Line 1805  void  freqsummary(char fileres[], int ag
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);      exit(0);
   }    }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   j1=0;    j1=0;
       
   j=cptcoveff;    j=cptcoveff;
Line 1272  void  freqsummary(char fileres[], int ag Line 1820  void  freqsummary(char fileres[], int ag
         scanf("%d", i);*/          scanf("%d", i);*/
       for (i=-1; i<=nlstate+ndeath; i++)          for (i=-1; i<=nlstate+ndeath; i++)  
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for (jk=-1; jk<=nlstate+ndeath; jk++)  
           for(m=agemin; m <= agemax+3; m++)            for(m=iagemin; m <= iagemax+3; m++)
             freq[i][jk][m]=0;              freq[i][jk][m]=0;
   
       for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
               
       dateintsum=0;        dateintsum=0;
       k2cpt=0;        k2cpt=0;
Line 1284  void  freqsummary(char fileres[], int ag Line 1836  void  freqsummary(char fileres[], int ag
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
               bool=0;                bool=0;
         }          }
         if (bool==1) {          if (bool==1){
           for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){
             k2=anint[m][i]+(mint[m][i]/12.);              k2=anint[m][i]+(mint[m][i]/12.);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
               if(agev[m][i]==0) agev[m][i]=agemax+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               if(agev[m][i]==1) agev[m][i]=agemax+2;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
               if (m<lastpass) {                if (m<lastpass) {
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               }                }
                               
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                 dateintsum=dateintsum+k2;                  dateintsum=dateintsum+k2;
                 k2cpt++;                  k2cpt++;
               }                }
             }                /*}*/
           }            }
         }          }
       }        }
                 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
Line 1315  void  freqsummary(char fileres[], int ag Line 1868  void  freqsummary(char fileres[], int ag
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       fprintf(ficresp, "\n");        fprintf(ficresp, "\n");
               
       for(i=(int)agemin; i <= (int)agemax+3; i++){        for(i=iagemin; i <= iagemax+3; i++){
         if(i==(int)agemax+3){          if(i==iagemax+3){
           fprintf(ficlog,"Total");            fprintf(ficlog,"Total");
         }else{          }else{
           if(first==1){            if(first==1){
Line 1347  void  freqsummary(char fileres[], int ag Line 1900  void  freqsummary(char fileres[], int ag
         for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             pp[jk] += freq[jk][m][i];              pp[jk] += freq[jk][m][i];
         }          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         for(jk=1,pos=0; jk <=nlstate ; jk++)  
           pos += pp[jk];            pos += pp[jk];
             posprop += prop[jk][i];
           }
         for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
           if(pos>=1.e-5){            if(pos>=1.e-5){
             if(first==1)              if(first==1)
Line 1361  void  freqsummary(char fileres[], int ag Line 1915  void  freqsummary(char fileres[], int ag
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           }            }
           if( i <= (int) agemax){            if( i <= iagemax){
             if(pos>=1.e-5){              if(pos>=1.e-5){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
               probs[i][jk][j1]= pp[jk]/pos;                /*probs[i][jk][j1]= pp[jk]/pos;*/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             }              }
             else              else
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           }            }
         }          }
                   
Line 1379  void  freqsummary(char fileres[], int ag Line 1933  void  freqsummary(char fileres[], int ag
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             }              }
         if(i <= (int) agemax)          if(i <= iagemax)
           fprintf(ficresp,"\n");            fprintf(ficresp,"\n");
         if(first==1)          if(first==1)
           printf("Others in log...\n");            printf("Others in log...\n");
Line 1390  void  freqsummary(char fileres[], int ag Line 1944  void  freqsummary(char fileres[], int ag
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
     
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
       free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /* End of Freq */    /* End of Freq */
 }  }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
 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)  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)
 {  /* Some frequencies */  {  
     /* 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).
        We still use firstpass and lastpass as another selection.
     */
     
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp;    double *pp, **prop;
   double pos, k2;    double pos,posprop; 
     double  y2; /* in fractional years */
   pp=vector(1,nlstate);    int iagemin, iagemax;
     
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    iagemin= (int) agemin;
     iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;    j1=0;
       
   j=cptcoveff;    j=cptcoveff;
Line 1417  void prevalence(int agemin, float agemax Line 1979  void prevalence(int agemin, float agemax
     for(i1=1; i1<=ncodemax[k1];i1++){      for(i1=1; i1<=ncodemax[k1];i1++){
       j1++;        j1++;
               
       for (i=-1; i<=nlstate+ndeath; i++)          for (i=1; i<=nlstate; i++)  
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for(m=iagemin; m <= iagemax+3; m++)
           for(m=agemin; m <= agemax+3; m++)            prop[i][m]=0.0;
             freq[i][jk][m]=0;  
             
       for (i=1; i<=imx; i++) {        for (i=1; i<=imx; i++) { /* Each individual */
         bool=1;          bool=1;
         if  (cptcovn>0) {          if  (cptcovn>0) {
           for (z1=1; z1<=cptcoveff; z1++)             for (z1=1; z1<=cptcoveff; z1++) 
Line 1430  void prevalence(int agemin, float agemax Line 1991  void prevalence(int agemin, float agemax
               bool=0;                bool=0;
         }           } 
         if (bool==1) {           if (bool==1) { 
           for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
             k2=anint[m][i]+(mint[m][i]/12.);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               if(agev[m][i]==0) agev[m][i]=agemax+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               if(agev[m][i]==1) agev[m][i]=agemax+2;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               if (m<lastpass) {                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); 
                 if (calagedate>0)                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                  /*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]]);*/
                 else                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];                 } 
               }  
             }              }
           }            } /* end selection of waves */
         }          }
       }        }
       for(i=(int)agemin; i <= (int)agemax+3; i++){         for(i=iagemin; i <= iagemax+3; i++){  
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];   
         }  
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  
         }  
           
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  
         }  
                   
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                     posprop += prop[jk][i]; 
         for(jk=1; jk <=nlstate ; jk++){              } 
           if( i <= (int) agemax){  
             if(pos>=1.e-5){          for(jk=1; jk <=nlstate ; jk++){     
               probs[i][jk][j1]= pp[jk]/pos;            if( i <=  iagemax){ 
             }              if(posprop>=1.e-5){ 
           }                probs[i][jk][j1]= prop[jk][i]/posprop;
         }/* end jk */              } 
       }/* end i */            } 
           }/* end jk */ 
         }/* end i */ 
     } /* end i1 */      } /* end i1 */
   } /* end k1 */    } /* end k1 */
   
     
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  
       
 }  /* End of Freq */    /*  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);
   }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 {  {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      Death is a valid wave (if date is known).       Death is a valid wave (if date is known).
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      and mw[mi+1][i]. dh depends on stepm.       and mw[mi+1][i]. dh depends on stepm.
      */       */
   
Line 1521  void  concatwav(int wav[], int **dh, int Line 2069  void  concatwav(int wav[], int **dh, int
   
     wav[i]=mi;      wav[i]=mi;
     if(mi==0){      if(mi==0){
         nbwarn++;
       if(first==0){        if(first==0){
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         first=1;          first=1;
       }        }
       if(first==1){        if(first==1){
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   }    } /* End individuals */
   
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
         dh[mi][i]=1;          dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           if (agedc[i] < 2*AGESUP) {            if (agedc[i] < 2*AGESUP) {
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           if(j==0) j=1;  /* Survives at least one month after exam */              if(j==0) j=1;  /* Survives at least one month after exam */
           k=k+1;              else if(j<0){
           if (j >= jmax) jmax=j;                nberr++;
           if (j <= jmin) jmin=j;                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]);
           sum=sum+j;                j=1; /* Temporary Dangerous patch */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                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.\n  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]);
                 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.\n  You MUST fix the contradiction between dates.\n",stepm);
               }
               k=k+1;
               if (j >= jmax) jmax=j;
               if (j <= jmin) jmin=j;
               sum=sum+j;
               /*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);*/
           }            }
         }          }
         else{          else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           k=k+1;            k=k+1;
           if (j >= jmax) jmax=j;            if (j >= jmax) jmax=j;
           else if (j <= jmin)jmin=j;            else if (j <= jmin)jmin=j;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            /*        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]);*/
             if(j<0){
               nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
           sum=sum+j;            sum=sum+j;
         }          }
         jk= j/stepm;          jk= j/stepm;
         jl= j -jk*stepm;          jl= j -jk*stepm;
         ju= j -(jk+1)*stepm;          ju= j -(jk+1)*stepm;
         if(jl <= -ju)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           dh[mi][i]=jk;            if(jl==0){
         else              dh[mi][i]=jk;
           dh[mi][i]=jk+1;              bh[mi][i]=0;
         if(dh[mi][i]==0)            }else{ /* We want a negative bias in order to only have interpolation ie
           dh[mi][i]=1; /* At least one step */                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
           }else{
             if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
             else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
           } /* end if mle */
       }        }
     }      } /* end wave */
   }    }
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
Line 1575  void  concatwav(int wav[], int **dh, int Line 2160  void  concatwav(int wav[], int **dh, int
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)  void tricode(int *Tvar, int **nbcode, int imx)
 {  {
   int Ndum[20],ij=1, k, j, i;    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   int cptcode=0;    int cptcode=0;
   cptcoveff=0;     cptcoveff=0; 
     
   for (k=0; k<19; k++) Ndum[k]=0;    for (k=0; k<maxncov; k++) Ndum[k]=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (k=1; k<=7; k++) ncodemax[k]=0;
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       ij=(int)(covar[Tvar[j]][i]);                                 modality*/ 
       Ndum[ij]++;         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       if (ij > cptcode) cptcode=ij;         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
     }      }
   
     for (i=0; i<=cptcode; i++) {      for (i=0; i<=cptcode; i++) {
       if(Ndum[i]!=0) ncodemax[j]++;        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 */
     }      }
     ij=1;   
   
   
       ij=1; 
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1; i<=ncodemax[j]; i++) {
       for (k=0; k<=19; k++) {        for (k=0; k<= maxncov; k++) {
         if (Ndum[k] != 0) {          if (Ndum[k] != 0) {
           nbcode[Tvar[j]][ij]=k;             nbcode[Tvar[j]][ij]=k; 
             /* 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; */
                       
           ij++;            ij++;
         }          }
Line 1608  void tricode(int *Tvar, int **nbcode, in Line 2197  void tricode(int *Tvar, int **nbcode, in
     }       } 
   }      }  
   
  for (k=0; k<19; k++) Ndum[k]=0;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
  for (i=1; i<=ncovmodel-2; i++) {   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    ij=Tvar[i];     ij=Tvar[i];
    Ndum[ij]++;      Ndum[ij]++;
  }   }
   
  ij=1;   ij=1;
  for (i=1; i<=10; i++) {   for (i=1; i<= maxncov; i++) {
    if((Ndum[i]!=0) && (i<=ncovcol)){     if((Ndum[i]!=0) && (i<=ncovcol)){
      Tvaraff[ij]=i;        Tvaraff[ij]=i; /*For printing */
      ij++;       ij++;
    }     }
  }   }
     
  cptcoveff=ij-1;   cptcoveff=ij-1; /*Number of simple covariates*/
 }  }
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
Line 1641  void evsij(char fileres[], double ***eij Line 2231  void evsij(char fileres[], double ***eij
   double ***gradg, ***trgradg;    double ***gradg, ***trgradg;
   int theta;    int theta;
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,nlstate*2,1,npar);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   doldm=matrix(1,nlstate*2,1,nlstate*2);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficreseij,"# Health expectancies\n");
   fprintf(ficreseij,"# Age");    fprintf(ficreseij,"# Age");
Line 1661  void evsij(char fileres[], double ***eij Line 2251  void evsij(char fileres[], double ***eij
    * This is mainly to measure the difference between two models: for example     * 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     * 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      * we are calculating an estimate of the Life Expectancy assuming a linear 
    * progression inbetween and thus overestimating or underestimating according     * progression in between and thus overestimating or underestimating according
    * to the curvature of the survival function. If, for the same date, we      * 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     * 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      * to compare the new estimate of Life expectancy with the same linear 
Line 1690  void evsij(char fileres[], double ***eij Line 2280  void evsij(char fileres[], double ***eij
     /* if (stepm >= YEARM) hstepm=1;*/      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     gp=matrix(0,nhstepm,1,nlstate*2);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*2);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
Line 1729  void evsij(char fileres[], double ***eij Line 2319  void evsij(char fileres[], double ***eij
         for(i=1;i<=nlstate;i++){          for(i=1;i<=nlstate;i++){
           cptj=cptj+1;            cptj=cptj+1;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           }            }
         }          }
       }        }
       for(j=1; j<= nlstate*2; j++)        for(j=1; j<= nlstate*nlstate; j++)
         for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         }          }
Line 1741  void evsij(char fileres[], double ***eij Line 2332  void evsij(char fileres[], double ***eij
         
 /* End theta */  /* End theta */
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   
      for(h=0; h<=nhstepm-1; h++)       for(h=0; h<=nhstepm-1; h++)
       for(j=1; j<=nlstate*2;j++)        for(j=1; j<=nlstate*nlstate;j++)
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
             
   
      for(i=1;i<=nlstate*2;i++)       for(i=1;i<=nlstate*nlstate;i++)
       for(j=1;j<=nlstate*2;j++)        for(j=1;j<=nlstate*nlstate;j++)
         varhe[i][j][(int)age] =0.;          varhe[i][j][(int)age] =0.;
   
      printf("%d|",(int)age);fflush(stdout);       printf("%d|",(int)age);fflush(stdout);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      for(h=0;h<=nhstepm-1;h++){       for(h=0;h<=nhstepm-1;h++){
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         for(i=1;i<=nlstate*2;i++)          for(i=1;i<=nlstate*nlstate;i++)
           for(j=1;j<=nlstate*2;j++)            for(j=1;j<=nlstate*nlstate;j++)
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
Line 1783  void evsij(char fileres[], double ***eij Line 2374  void evsij(char fileres[], double ***eij
       }        }
     fprintf(ficreseij,"\n");      fprintf(ficreseij,"\n");
         
     free_matrix(gm,0,nhstepm,1,nlstate*2);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*2);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    }
   printf("\n");    printf("\n");
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(dnewm,1,nlstate*2,1,npar);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 }  }
   
 /************ Variance ******************/  /************ Variance ******************/
Line 1824  void varevsij(char optionfilefiname[], d Line 2415  void varevsij(char optionfilefiname[], d
   char fileresprobmorprev[FILENAMELENGTH];    char fileresprobmorprev[FILENAMELENGTH];
   
   if(popbased==1){    if(popbased==1){
     if(mobilav==1)      if(mobilav!=0)
       strcpy(digitp,"-populbased-mobilav-");        strcpy(digitp,"-populbased-mobilav-");
     else strcpy(digitp,"-populbased-nomobil-");      else strcpy(digitp,"-populbased-nomobil-");
   }    }
Line 1851  void varevsij(char optionfilefiname[], d Line 2442  void varevsij(char optionfilefiname[], d
   }    }
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    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,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficresprobmorprev," p.%-d SE",j);      fprintf(ficresprobmorprev," p.%-d SE",j);
Line 1859  void varevsij(char optionfilefiname[], d Line 2450  void varevsij(char optionfilefiname[], d
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   }      }  
   fprintf(ficresprobmorprev,"\n");    fprintf(ficresprobmorprev,"\n");
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficgp,"\n# Routine varevsij");
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    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(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     exit(0);  /*   } */
   }  
   else{  
     fprintf(ficgp,"\n# Routine varevsij");  
   }  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);  
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);  
   }  
   else{  
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");  
     fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);  
   }  
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   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");    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");
Line 1908  void varevsij(char optionfilefiname[], d Line 2486  void varevsij(char optionfilefiname[], d
      and note for a fixed period like k years */       and note for a fixed period like k years */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* 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       survival function given by stepm (the optimization length). Unfortunately it
      means that if the survival funtion is printed only each two years of age and if       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        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.       results. So we changed our mind and took the option of the best precision.
   */    */
Line 1924  void varevsij(char optionfilefiname[], d Line 2502  void varevsij(char optionfilefiname[], d
   
   
     for(theta=1; theta <=npar; theta++){      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
Line 1946  void varevsij(char optionfilefiname[], d Line 2524  void varevsij(char optionfilefiname[], d
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
       /* This for computing forces of mortality (h=1)as a weighted average */        /* This for computing probability of death (h=1 means
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){           computed over hstepm matrices product = hstepm*stepm months) 
         for(i=1; i<= nlstate; i++)           as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
           gpp[j] += prlim[i][i]*p3mat[i][j][1];            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       }            }    
       /* end force of mortality */        /* end probability of death */
   
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
Line 1974  void varevsij(char optionfilefiname[], d Line 2555  void varevsij(char optionfilefiname[], d
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
       /* This for computing force of mortality (h=1)as a weighted average */        /* This for computing probability of death (h=1 means
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){           computed over hstepm matrices product = hstepm*stepm months) 
         for(i=1; i<= nlstate; i++)           as a weighted average of prlim.
           gmp[j] += prlim[i][i]*p3mat[i][j][1];        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
       }            }    
       /* end force of mortality */        /* end probability of death */
   
       for(j=1; j<= nlstate; j++) /* vareij */        for(j=1; j<= nlstate; j++) /* vareij */
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         }          }
   
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       }        }
Line 2001  void varevsij(char optionfilefiname[], d Line 2586  void varevsij(char optionfilefiname[], d
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       for(theta=1; theta <=npar; theta++)        for(theta=1; theta <=npar; theta++)
         trgradgp[j][theta]=gradgp[theta][j];          trgradgp[j][theta]=gradgp[theta][j];
     
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
Line 2016  void varevsij(char optionfilefiname[], d Line 2602  void varevsij(char optionfilefiname[], d
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
     
     /* pptj */      /* pptj */
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);      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);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
Line 2024  void varevsij(char optionfilefiname[], d Line 2610  void varevsij(char optionfilefiname[], d
       for(i=nlstate+1;i<=nlstate+ndeath;i++)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         varppt[j][i]=doldmp[j][i];          varppt[j][i]=doldmp[j][i];
     /* end ppptj */      /* end ppptj */
       /*  x centered again */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     
Line 2036  void varevsij(char optionfilefiname[], d Line 2623  void varevsij(char optionfilefiname[], d
           prlim[i][i]=mobaverage[(int)age][i][ij];            prlim[i][i]=mobaverage[(int)age][i][ij];
       }        }
     }      }
                    
     /* This for computing force of mortality (h=1)as a weighted average */      /* This for computing probability of death (h=1 means
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       for(i=1; i<= nlstate; i++)         as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     }          }    
     /* end force of mortality */      /* end probability of death */
   
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2072  void varevsij(char optionfilefiname[], d Line 2662  void varevsij(char optionfilefiname[], d
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    /* 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 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);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);    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);    /*  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);
 */  */
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);    free_matrix(doldm,1,nlstate,1,nlstate);
Line 2089  void varevsij(char optionfilefiname[], d Line 2683  void varevsij(char optionfilefiname[], d
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficresprobmorprev);    fclose(ficresprobmorprev);
   fclose(ficgp);    fflush(ficgp);
   fclose(fichtm);    fflush(fichtm); 
 }  }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ 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)  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)
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double **newm;    double **newm;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
Line 2237  void varprob(char optionfilefiname[], do Line 2831  void varprob(char optionfilefiname[], do
       fprintf(ficresprobcov," p%1d-%1d ",i,j);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     }        }  
   fprintf(ficresprob,"\n");   /* fprintf(ficresprob,"\n");
   fprintf(ficresprobcov,"\n");    fprintf(ficresprobcov,"\n");
   fprintf(ficresprobcor,"\n");    fprintf(ficresprobcor,"\n");
   xp=vector(1,npar);   */
    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   first=1;    first=1;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficgp,"\n# Routine varprob");
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(fichtm,"\n");
     exit(0);  
   }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
   else{    fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
     fprintf(ficgp,"\n# Routine varprob");    file %s<br>\n",optionfilehtmcov);
   }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  and drawn. It helps understanding how is the covariance between two incidences.\
     printf("Problem with html file: %s\n", optionfilehtm);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    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. \
     exit(0);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   else{  standard deviations wide on each axis. <br>\
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     fprintf(fichtm,"\n");   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");  
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");  
     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");  
   
   }  
   
    
   cov[1]=1;    cov[1]=1;
   tj=cptcoveff;    tj=cptcoveff;
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
Line 2277  void varprob(char optionfilefiname[], do Line 2866  void varprob(char optionfilefiname[], do
   for(t=1; t<=tj;t++){    for(t=1; t<=tj;t++){
     for(i1=1; i1<=ncodemax[t];i1++){       for(i1=1; i1<=ncodemax[t];i1++){ 
       j1++;        j1++;
         
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");           fprintf(ficresprob, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresprob, "**********\n#");          fprintf(ficresprob, "**********\n#\n");
         fprintf(ficresprobcov, "\n#********** Variable ");           fprintf(ficresprobcov, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresprobcov, "**********\n#");          fprintf(ficresprobcov, "**********\n#\n");
                   
         fprintf(ficgp, "\n#********** Variable ");           fprintf(ficgp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp, "**********\n#");          fprintf(ficgp, "**********\n#\n");
                   
                   
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
Line 2297  void varprob(char optionfilefiname[], do Line 2885  void varprob(char optionfilefiname[], do
                   
         fprintf(ficresprobcor, "\n#********** Variable ");              fprintf(ficresprobcor, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp, "**********\n#");              fprintf(ficresprobcor, "**********\n#");    
       }        }
               
       for (age=bage; age<=fage; age ++){         for (age=bage; age<=fage; age ++){ 
Line 2316  void varprob(char optionfilefiname[], do Line 2904  void varprob(char optionfilefiname[], do
           
         for(theta=1; theta <=npar; theta++){          for(theta=1; theta <=npar; theta++){
           for(i=1; i<=npar; i++)            for(i=1; i<=npar; i++)
             xp[i] = x[i] + (i==theta ?delti[theta]:0);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                       
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                       
Line 2329  void varprob(char optionfilefiname[], do Line 2917  void varprob(char optionfilefiname[], do
           }            }
                       
           for(i=1; i<=npar; i++)            for(i=1; i<=npar; i++)
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           k=0;            k=0;
Line 2341  void varprob(char optionfilefiname[], do Line 2929  void varprob(char optionfilefiname[], do
           }            }
             
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         }          }
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
Line 2350  void varprob(char optionfilefiname[], do Line 2938  void varprob(char optionfilefiname[], do
                   
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);           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);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                   free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
         pmij(pmmij,cov,ncovmodel,x,nlstate);          pmij(pmmij,cov,ncovmodel,x,nlstate);
                   
         k=0;          k=0;
Line 2365  void varprob(char optionfilefiname[], do Line 2957  void varprob(char optionfilefiname[], do
             varpij[i][j][(int)age] = doldm[i][j];              varpij[i][j][(int)age] = doldm[i][j];
   
         /*printf("\n%d ",(int)age);          /*printf("\n%d ",(int)age);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);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]));            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      }*/            }*/
   
         fprintf(ficresprob,"\n%d ",(int)age);          fprintf(ficresprob,"\n%d ",(int)age);
         fprintf(ficresprobcov,"\n%d ",(int)age);          fprintf(ficresprobcov,"\n%d ",(int)age);
Line 2396  void varprob(char optionfilefiname[], do Line 2988  void varprob(char optionfilefiname[], do
   
       /* Confidence intervalle of pij  */        /* Confidence intervalle of pij  */
       /*        /*
       fprintf(ficgp,"\nset noparametric;unset label");          fprintf(ficgp,"\nset noparametric;unset label");
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       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>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(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       */        */
   
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
Line 2447  void varprob(char optionfilefiname[], do Line 3039  void varprob(char optionfilefiname[], do
                     fprintf(ficgp,"\nset parametric;unset label");                      fprintf(ficgp,"\nset parametric;unset label");
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                      fprintf(ficgp,"\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",\                      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",\
Line 2458  void varprob(char optionfilefiname[], do Line 3054  void varprob(char optionfilefiname[], do
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   }else{                    }else{
                     first=0;                      first=0;
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);                      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,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\                      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",\
Line 2467  void varprob(char optionfilefiname[], do Line 3063  void varprob(char optionfilefiname[], do
                   }/* if first */                    }/* if first */
                 } /* age mod 5 */                  } /* age mod 5 */
               } /* end loop age */                } /* end loop age */
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               first=1;                first=1;
             } /*l12 */              } /*l12 */
           } /* k12 */            } /* k12 */
         } /*l1 */          } /*l1 */
       }/* k1 */        }/* k1 */
     } /* loop covariates */      } /* loop covariates */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   fclose(ficresprob);    fclose(ficresprob);
   fclose(ficresprobcov);    fclose(ficresprobcov);
   fclose(ficresprobcor);    fclose(ficresprobcor);
   fclose(ficgp);    fflush(ficgp);
   fclose(fichtm);    fflush(fichtmcov);
 }  }
   
   
Line 2499  void printinghtml(char fileres[], char t Line 3091  void printinghtml(char fileres[], char t
                   double jprev2, double mprev2,double anprev2){                    double jprev2, double mprev2,double anprev2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   /*char optionfilehtm[FILENAMELENGTH];*/    /*char optionfilehtm[FILENAMELENGTH];*/
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
     printf("Problem with %s \n",optionfilehtm), exit(0);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   }  /*   } */
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
  - Life expectancies by age and initial health status (estepm=%2d months):    - Life expectancies by age and initial health status (estepm=%2d months): \
    <a href=\"e%s\">e%s</a> <br>\n</li>", \     <a href=\"%s\">%s</a> <br>\n</li>", \
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
Line 2528  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 3123  fprintf(fichtm," \n<ul><li><b>Graphs</b>
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      /* Pij */       /* Pij */
      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>       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
      /* Quasi-incidences */       /* 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>       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Stable prevalence in each health state */         /* Stable prevalence in each health state */
        for(cpt=1; cpt<nlstate;cpt++){         for(cpt=1; cpt<nlstate;cpt++){
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }         }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2): e%s%d.png<br>  health expectancies in states (1) and (2): %s%d.png<br>\
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
   
   
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            rfileres,rfileres,\
  if(popforecast==1) fprintf(fichtm,"\n           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
         <br>",fileres,fileres,fileres,fileres);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
  else            subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
    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);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
  m=cptcoveff;   m=cptcoveff;
Line 2581  fprintf(fichtm," <ul><li><b>Graphs</b></ Line 3184  fprintf(fichtm," <ul><li><b>Graphs</b></
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
 interval) in state (%d): v%s%d%d.png <br>  interval) in state (%d): %s%d%d.png <br>\
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }       }
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
 fclose(fichtm);   fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   int ng;    int ng;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     printf("Problem with file %s",optionfilegnuplot);  /*     printf("Problem with file %s",optionfilegnuplot); */
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   }  /*   } */
   
   /*#ifdef windows */    /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */      /*#endif */
 m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
  /* 1eme*/   /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
    for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) {
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
      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);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }        } 
      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       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));
    }     }
   }    }
   /*2 eme*/    /*2 eme*/
       
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           
     for (i=1; i<= nlstate+1 ; i ++) {      for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;        k=2*i;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }           }   
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        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);        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 ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }           }   
       fprintf(ficgp,"\" t\"\" w l 0,");        fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
Line 2665  m=pow(2,cptcoveff); Line 3276  m=pow(2,cptcoveff);
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(2*cpt-2);        k=2+nlstate*(2*cpt-2);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 2676  m=pow(2,cptcoveff); Line 3289  m=pow(2,cptcoveff);
                   
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         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(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);
                   
       }         } 
     }      }
   }    }
       
   /* CV preval stat */    /* CV preval stable (period) */
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<nlstate ; cpt ++) {      for (cpt=1; cpt<=nlstate ; cpt ++) {
       k=3;        k=3;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
       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(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
               
       for (i=1; i< nlstate ; i ++)        for (i=1; i< nlstate ; i ++)
         fprintf(ficgp,"+$%d",k+i+1);          fprintf(ficgp,"+$%d",k+i+1);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
               
       l=3+(nlstate+ndeath)*cpt;        l=3+(nlstate+ndeath)*cpt;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         l=3+(nlstate+ndeath)*cpt;          l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,"+$%d",l+i+1);          fprintf(ficgp,"+$%d",l+i+1);
Line 2718  m=pow(2,cptcoveff); Line 3334  m=pow(2,cptcoveff);
   
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      for(jk=1; jk <=m; jk++) {       for(jk=1; jk <=m; jk++) {
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
        if (ng==2)         if (ng==2)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        else         else
Line 2765  m=pow(2,cptcoveff); Line 3381  m=pow(2,cptcoveff);
        } /* end k2 */         } /* end k2 */
      } /* end jk */       } /* end jk */
    } /* end ng */     } /* end ng */
    fclose(ficgp);      fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
Line 2773  m=pow(2,cptcoveff); Line 3389  m=pow(2,cptcoveff);
 int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
   int i, cpt, cptcod;    int i, cpt, cptcod;
     int modcovmax =1;
   int mobilavrange, mob;    int mobilavrange, mob;
   double age;    double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     if(mobilav==1) mobilavrange=5; /* default */      if(mobilav==1) mobilavrange=5; /* default */
     else mobilavrange=mobilav;      else mobilavrange=mobilav;
     for (age=bage; age<=fage; age++)      for (age=bage; age<=fage; age++)
       for (i=1; i<=nlstate;i++)        for (i=1; i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for (cptcod=1;cptcod<=modcovmax;cptcod++)
           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     /* We keep the original values on the extreme ages bage, fage and for       /* We keep the original values on the extreme ages bage, fage and for 
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
Line 2789  int movingaverage(double ***probs, doubl Line 3411  int movingaverage(double ***probs, doubl
     for (mob=3;mob <=mobilavrange;mob=mob+2){      for (mob=3;mob <=mobilavrange;mob=mob+2){
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
         for (i=1; i<=nlstate;i++){          for (i=1; i<=nlstate;i++){
           for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for (cptcod=1;cptcod<=modcovmax;cptcod++){
             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
               for (cpt=1;cpt<=(mob-1)/2;cpt++){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
Line 2806  int movingaverage(double ***probs, doubl Line 3428  int movingaverage(double ***probs, doubl
   
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 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){  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
       /* proj1, year, month, day of starting projection 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   int *popage;    int *popage;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    double ***mobaverage;
   char fileresf[FILENAMELENGTH];    char fileresf[FILENAMELENGTH];
   
  agelim=AGESUP;    agelim=AGESUP;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
    
     
   strcpy(fileresf,"f");     strcpy(fileresf,"f"); 
   strcat(fileresf,fileres);    strcat(fileresf,fileres);
Line 2843  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 3467  calagedate=(anproj1+mproj1/12.+jproj1/36
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
       if(estepm < stepm){
   agelim=AGESUP;      printf ("Problem %d lower than %d\n",estepm, stepm);
       }
   hstepm=1;    else  hstepm=estepm;   
   
   hstepm=hstepm/stepm;     hstepm=hstepm/stepm; 
   yp1=modf(dateintmean,&yp);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
   anprojmean=yp;    anprojmean=yp;
   yp2=modf((yp1*12),&yp);    yp2=modf((yp1*12),&yp);
   mprojmean=yp;    mprojmean=yp;
Line 2856  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 3482  calagedate=(anproj1+mproj1/12.+jproj1/36
   jprojmean=yp;    jprojmean=yp;
   if(jprojmean==0) jprojmean=1;    if(jprojmean==0) jprojmean=1;
   if(mprojmean==0) jprojmean=1;    if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
       
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#******");        fprintf(ficresf,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }        }
       fprintf(ficresf,"******\n");        fprintf(ficresf,"******\n");
       fprintf(ficresf,"# StartingAge FinalAge");        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for(j=1; j<=nlstate+ndeath;j++){ 
                 for(i=1; i<=nlstate;i++)              
                   fprintf(ficresf," p%d%d",i,j);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);             fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){           for (agec=fage; agec>=(ageminpar-1); agec--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;             nhstepm = nhstepm/hstepm; 
             
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;            oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {              if (h*hstepm/YEARM*stepm ==yearp) {
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);                fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
               kk1=0.;kk2=0;                ppij=0.;
               for(i=1; i<=nlstate;i++) {                              for(i=1; i<=nlstate;i++) {
                 if (mobilav==1)                   if (mobilav==1) 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                 else {                  else {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                 }                  }
                                   if (h*hstepm/YEARM*stepm== yearp) {
               }                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
               if (h==(int)(calagedate+12*cpt)){                  }
                 fprintf(ficresf," %.3f", kk1);                } /* end i */
                                         if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
               }                }
             }              }/* end j */
           }            } /* end h */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }          } /* end agec */
       }        } /* end yearp */
     }      } /* end cptcod */
   }    } /* end  cptcov */
                 
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   fclose(ficresf);    fclose(ficresf);
 }  }
 /************** Forecasting ******************/  
   /************** 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){  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
       
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double calagedatem, agelim, kk1, kk2;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat,***tabpop,***tabpopprev;    double ***p3mat,***tabpop,***tabpopprev;
   double ***mobaverage;    double ***mobaverage;
Line 2927  populforecast(char fileres[], double anp Line 3565  populforecast(char fileres[], double anp
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   agelim=AGESUP;    agelim=AGESUP;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
       
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       
       
   strcpy(filerespop,"pop");     strcpy(filerespop,"pop"); 
Line 2975  populforecast(char fileres[], double anp Line 3613  populforecast(char fileres[], double anp
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   }    }
   
   for(cptcov=1;cptcov<=i2;cptcov++){    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficrespop,"\n#******");        fprintf(ficrespop,"\n#******");
Line 2990  populforecast(char fileres[], double anp Line 3628  populforecast(char fileres[], double anp
       for (cpt=0; cpt<=0;cpt++) {         for (cpt=0; cpt<=0;cpt++) { 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);             fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;             nhstepm = nhstepm/hstepm; 
                       
Line 2999  populforecast(char fileres[], double anp Line 3637  populforecast(char fileres[], double anp
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {              if (h==(int) (calagedatem+YEARM*cpt)) {
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
Line 3011  populforecast(char fileres[], double anp Line 3649  populforecast(char fileres[], double anp
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                 }                  }
               }                }
               if (h==(int)(calagedate+12*cpt)){                if (h==(int)(calagedatem+12*cpt)){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   /*fprintf(ficrespop," %.3f", kk1);                    /*fprintf(ficrespop," %.3f", kk1);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
Line 3022  populforecast(char fileres[], double anp Line 3660  populforecast(char fileres[], double anp
                 for(j=1; j<=nlstate;j++){                  for(j=1; j<=nlstate;j++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                 }                  }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
             }              }
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3036  populforecast(char fileres[], double anp Line 3674  populforecast(char fileres[], double anp
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);             fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;             nhstepm = nhstepm/hstepm; 
                       
Line 3044  populforecast(char fileres[], double anp Line 3682  populforecast(char fileres[], double anp
           oldm=oldms;savm=savms;            oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {              if (h==(int) (calagedatem+YEARM*cpt)) {
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
Line 3052  populforecast(char fileres[], double anp Line 3690  populforecast(char fileres[], double anp
               for(i=1; i<=nlstate;i++) {                              for(i=1; i<=nlstate;i++) {              
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                      kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
               }                }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
             }              }
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3071  populforecast(char fileres[], double anp Line 3709  populforecast(char fileres[], double anp
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrespop);    fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
 }  }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   
 /***********************************************/  /***********************************************/
 /**************** Main Program *****************/  /**************** Main Program *****************/
 /***********************************************/  /***********************************************/
   
 int main(int argc, char *argv[])  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,cptcode, cptcod;    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
   double agedeb, agefin,hf;    double agedeb, agefin,hf;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
Line 3092  int main(int argc, char *argv[]) Line 3870  int main(int argc, char *argv[])
   double ***mobaverage;    double ***mobaverage;
   int *indx;    int *indx;
   char line[MAXLINE], linepar[MAXLINE];    char line[MAXLINE], linepar[MAXLINE];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */    int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;    int c,  h , cpt,l;
   int ju,jl, mi;    int ju,jl, mi;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;     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 mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm, nhstepm;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    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 bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;    double ftolpl=FTOL;
Line 3116  int main(int argc, char *argv[]) Line 3897  int main(int argc, char *argv[])
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;    double *epj, vepp;
   double kk1, kk2;    double kk1, kk2;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
   char z[1]="c", occ;    char z[1]="c", occ;
 #include <sys/time.h>  
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     
   /* long total_usecs;    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   struct timeval start_time, end_time;    (void) gettimeofday(&start_time,&tzp);
       curr_time=start_time;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first 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);    getcwd(pathcd, size);
   
   printf("\n%s",version);    printf("\n%s\n%s",version,fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     scanf("%s",pathtot);      scanf("%s",pathtot);
Line 3141  int main(int argc, char *argv[]) Line 3946  int main(int argc, char *argv[])
   else{    else{
     strcpy(pathtot,argv[1]);      strcpy(pathtot,argv[1]);
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);    /*cygwin_split_path(pathtot,path,optionfile);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   /* cutv(path,optionfile,pathtot,'\\');*/    /* cutv(path,optionfile,pathtot,'\\');*/
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);    chdir(path);
   replace(pathc,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 --------*/    /*-------- arguments in the command line --------*/
   
   /* Log file */    /* Log file */
   strcat(filelog, optionfilefiname);    strcat(filelog, optionfilefiname);
Line 3161  int main(int argc, char *argv[]) Line 3976  int main(int argc, char *argv[])
     goto end;      goto end;
   }    }
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s",version);    fprintf(ficlog,"\n%s\n%s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: ");    fprintf(ficlog,"\nEnter the parameter file name: ");
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
   fflush(ficlog);    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");    strcpy(fileres,"r");
Line 3176  int main(int argc, char *argv[]) Line 4000  int main(int argc, char *argv[])
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile %s\n",optionfile);      printf("Problem with optionfile %s\n",optionfile);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
     goto end;      goto end;
   }    }
   
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileres);    strcat(filereso,fileres);
   if((ficparo=fopen(filereso,"w"))==NULL) {    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);      printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
     goto end;      goto end;
   }    }
   
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
     numlinepar=0;
   while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
       numlinepar++;
     puts(line);      puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
       fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    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);    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);    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(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);
 while((c=getc(ficpar))=='#' && c!= EOF){    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);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
       numlinepar++;
     puts(line);      puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
       fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
     
         
   covar=matrix(0,NCOVMAX,1,n);     covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0;     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
   ncovmodel=2+cptcovn;    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
      
     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);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
   /* Read guess parameters */    /* Read guess parameters */
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
       numlinepar++;
     puts(line);      puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
       fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
     
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)    for(i=1; i <=nlstate; i++){
     for(j=1; j <=nlstate+ndeath-1; j++){      j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
       fscanf(ficpar,"%1d%1d",&i1,&j1);        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);        fprintf(ficparo,"%1d%1d",i1,j1);
       if(mle==1)        if(mle==1)
         printf("%1d%1d",i,j);          printf("%1d%1d",i,j);
Line 3244  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4097  while((c=getc(ficpar))=='#' && c!= EOF){
         fprintf(ficparo," %lf",param[i][j][k]);          fprintf(ficparo," %lf",param[i][j][k]);
       }        }
       fscanf(ficpar,"\n");        fscanf(ficpar,"\n");
         numlinepar++;
       if(mle==1)        if(mle==1)
         printf("\n");          printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
       }  
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
   p=param[1][1];    p=param[1][1];
       
Line 3258  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4114  while((c=getc(ficpar))=='#' && c!= EOF){
   while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
       numlinepar++;
     puts(line);      puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
       fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
   for(i=1; i <=nlstate; i++){    for(i=1; i <=nlstate; i++){
     for(j=1; j <=nlstate+ndeath-1; j++){      for(j=1; j <=nlstate+ndeath-1; j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        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);        printf("%1d%1d",i,j);
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
       for(k=1; k<=ncovmodel;k++){        for(k=1; k<=ncovmodel;k++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);          fscanf(ficpar,"%le",&delti3[i][j][k]);
         printf(" %le",delti3[i][j][k]);          printf(" %le",delti3[i][j][k]);
         fprintf(ficparo," %le",delti3[i][j][k]);          fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
       }        }
       fscanf(ficpar,"\n");        fscanf(ficpar,"\n");
         numlinepar++;
       printf("\n");        printf("\n");
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
     }      }
   }    }
     fflush(ficlog);
   
   delti=delti3[1][1];    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 '#' */    /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
       numlinepar++;
     puts(line);      puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
       fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
       
Line 3302  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4175  while((c=getc(ficpar))=='#' && c!= EOF){
       fscanf(ficpar," %le",&matcov[i][j]);        fscanf(ficpar," %le",&matcov[i][j]);
       if(mle==1){        if(mle==1){
         printf(" %.5le",matcov[i][j]);          printf(" %.5le",matcov[i][j]);
         fprintf(ficlog," %.5le",matcov[i][j]);  
       }        }
       else        fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficlog," %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);        fprintf(ficparo," %.5le",matcov[i][j]);
     }      }
     fscanf(ficpar,"\n");      fscanf(ficpar,"\n");
       numlinepar++;
     if(mle==1)      if(mle==1)
       printf("\n");        printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
Line 3322  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4194  while((c=getc(ficpar))=='#' && c!= EOF){
     printf("\n");      printf("\n");
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/    /*-------- Rewriting paramater file ----------*/
      strcpy(rfileres,"r");    /* "Rparameterfile */    strcpy(rfileres,"r");    /* "Rparameterfile */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
      strcat(rfileres,".");    /* */    strcat(rfileres,".");    /* */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {    if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"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);    fprintf(ficres,"#%s\n",version);
           
     /*-------- data file ----------*/    /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;      printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }    }
   
     n= lastobs;    n= lastobs;
     severity = vector(1,maxwav);    severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);    outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);    num=lvector(1,n);
     moisnais=vector(1,n);    moisnais=vector(1,n);
     annais=vector(1,n);    annais=vector(1,n);
     moisdc=vector(1,n);    moisdc=vector(1,n);
     andc=vector(1,n);    andc=vector(1,n);
     agedc=vector(1,n);    agedc=vector(1,n);
     cod=ivector(1,n);    cod=ivector(1,n);
     weight=vector(1,n);    weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);    s=imatrix(1,maxwav+1,1,n);
     adl=imatrix(1,maxwav+1,1,n);        tab=ivector(1,NCOVMAX);
     tab=ivector(1,NCOVMAX);    ncodemax=ivector(1,8);
     ncodemax=ivector(1,8);  
     i=1;
     i=1;    while (fgets(line, MAXLINE, fic) != NULL)    {
     while (fgets(line, MAXLINE, fic) != NULL)    {      if ((i >= firstobs) && (i <=lastobs)) {
       if ((i >= firstobs) && (i <=lastobs)) {  
                   
         for (j=maxwav;j>=1;j--){        for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);          strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }        }
                   
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){        for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); 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);          num[i]=atol(stra);
                   
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          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;        i=i+1;
       }      }
     }     }
     /* printf("ii=%d", ij);    /* printf("ii=%d", ij);
        scanf("%d",i);*/       scanf("%d",i);*/
   imx=i-1; /* Number of individuals */    imx=i-1; /* Number of individuals */
   
   /* for (i=1; i<=imx; i++){    /* for (i=1; i<=imx; i++){
Line 3399  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4277  while((c=getc(ficpar))=='#' && c!= EOF){
     }*/      }*/
    /*  for (i=1; i<=imx; i++){     /*  for (i=1; i<=imx; i++){
      if (s[4][i]==9)  s[4][i]=-1;        if (s[4][i]==9)  s[4][i]=-1; 
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/       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 parameter from char model*/    /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
   Tprod=ivector(1,15);     Tprod=ivector(1,15); 
Line 3409  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4291  while((c=getc(ficpar))=='#' && c!= EOF){
   Tvard=imatrix(1,15,1,2);    Tvard=imatrix(1,15,1,2);
   Tage=ivector(1,15);          Tage=ivector(1,15);      
         
   if (strlen(model) >1){    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=1, k2=1;      j=0, j1=0, k1=1, k2=1;
     j=nbocc(model,'+');      j=nbocc(model,'+'); /* j=Number of '+' */
     j1=nbocc(model,'*');      j1=nbocc(model,'*'); /* j1=Number of '*' */
     cptcovn=j+1;      cptcovn=j+1; 
     cptcovprod=j1;      cptcovprod=j1; /*Number of products */
           
     strcpy(modelsav,model);       strcpy(modelsav,model); 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
Line 3423  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4305  while((c=getc(ficpar))=='#' && c!= EOF){
       goto end;        goto end;
     }      }
           
       /* This loop fills the array Tvar from the string 'model'.*/
   
     for(i=(j+1); i>=1;i--){      for(i=(j+1); i>=1;i--){
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
       /*scanf("%d",i);*/        /*scanf("%d",i);*/
       if (strchr(strb,'*')) {  /* Model includes a product */        if (strchr(strb,'*')) {  /* Model includes a product */
Line 3472  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4356  while((c=getc(ficpar))=='#' && c!= EOF){
     } /* end of loop + */      } /* end of loop + */
   } /* end model */    } /* 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("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   printf("cptcovprod=%d ", cptcovprod);    printf("cptcovprod=%d ", cptcovprod);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   scanf("%d ",i);*/  
     fclose(fic);    scanf("%d ",i);
     fclose(fic);*/
   
     /*  if(mle==1){*/      /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/    if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;      for(i=1;i<=n;i++) weight[i]=1.0;
     }    }
     /*-calculation of age at interview from date of interview and age at death -*/      /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);    agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {    for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {      for(m=2; (m<= maxwav); m++) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;          anint[m][i]=9999;
          s[m][i]=-1;          s[m][i]=-1;
        }        }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) 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++)  {    for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){      for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){        if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)            if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
            else {              else {
               if (andc[i]!=9999){                if ((int)andc[i]!=9999){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                  nbwarn++;
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
               agev[m][i]=-1;                  fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
               }                }
             }              }
           }          }
           else if(s[m][i] !=9){ /* Should no more exist */          else if(s[m][i] !=9){ /* Standard case, age in fractional
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                                   years but with the precision of a
             if(mint[m][i]==99 || anint[m][i]==9999)                                   month */
               agev[m][i]=1;            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             else if(agev[m][i] <agemin){             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               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;              agev[m][i]=1;
             s[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 /*= 0 Unknown */          else { /* =9 */
           agev[m][i]=1;            agev[m][i]=1;
             s[m][i]=-1;
           }
       }        }
             else /*= 0 Unknown */
           agev[m][i]=1;
     }      }
     for (i=1; i<=imx; i++)  {      
       for(m=1; (m<= maxwav); m++){    }
         if (s[m][i] > (nlstate+ndeath)) {    for (i=1; i<=imx; i++)  {
           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);         for(m=firstpass; (m<=lastpass); m++){
           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);           if (s[m][i] > (nlstate+ndeath)) {
           goto end;          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); 
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    free_vector(severity,1,maxwav);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(severity,1,maxwav);    free_vector(annais,1,n);
     free_imatrix(outcome,1,maxwav+1,1,n);    /* free_matrix(mint,1,maxwav,1,n);
     free_vector(moisnais,1,n);       free_matrix(anint,1,maxwav,1,n);*/
     free_vector(annais,1,n);    free_vector(moisdc,1,n);
     /* free_matrix(mint,1,maxwav,1,n);    free_vector(andc,1,n);
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);  
   
         
     wav=ivector(1,imx);    wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    dh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=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 */    /* Concatenates waves */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    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);    Tcode=ivector(1,100);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
       ncodemax[1]=1;    ncodemax[1]=1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
               
    codtab=imatrix(1,100,1,10);    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
    h=0;                                   the estimations*/
    m=pow(2,cptcoveff);    h=0;
     m=pow(2,cptcoveff);
     
    for(k=1;k<=cptcoveff; k++){    for(k=1;k<=cptcoveff; k++){
      for(i=1; i <=(m/pow(2,k));i++){      for(i=1; i <=(m/pow(2,k));i++){
        for(j=1; j <= ncodemax[k]; j++){        for(j=1; j <= ncodemax[k]; j++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
            h++;            h++;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            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("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);*/      }
     } 
     /* 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);*/
           
    /* Calculates basic frequencies. Computes observed prevalence at single age    /*------------ gnuplot -------------*/
        and prints on file fileres'p'. */    strcpy(optionfilegnuplot,optionfilefiname);
     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 */
        strcat(optionfilehtm,".htm");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    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\
    - 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,\
             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);
   
     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 */      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= 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 */      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      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] */    /* For Powell, parameters are in a vector p[] starting at p[1]
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */       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) */
     if(mle==1){  
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     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);      mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }    }
           
     /*--------- results files --------------*/    /*--------- 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,"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);
       
   
    jk=1;    jk=1;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    printf("# 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");    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
      for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i)         if (k != i) 
          {          {
            printf("%d%d ",i,k);            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficres,"%1d%1d ",i,k);
            for(j=1; j <=ncovmodel; j++){            for(j=1; j <=ncovmodel; j++){
              printf("%f ",p[jk]);              printf("%f ",p[jk]);
              fprintf(ficlog,"%f ",p[jk]);              fprintf(ficlog,"%f ",p[jk]);
              fprintf(ficres,"%f ",p[jk]);              fprintf(ficres,"%f ",p[jk]);
              jk++;               jk++; 
            }            }
            printf("\n");            printf("\n");
            fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");            fprintf(ficres,"\n");
          }          }
      }      }
    }    }
    if(mle==1){    if(mle!=0){
      /* Computing hessian and covariance matrix */      /* Computing hessian and covariance matrix */
      ftolhess=ftol; /* Usually correct */      ftolhess=ftol; /* Usually correct */
      hesscov(matcov, p, npar, delti, ftolhess, func);      hesscov(matcov, p, npar, delti, ftolhess, func);
    }    }
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
    printf("# Scales (for hessian or gradient estimation)\n");    printf("# Scales (for hessian or gradient estimation)\n");
    fprintf(ficlog,"# 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(i=1,jk=1; i <=nlstate; i++){
      for(j=1; j <=nlstate+ndeath; j++){      for(j=1; j <=nlstate+ndeath; j++){
        if (j!=i) {        if (j!=i) {
          fprintf(ficres,"%1d%1d",i,j);          fprintf(ficres,"%1d%1d",i,j);
          printf("%1d%1d",i,j);          printf("%1d%1d",i,j);
          fprintf(ficlog,"%1d%1d",i,j);          fprintf(ficlog,"%1d%1d",i,j);
          for(k=1; k<=ncovmodel;k++){          for(k=1; k<=ncovmodel;k++){
            printf(" %.5e",delti[jk]);            printf(" %.5e",delti[jk]);
            fprintf(ficlog," %.5e",delti[jk]);            fprintf(ficlog," %.5e",delti[jk]);
            fprintf(ficres," %.5e",delti[jk]);            fprintf(ficres," %.5e",delti[jk]);
            jk++;            jk++;
          }          }
          printf("\n");          printf("\n");
          fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
          fprintf(ficres,"\n");          fprintf(ficres,"\n");
        }        }
      }      }
    }    }
         
    k=1;    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
    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)
    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");
      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");
    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,k=1;i<=npar;i++){
    for(i=1;i<=npar;i++){      /*  if (k>nlstate) k=1;
      /*  if (k>nlstate) k=1;          i1=(i-1)/(ncovmodel*nlstate)+1; 
          i1=(i-1)/(ncovmodel*nlstate)+1;           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          printf("%s%d%d",alph[k],i1,tab[i]);
          printf("%s%d%d",alph[k],i1,tab[i]);*/      */
      fprintf(ficres,"%3d",i);      fprintf(ficres,"%3d",i);
      if(mle==1)      if(mle==1)
        printf("%3d",i);        printf("%3d",i);
      fprintf(ficlog,"%3d",i);      fprintf(ficlog,"%3d",i);
      for(j=1; j<=i;j++){      for(j=1; j<=i;j++){
        fprintf(ficres," %.5e",matcov[i][j]);        fprintf(ficres," %.5e",matcov[i][j]);
        if(mle==1)        if(mle==1)
          printf(" %.5e",matcov[i][j]);          printf(" %.5e",matcov[i][j]);
        fprintf(ficlog," %.5e",matcov[i][j]);        fprintf(ficlog," %.5e",matcov[i][j]);
      }      }
      fprintf(ficres,"\n");      fprintf(ficres,"\n");
      if(mle==1)      if(mle==1)
        printf("\n");        printf("\n");
      fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
      k++;      k++;
    }    }
         
    while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
      puts(line);      puts(line);
      fputs(line,ficparo);      fputs(line,ficparo);
    }    }
    ungetc(c,ficpar);    ungetc(c,ficpar);
    estepm=0;  
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    estepm=0;
    if (estepm==0 || estepm < stepm) estepm=stepm;    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
    if (fage <= 2) {    if (estepm==0 || estepm < stepm) estepm=stepm;
      bage = ageminpar;    if (fage <= 2) {
      fage = agemaxpar;      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 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(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);    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
         
    while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
      puts(line);      puts(line);
      fputs(line,ficparo);      fputs(line,ficparo);
    }    }
    ungetc(c,ficpar);    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);    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(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);    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){    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
      puts(line);      puts(line);
      fputs(line,ficparo);      fputs(line,ficparo);
    }    }
    ungetc(c,ficpar);    ungetc(c,ficpar);
     
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    fscanf(ficpar,"pop_based=%d\n",&popbased);
   fprintf(ficparo,"pop_based=%d\n",popbased);       fprintf(ficparo,"pop_based=%d\n",popbased);   
Line 3753  printf("Total number of individuals= %d, Line 4737  printf("Total number of individuals= %d,
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    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,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    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);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    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.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     puts(line);      puts(line);
Line 3770  while((c=getc(ficpar))=='#' && c!= EOF){ Line 4756  while((c=getc(ficpar))=='#' && c!= EOF){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
 /*------------ gnuplot -------------*/    /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
  strcpy(optionfilegnuplot,optionfilefiname);  
  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);  
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  
 /*--------- index.htm --------*/  
   
   strcpy(optionfilehtm,optionfile);    replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
   strcat(optionfilehtm,".htm");    printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }  
   
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n                 model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
 \n                 jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li><h4>Parameter files</h4>\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></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);  
   fclose(fichtm);  
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
     
 /*------------ free_vector  -------------*/    /*------------ free_vector  -------------*/
  chdir(path);    /*  chdir(path); */
     
  free_ivector(wav,1,imx);    free_ivector(wav,1,imx);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
  free_ivector(num,1,n);    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
  free_vector(agedc,1,n);    free_lvector(num,1,n);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    free_vector(agedc,1,n);
  fclose(ficparo);    /*free_matrix(covar,0,NCOVMAX,1,n);*/
  fclose(ficres);    /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
   /*--------------- Prevalence limit  (stable prevalence) --------------*/    /*--------------- Prevalence limit  (stable prevalence) --------------*/
Line 3835  Interval (in months) between two waves: Line 4797  Interval (in months) between two waves:
   fprintf(ficrespl,"\n");    fprintf(ficrespl,"\n");
       
   prlim=matrix(1,nlstate,1,nlstate);    prlim=matrix(1,nlstate,1,nlstate);
   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 */  
   k=0;  
   agebase=ageminpar;    agebase=ageminpar;
   agelim=agemaxpar;    agelim=agemaxpar;
   ftolpl=1.e-10;    ftolpl=1.e-10;
   i1=cptcoveff;    i1=cptcoveff;
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;        k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");        fprintf(ficrespl,"\n#******");
         printf("\n#******");        printf("\n#******");
         fprintf(ficlog,"\n#******");        fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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]]);          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(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }        }
         fprintf(ficrespl,"******\n");        fprintf(ficrespl,"******\n");
         printf("******\n");        printf("******\n");
         fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
                   
         for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f",age );          fprintf(ficrespl,"%.0f ",age );
           for(i=1; i<=nlstate;i++)          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," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");          fprintf(ficrespl,"\n");
         }  
       }        }
     }      }
     }
   fclose(ficrespl);    fclose(ficrespl);
   
   /*------------- h Pij x at various ages ------------*/    /*------------- h Pij x at various ages ------------*/
Line 3893  Interval (in months) between two waves: Line 4852  Interval (in months) between two waves:
   
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   
   k=0;    fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;        k=k+1;
         fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
                   
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        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=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");          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(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)              for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);                fprintf(ficrespij," %.5f", p3mat[i][j][h]);
           fprintf(ficrespij,"\n");  
            for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %f %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");            fprintf(ficrespij,"\n");
         }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
     }      }
   }    }
   
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
   fclose(ficrespij);    fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   /*---------- Forecasting ------------------*/    /*---------- Forecasting ------------------*/
   if((stepm == 1) && (strcmp(model,".")==0)){    /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    if(prevfcast==1){
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      /*    if(stepm ==1){*/
   }         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
   else{        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
     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);  /*      else{ */
     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);  /*        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); */
   /*      } */
   }    }
       
   
Line 3975  Interval (in months) between two waves: Line 4938  Interval (in months) between two waves:
   }    }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   calagedate=-1;  
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    /* 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) {    if (mobilav!=0) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
Line 3985  Interval (in months) between two waves: Line 4953  Interval (in months) between two waves:
     }      }
   }    }
   
   k=0;    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;         k=k+1; 
       fprintf(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
Line 4013  Interval (in months) between two waves: Line 4980  Interval (in months) between two waves:
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);        varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
       if(popbased==1){        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);          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
        }        }
   
     
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
Line 4051  Interval (in months) between two waves: Line 5018  Interval (in months) between two waves:
         }          }
         fprintf(ficrest,"\n");          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_matrix(mint,1,maxwav,1,n);    free_vector(weight,1,n);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    free_imatrix(Tvard,1,15,1,2);
     free_vector(weight,1,n);    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(ficreseij);
   fclose(ficresvij);    fclose(ficresvij);
   fclose(ficrest);    fclose(ficrest);
   fclose(ficpar);    fclose(ficpar);
   free_vector(epj,1,nlstate+1);  
       
   /*------- Variance of stable prevalence------*/       /*------- Variance of stable prevalence------*/   
   
Line 4072  free_matrix(mint,1,maxwav,1,n); Line 5045  free_matrix(mint,1,maxwav,1,n);
   }    }
   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);    printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
   k=0;    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficresvpl,"\n#****** ");        fprintf(ficresvpl,"\n#****** ");
Line 4083  free_matrix(mint,1,maxwav,1,n); Line 5055  free_matrix(mint,1,maxwav,1,n);
               
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        varpl=matrix(1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     }      }
  }    }
   
   fclose(ficresvpl);    fclose(ficresvpl);
   
   /*---------- End : free ----------------*/    /*---------- End : free ----------------*/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
     
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
     
     
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(oldms, 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(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(savms, 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_matrix(matcov,1,npar,1,npar);
   free_vector(delti,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_matrix(agev,1,maxwav,1,imx);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   fprintf(fichtm,"\n</body>");    free_ivector(ncodemax,1,8);
   fclose(fichtm);    free_ivector(Tvar,1,15);
   fclose(ficgp);    free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
   if(erreur >0){    free_ivector(Tcode,1,100);
     printf("End of Imach with error or warning %d\n",erreur);  
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
   }else{    }else{
    printf("End of Imach\n");      printf("End of Imach\n");
    fprintf(ficlog,"End of Imach\n");      fprintf(ficlog,"End of Imach\n");
   }    }
   printf("See log file on %s\n",filelog);    printf("See log file on %s\n",filelog);
   fclose(ficlog);  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
       (void) gettimeofday(&end_time,&tzp);
   /* 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);*/    tm = *localtime(&end_time.tv_sec);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime 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 -----------*/    /*------ End -----------*/
   
     chdir(path);
  end:    strcpy(plotcmd,GNUPLOTPROGRAM);
 #ifdef windows    strcat(plotcmd," ");
   /* chdir(pathcd);*/    strcat(plotcmd,optionfilegnuplot);
 #endif     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
  /*system("wgnuplot graph.plt");*/    if((outcmd=system(plotcmd)) != 0){
  /*system("../gp37mgw/wgnuplot graph.plt");*/      printf(" Problem with gnuplot\n");
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    printf(" Wait...");
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);  
  printf("Starting: %s\n",plotcmd);fflush(stdout);  
  system(plotcmd);  
   
  /*#ifdef windows*/  
   while (z[0] != 'q') {    while (z[0] != 'q') {
     /* chdir(path); */      /* chdir(path); */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      printf("\nType e to edit output files, g to graph again and q for exiting: ");
     scanf("%s",z);      scanf("%s",z);
     if (z[0] == 'c') system("./imach");  /*     if (z[0] == 'c') system("./imach"); */
     else if (z[0] == 'e') system(optionfilehtm);      if (z[0] == 'e') system(optionfilehtm);
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
   /*#endif */    end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
 }  }
   
   
   
Removed from v.1.56  
changed lines
  Added in v.1.94

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