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Diff for /imach/src/imach.c between versions 1.97 and 1.106

version 1.97, 2004/02/20 13:25:42 version 1.106, 2006/01/19 13:24:36
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
   
     Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
   
     Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
   
     Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   
     Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
   
     Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
   
     Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
   
     Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
   
     Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
   
     The same imach parameter file can be used but the option for mle should be -3.
   
     Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   
     The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
   
     Current limitations:
     A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
   
   Revision 1.97  2004/02/20 13:25:42  lievre    Revision 1.97  2004/02/20 13:25:42  lievre
   Version 0.96d. Population forecasting command line is (temporarily)    Version 0.96d. Population forecasting command line is (temporarily)
   suppressed.    suppressed.
Line 172 Line 224
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
   #include <string.h>
 #include <unistd.h>  #include <unistd.h>
   
 #include <sys/time.h>  /* #include <sys/time.h> */
 #include <time.h>  #include <time.h>
 #include "timeval.h"  #include "timeval.h"
   
Line 201 Line 254
 #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 unix  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 #define DIRSEPARATOR '/'  #define DIRSEPARATOR '/'
 #define ODIRSEPARATOR '\\'  #define ODIRSEPARATOR '\\'
 #else  #else
Line 212 Line 266
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;  int nvar;
Line 242  int globpr; /* Global variable for print Line 296  int globpr; /* Global variable for print
 double fretone; /* Only one call to likelihood */  double fretone; /* Only one call to likelihood */
 long ipmx; /* Number of contributions */  long ipmx; /* Number of contributions */
 double sw; /* Sum of weights */  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 FILE *ficresilk;  FILE *ficresilk;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
Line 304  static double maxarg1,maxarg2; Line 359  static double maxarg1,maxarg2;
 static double sqrarg;  static double sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   
 int imx;   int imx; 
 int stepm;  int stepm=1;
 /* Stepm, step in month: minimum step interpolation*/  /* Stepm, step in month: minimum step interpolation*/
   
 int estepm;  int estepm;
Line 314  int estepm; Line 370  int estepm;
   
 int m,nb;  int m,nb;
 long *num;  long *num;
 int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
 double *agedc, **covar, idx;  double *agedc, **covar, idx;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 double ftolhess; /* Tolerance for computing hessian */  double ftolhess; /* Tolerance for computing hessian */
Line 330  double ftolhess; /* Tolerance for comput Line 388  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 )
 {  {
     /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   char  *ss;                            /* pointer */    char  *ss;                            /* pointer */
   int   l1, l2;                         /* length counters */    int   l1, l2;                         /* length counters */
   
Line 361  static int split( char *path, char *dirc Line 422  static int split( char *path, char *dirc
 #endif  #endif
   */    */
   ss = strrchr( name, '.' );            /* find last / */    ss = strrchr( name, '.' );            /* find last / */
   ss++;    if (ss >0){
   strcpy(ext,ss);                       /* save extension */      ss++;
   l1= strlen( name);      strcpy(ext,ss);                     /* save extension */
   l2= strlen(ss)+1;      l1= strlen( name);
   strncpy( finame, name, l1-l2);      l2= strlen(ss)+1;
   finame[l1-l2]= 0;      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
     }
   return( 0 );                          /* we're done */    return( 0 );                          /* we're done */
 }  }
   
Line 399  int nbocc(char *s, char occ) Line 462  int nbocc(char *s, char occ)
   
 void cutv(char *u,char *v, char*t, char occ)  void cutv(char *u,char *v, char*t, char occ)
 {  {
   /* cuts string t into u and v where u is ended by char occ excluding it    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
      gives u="abcedf" and v="ghi2j" */       gives u="abcedf" and v="ghi2j" */
   int i,lg,j,p=0;    int i,lg,j,p=0;
   i=0;    i=0;
Line 829  void powell(double p[], double **xi, int Line 892  void powell(double p[], double **xi, int
     last_time=curr_time;      last_time=curr_time;
     (void) gettimeofday(&curr_time,&tzp);      (void) gettimeofday(&curr_time,&tzp);
     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);      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(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);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     for (i=1;i<=n;i++) {      */
      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 841  void powell(double p[], double **xi, int Line 905  void powell(double p[], double **xi, int
     fprintf(ficrespow,"\n");fflush(ficrespow);      fprintf(ficrespow,"\n");fflush(ficrespow);
     if(*iter <=3){      if(*iter <=3){
       tm = *localtime(&curr_time.tv_sec);        tm = *localtime(&curr_time.tv_sec);
       strcpy(strcurr,asctime(&tmf));        strcpy(strcurr,asctime(&tm));
 /*       asctime_r(&tm,strcurr); */  /*       asctime_r(&tm,strcurr); */
       forecast_time=curr_time;        forecast_time=curr_time; 
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         strcurr[itmp-1]='\0';          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);        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);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
Line 857  void powell(double p[], double **xi, int Line 921  void powell(double p[], double **xi, int
         itmp = strlen(strfor);          itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')          if(strfor[itmp-1]=='\n')
         strfor[itmp-1]='\0';          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);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s 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 i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) {       for (i=1;i<=n;i++) { 
Line 1023  double **pmij(double **ps, double *cov, Line 1087  double **pmij(double **ps, double *cov,
   int i,j,j1, nc, ii, jj;    int i,j,j1, nc, ii, jj;
   
     for(i=1; i<= nlstate; i++){      for(i=1; i<= nlstate; i++){
     for(j=1; j<i;j++){        for(j=1; j<i;j++){
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         /*s2 += param[i][j][nc]*cov[nc];*/            /*s2 += param[i][j][nc]*cov[nc];*/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       }          }
       ps[i][j]=s2;          ps[i][j]=s2;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     }        }
     for(j=i+1; j<=nlstate+ndeath;j++){        for(j=i+1; j<=nlstate+ndeath;j++){
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
           }
           ps[i][j]=s2;
       }        }
       ps[i][j]=s2;  
     }      }
   }  
     /*ps[3][2]=1;*/      /*ps[3][2]=1;*/
       
   for(i=1; i<= nlstate; i++){      for(i=1; i<= nlstate; i++){
      s1=0;        s1=0;
     for(j=1; j<i; j++)        for(j=1; j<i; j++)
       s1+=exp(ps[i][j]);          s1+=exp(ps[i][j]);
     for(j=i+1; j<=nlstate+ndeath; j++)        for(j=i+1; j<=nlstate+ndeath; j++)
       s1+=exp(ps[i][j]);          s1+=exp(ps[i][j]);
     ps[i][i]=1./(s1+1.);        ps[i][i]=1./(s1+1.);
     for(j=1; j<i; j++)        for(j=1; j<i; j++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     for(j=i+1; j<=nlstate+ndeath; j++)        for(j=i+1; j<=nlstate+ndeath; j++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   } /* end i */      } /* end i */
       
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for(jj=1; jj<= nlstate+ndeath; jj++){        for(jj=1; jj<= nlstate+ndeath; jj++){
       ps[ii][jj]=0;          ps[ii][jj]=0;
       ps[ii][ii]=1;          ps[ii][ii]=1;
         }
     }      }
   }      
   
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
      printf("%lf ",ps[ii][jj]);  /*         printf("ddd %lf ",ps[ii][jj]); */
    }  /*       } */
     printf("\n ");  /*       printf("\n "); */
     }  /*        } */
     printf("\n ");printf("%lf ",cov[2]);*/  /*        printf("\n ");printf("%lf ",cov[2]); */
 /*         /*
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   goto end;*/        goto end;*/
     return ps;      return ps;
 }  }
   
Line 1197  double func( double *x) Line 1261  double func( double *x)
         } /* end mult */          } /* end mult */
               
         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */          /*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.          /* But now since version 0.9 we anticipate for bias at large stepm.
          * If stepm is larger than one month (smallest stepm) and if the exact delay            * 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            * (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           * 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           * 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           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
          * probability in order to take into account the bias as a fraction of the way           * 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           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
          * -stepm/2 to stepm/2 .           * -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 the same as for previous versions of Imach.
          * For stepm > 1 the results are less biased than in previous versions.            * For stepm > 1 the results are less biased than in previous versions. 
Line 1212  double func( double *x) Line 1276  double func( double *x)
         s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration          /* bias bh is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.           * 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]));*/          /* 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){           if( s2 > nlstate){ 
           /* i.e. if s2 is a death state and if the date of death is known then the contribution            /* i.e. if s2 is a death state and if the date of death is known 
              to the likelihood is the probability to die between last step unit time and current                then the contribution to the likelihood is the probability to 
              step unit time, which is also the differences between probability to die before dh                die between last step unit time and current  step unit time, 
              and probability to die before dh-stepm .                which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
              In version up to 0.92 likelihood was computed               In version up to 0.92 likelihood was computed
         as if date of death was unknown. Death was treated as any other          as if date of death was unknown. Death was treated as any other
         health state: the date of the interview describes the actual state          health state: the date of the interview describes the actual state
Line 1240  double func( double *x) Line 1305  double func( double *x)
         lower mortality.          lower mortality.
           */            */
           lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
         }else{  
   
           } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += out[s1][j];
             lli= survp;
           }
           
           else if  (s2==-4) {
             for (j=3,survp=0. ; j<=nlstate; j++) 
               survp += out[s1][j];
             lli= survp;
           }
           
           else if  (s2==-5) {
             for (j=1,survp=0. ; j<=2; j++) 
               survp += out[s1][j];
             lli= survp;
           }
   
   
           else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            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= (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 */
         }           } 
Line 1516  void mlikeli(FILE *ficres,double p[], in Line 1602  void mlikeli(FILE *ficres,double p[], in
   double **xi;    double **xi;
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
   char filerespow[FILENAMELENGTH];    /*  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++)
Line 1551  void hesscov(double **matcov, double p[] Line 1637  void hesscov(double **matcov, double p[]
   int i, j,jk;    int i, j,jk;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[]);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double hessij(double p[], double delti[], int i, int j);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   void lubksb(double **a, int npar, int *indx, double b[]) ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
   hess=matrix(1,npar,1,npar);    hess=matrix(1,npar,1,npar);
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
Line 1563  void hesscov(double **matcov, double p[] Line 1649  void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++){    for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);      printf("%d",i);fflush(stdout);
     fprintf(ficlog,"%d",i);fflush(ficlog);      fprintf(ficlog,"%d",i);fflush(ficlog);
     hess[i][i]=hessii(p,ftolhess,i,delti);     
     /*printf(" %f ",p[i]);*/       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     /*printf(" %lf ",hess[i][i]);*/      
       /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }    }
       
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
Line 1573  void hesscov(double **matcov, double p[] Line 1661  void hesscov(double **matcov, double p[]
       if (j>i) {         if (j>i) { 
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d%d",i,j);fflush(stdout);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         hess[i][j]=hessij(p,delti,i,j);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
         hess[j][i]=hess[i][j];              hess[j][i]=hess[i][j];    
         /*printf(" %lf ",hess[i][j]);*/          /*printf(" %lf ",hess[i][j]);*/
       }        }
Line 1644  void hesscov(double **matcov, double p[] Line 1733  void hesscov(double **matcov, double p[]
 }  }
   
 /*************** hessian matrix ****************/  /*************** hessian matrix ****************/
 double hessii( double x[], double delta, int theta, double delti[])  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  {
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2;    double k1,k2;
   double p2[NPARMAX+1];    double p2[NPARMAX+1];
   double res;    double res;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;    double fx;
   int k=0,kmax=10;    int k=0,kmax=10;
   double l1;    double l1;
Line 1691  double hessii( double x[], double delta, Line 1780  double hessii( double x[], double delta,
       
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, l1, lmax=20;    int l=1, l1, lmax=20;
Line 1801  void lubksb(double **a, int n, int *indx Line 1890  void lubksb(double **a, int n, int *indx
 }   } 
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 {  /* 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;
Line 1821  void  freqsummary(char fileres[], int ia Line 1910  void  freqsummary(char fileres[], int ia
     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,iagemin,iagemax+3);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   j1=0;    j1=0;
       
   j=cptcoveff;    j=cptcoveff;
Line 1834  void  freqsummary(char fileres[], int ia Line 1923  void  freqsummary(char fileres[], int ia
       j1++;        j1++;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
       for (i=-1; i<=nlstate+ndeath; i++)          for (i=-5; i<=nlstate+ndeath; i++)  
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for (jk=-5; jk<=nlstate+ndeath; jk++)  
           for(m=iagemin; m <= iagemax+3; m++)            for(m=iagemin; m <= iagemax+3; m++)
             freq[i][jk][m]=0;              freq[i][jk][m]=0;
   
Line 1874  void  freqsummary(char fileres[], int ia Line 1963  void  freqsummary(char fileres[], int ia
       }        }
                 
       /*      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);*/
   fprintf(ficresp, "#Local time at start: %s", strstart);
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 1960  void  freqsummary(char fileres[], int ia Line 2049  void  freqsummary(char fileres[], int ia
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
     
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /* End of Freq */    /* End of Freq */
Line 2069  void  concatwav(int wav[], int **dh, int Line 2158  void  concatwav(int wav[], int **dh, int
     mi=0;      mi=0;
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){      while(s[m][i] <= nlstate){
       if(s[m][i]>=1)        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         mw[++mi][i]=m;          mw[++mi][i]=m;
       if(m >=lastpass)        if(m >=lastpass)
         break;          break;
Line 2109  void  concatwav(int wav[], int **dh, int Line 2198  void  concatwav(int wav[], int **dh, int
               nberr++;                nberr++;
               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               j=1; /* Temporary Dangerous patch */                j=1; /* Temporary Dangerous patch */
               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                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);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }              }
             k=k+1;              k=k+1;
             if (j >= jmax) jmax=j;              if (j >= jmax) jmax=j;
Line 2123  void  concatwav(int wav[], int **dh, int Line 2212  void  concatwav(int wav[], int **dh, int
         }          }
         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);*/  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   
           k=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;
Line 2216  void tricode(int *Tvar, int **nbcode, in Line 2306  void tricode(int *Tvar, int **nbcode, in
  for (k=0; k< maxncov; 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.*/     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    ij=Tvar[i];     ij=Tvar[i];
    Ndum[ij]++;     Ndum[ij]++;
  }   }
Line 2234  void tricode(int *Tvar, int **nbcode, in Line 2324  void tricode(int *Tvar, int **nbcode, in
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
   
 {  {
   /* Health expectancies */    /* Health expectancies */
Line 2252  void evsij(char fileres[], double ***eij Line 2342  void evsij(char fileres[], double ***eij
   dnewm=matrix(1,nlstate*nlstate,1,npar);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       
     fprintf(ficreseij,"# Local time at start: %s", strstart);
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficreseij,"# Health expectancies\n");
   fprintf(ficreseij,"# Age");    fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
Line 2406  void evsij(char fileres[], double ***eij Line 2497  void evsij(char fileres[], double ***eij
 }  }
   
 /************ Variance ******************/  /************ Variance ******************/
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
 {  {
   /* Variance of health expectancies */    /* Variance of health expectancies */
   /*  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);*/
Line 2457  void varevsij(char optionfilefiname[], d Line 2548  void varevsij(char optionfilefiname[], d
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
   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, "#Local time at start: %s", strstart);
   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,"# 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++){
Line 2467  void varevsij(char optionfilefiname[], d Line 2560  void varevsij(char optionfilefiname[], d
   }      }  
   fprintf(ficresprobmorprev,"\n");    fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n# Routine varevsij");    fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);    fprintf(fichtm,"\n<br>%s  <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, "#Local time at start: %s", strstart);
   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");
   fprintf(ficresvij,"# Age");    fprintf(ficresvij,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
Line 2704  void varevsij(char optionfilefiname[], d Line 2798  void varevsij(char optionfilefiname[], d
 }  /* end varevsij */  }  /* 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, char strstart[])
 {  {
   /* 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);*/
Line 2717  void varprevlim(char fileres[], double * Line 2811  void varprevlim(char fileres[], double *
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double age,agelim;    double age,agelim;
   int theta;    int theta;
        fprintf(ficresvpl, "#Local time at start: %s", strstart); 
   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   fprintf(ficresvpl,"# Age");    fprintf(ficresvpl,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
Line 2787  void varprevlim(char fileres[], double * Line 2881  void varprevlim(char fileres[], double *
 }  }
   
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {  {
   int i, j=0,  i1, k1, l1, t, tj;    int i, j=0,  i1, k1, l1, t, tj;
   int k2, l2, j1,  z1;    int k2, l2, j1,  z1;
Line 2832  void varprob(char optionfilefiname[], do Line 2926  void varprob(char optionfilefiname[], do
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       fprintf(ficresprob, "#Local time at start: %s", strstart);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov, "#Local time at start: %s", strstart);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor, "#Local time at start: %s", strstart);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcov,"# Age");    fprintf(ficresprobcov,"# Age");
   
Line 3107  void printinghtml(char fileres[], char t Line 3203  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;
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \     fprintf(fichtm,"<ul><li><a> href="#firstorder">Result files (first order: no variance)</a>\n \
      <li><a> href="#secondorder">Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name="firstorder">Result files (first order: no variance)</a></h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
Line 3158  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 3257  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   
   
  fprintf(fichtm,"\   fprintf(fichtm,"\
 \n<br><li><h4> Result files (second order: variances)</h4>\n\  \n<br><li><h4> <a name="secondorder">Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 3867  void prwizard(int ncovmodel, int nlstate Line 3966  void prwizard(int ncovmodel, int nlstate
   } /* end itimes */    } /* end itimes */
   
 } /* end of prwizard */  } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
 /***********************************************/  /***********************************************/
Line 3880  int main(int argc, char *argv[]) Line 4062  int main(int argc, char *argv[])
   int jj, ll, li, lj, lk, imk;    int jj, ll, li, lj, lk, imk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
   int itimes;    int itimes;
     int NDIM=2;
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32], cc[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
Line 3896  int main(int argc, char *argv[]) Line 4079  int main(int argc, char *argv[])
   int *indx;    int *indx;
   char line[MAXLINE], linepar[MAXLINE];    char line[MAXLINE], linepar[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
   char pathr[MAXLINE];     char pathr[MAXLINE], pathimach[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;
Line 3906  int main(int argc, char *argv[]) Line 4089  int main(int argc, char *argv[])
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    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;
     int agemortsup;
     float  sumlpop=0.;
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;    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 jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
Line 3923  int main(int argc, char *argv[]) Line 4108  int main(int argc, char *argv[])
   double *epj, vepp;    double *epj, vepp;
   double kk1, kk2;    double kk1, kk2;
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
   char z[1]="c", occ;    char z[1]="c", occ;
   
Line 3982  int main(int argc, char *argv[]) Line 4167  int main(int argc, char *argv[])
     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(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);    chdir(path);
   strcpy(command,"mkdir ");    strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);    strcat(command,optionfilefiname);
Line 4008  int main(int argc, char *argv[]) Line 4195  int main(int argc, char *argv[])
   }    }
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s\n%s",version,fullversion);    fprintf(ficlog,"\n%s\n%s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: ");    fprintf(ficlog,"\nEnter the parameter file name: \n");
   fprintf(ficlog,"pathtot=%s\n\    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
  path=%s \n\   path=%s \n\
  optionfile=%s\n\   optionfile=%s\n\
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   printf("Local time (at start):%s",strstart);    printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"Local time (at start): %s",strstart);
Line 4081  int main(int argc, char *argv[]) Line 4268  int main(int argc, char *argv[])
   
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */    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 */
      npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      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);      fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     fclose (ficparo);      fclose (ficparo);
     fclose (ficlog);      fclose (ficlog);
     exit(0);      exit(0);
   }    }
   /* Read guess parameters */    else if(mle==-3) {
   /* Reads comments: lines beginning with '#' */      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
   while((c=getc(ficpar))=='#' && c!= EOF){      printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     ungetc(c,ficpar);      fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fgets(line, MAXLINE, ficpar);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     numlinepar++;      matcov=matrix(1,npar,1,npar);
     puts(line);  
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }    }
   ungetc(c,ficpar);    else{
       /* Read guess parameters */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      /* Reads comments: lines beginning with '#' */
   for(i=1; i <=nlstate; i++){      while((c=getc(ficpar))=='#' && c!= EOF){
     j=0;        ungetc(c,ficpar);
     for(jj=1; jj <=nlstate+ndeath; jj++){        fgets(line, MAXLINE, ficpar);
       if(jj==i) continue;  
       j++;  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       if ((i1 != i) && (j1 != j)){  
         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);  
         exit(1);  
       }  
       fprintf(ficparo,"%1d%1d",i1,j1);  
       if(mle==1)  
         printf("%1d%1d",i,j);  
       fprintf(ficlog,"%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  
         if(mle==1){  
           printf(" %lf",param[i][j][k]);  
           fprintf(ficlog," %lf",param[i][j][k]);  
         }  
         else  
           fprintf(ficlog," %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  
       }  
       fscanf(ficpar,"\n");  
       numlinepar++;        numlinepar++;
       if(mle==1)        puts(line);
         printf("\n");        fputs(line,ficparo);
       fprintf(ficlog,"\n");        fputs(line,ficlog);
       fprintf(ficparo,"\n");  
     }      }
   }        ungetc(c,ficpar);
   fflush(ficlog);      
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/  
   
   p=param[1][1];      p=param[1][1];
         
   /* 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);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);  
     numlinepar++;  
     puts(line);  
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }  
   ungetc(c,ficpar);  
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(i=1; i <=nlstate; i++){
   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */        for(j=1; j <=nlstate+ndeath-1; j++){
   for(i=1; i <=nlstate; i++){          fscanf(ficpar,"%1d%1d",&i1,&j1);
     for(j=1; j <=nlstate+ndeath-1; j++){          if ((i1-i)*(j1-j)!=0){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
       if ((i1-i)*(j1-j)!=0){            exit(1);
         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);          }
         exit(1);          printf("%1d%1d",i,j);
       }          fprintf(ficparo,"%1d%1d",i1,j1);
       printf("%1d%1d",i,j);          fprintf(ficlog,"%1d%1d",i1,j1);
       fprintf(ficparo,"%1d%1d",i1,j1);          for(k=1; k<=ncovmodel;k++){
       fprintf(ficlog,"%1d%1d",i1,j1);            fscanf(ficpar,"%le",&delti3[i][j][k]);
       for(k=1; k<=ncovmodel;k++){            printf(" %le",delti3[i][j][k]);
         fscanf(ficpar,"%le",&delti3[i][j][k]);            fprintf(ficparo," %le",delti3[i][j][k]);
         printf(" %le",delti3[i][j][k]);            fprintf(ficlog," %le",delti3[i][j][k]);
         fprintf(ficparo," %le",delti3[i][j][k]);          }
         fprintf(ficlog," %le",delti3[i][j][k]);          fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
       }        }
       fscanf(ficpar,"\n");  
       numlinepar++;  
       printf("\n");  
       fprintf(ficparo,"\n");  
       fprintf(ficlog,"\n");  
     }      }
   }      fflush(ficlog);
   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 */      /* 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);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);  
     numlinepar++;  
     puts(line);  
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }  
   ungetc(c,ficpar);  
       
   matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
   for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
     fscanf(ficpar,"%s",&str);        fscanf(ficpar,"%s",&str);
     if(mle==1)        if(mle==1)
       printf("%s",str);          printf("%s",str);
     fprintf(ficlog,"%s",str);        fprintf(ficlog,"%s",str);
     fprintf(ficparo,"%s",str);        fprintf(ficparo,"%s",str);
     for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
       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]);
           fprintf(ficparo," %.5le",matcov[i][j]);
       }        }
       fprintf(ficlog," %.5le",matcov[i][j]);        fscanf(ficpar,"\n");
       fprintf(ficparo," %.5le",matcov[i][j]);        numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
     }      }
     fscanf(ficpar,"\n");      for(i=1; i <=npar; i++)
     numlinepar++;        for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
     if(mle==1)      if(mle==1)
       printf("\n");        printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficparo,"\n");  
   }  
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];  
      
   if(mle==1)  
     printf("\n");  
   fprintf(ficlog,"\n");  
   
   fflush(ficlog);  
   
   /*-------- Rewriting paramater file ----------*/  
   strcpy(rfileres,"r");    /* "Rparameterfile */  
   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
   strcat(rfileres,".");    /* */  
   strcat(rfileres,optionfilext);    /* Other files have txt extension */  
   if((ficres =fopen(rfileres,"w"))==NULL) {  
     printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;  
   }  
   fprintf(ficres,"#%s\n",version);  
           
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   /*-------- data file ----------*/    /*-------- 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;
Line 4265  int main(int argc, char *argv[]) Line 4463  int main(int argc, char *argv[])
   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=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
       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);
Line 4310  int main(int argc, char *argv[]) Line 4511  int main(int argc, char *argv[])
      if (s[4][i]==9)  s[4][i]=-1;        if (s[4][i]==9)  s[4][i]=-1; 
      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/       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++)    /* for (i=1; i<=imx; i++) */
     
    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;     /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
      else weight[i]=1;*/       else weight[i]=1;*/
   
   /* Calculation of the number of parameter from char model*/    /* Calculation of the number of parameters from char model */
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */    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); 
   Tvaraff=ivector(1,15);     Tvaraff=ivector(1,15); 
Line 4428  int main(int argc, char *argv[]) Line 4629  int main(int argc, char *argv[])
   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=firstpass; (m<= lastpass); m++){      for(m=firstpass; (m<= lastpass); m++){
       if(s[m][i] >0){        if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
         if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
           if(agedc[i]>0)            if(agedc[i]>0)
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
Line 4492  int main(int argc, char *argv[]) Line 4693  int main(int argc, char *argv[])
   printf("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);
   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
   free_vector(severity,1,maxwav);    free_vector(severity,1,maxwav);
   free_imatrix(outcome,1,maxwav+1,1,n);    free_imatrix(outcome,1,maxwav+1,1,n);
   free_vector(moisnais,1,n);    free_vector(moisnais,1,n);
Line 4545  int main(int argc, char *argv[]) Line 4747  int main(int argc, char *argv[])
           
   /*------------ gnuplot -------------*/    /*------------ gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
   strcat(optionfilegnuplot,".gp");    strcat(optionfilegnuplot,".gp");
   
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
   }    }
Line 4558  int main(int argc, char *argv[]) Line 4763  int main(int argc, char *argv[])
   /*--------- index.htm --------*/    /*--------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm), exit(0);      printf("Problem with %s \n",optionfilehtm), exit(0);
Line 4596  Title=%s <br>Datafile=%s Firstpass=%d La Line 4803  Title=%s <br>Datafile=%s Firstpass=%d La
       
   /* Calculates basic frequencies. Computes observed prevalence at single age    /* Calculates basic frequencies. Computes observed prevalence at single age
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 4615  Interval (in months) between two waves: Line 4822  Interval (in months) between two waves:
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/    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 */    if (mle==-3){
   printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      ximort=matrix(1,NDIM,1,NDIM);
   for (k=1; k<=npar;k++)      cens=ivector(1,n);
     printf(" %d %8.5f",k,p[k]);      ageexmed=vector(1,n);
   printf("\n");      agecens=vector(1,n);
   globpr=1; /* to print the contributions */      dcwave=ivector(1,n);
   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 (i=1; i<=imx; i++){
   for (k=1; k<=npar;k++)        dcwave[i]=-1;
     printf(" %d %8.5f",k,p[k]);        for (j=1; j<=lastpass; j++)
   printf("\n");          if (s[j][i]>nlstate) {
   if(mle>=1){ /* Could be 1 or 2 */            dcwave[i]=j;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
   }            break;
       
   /*--------- results files --------------*/  
   fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);  
     
   
   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
   for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {  
         printf("%d%d ",i,k);  
         fprintf(ficlog,"%d%d ",i,k);  
         fprintf(ficres,"%1d%1d ",i,k);  
         for(j=1; j <=ncovmodel; j++){  
           printf("%f ",p[jk]);  
           fprintf(ficlog,"%f ",p[jk]);  
           fprintf(ficres,"%f ",p[jk]);  
           jk++;   
         }          }
         printf("\n");      }
         fprintf(ficlog,"\n");  
         fprintf(ficres,"\n");      for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
       }        }
         else cens[i]=-1;
     }      }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
   if(mle!=0){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /* Computing hessian and covariance matrix */    /*  for (i=1;i<=nlstate;i++)
     ftolhess=ftol; /* Usually correct */      for(j=1;j<=nlstate+ndeath;j++)
     hesscov(matcov, p, npar, delti, ftolhess, func);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   }    */
   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    fprintf(ficrespow,"\n");
   printf("# Scales (for hessian or gradient estimation)\n");  
   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   for(i=1,jk=1; i <=nlstate; i++){      fclose(ficrespow);
     for(j=1; j <=nlstate+ndeath; j++){      
       if (j!=i) {      hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
         fprintf(ficres,"%1d%1d",i,j);  
         printf("%1d%1d",i,j);      for(i=1; i <=NDIM; i++)
         fprintf(ficlog,"%1d%1d",i,j);        for(j=i+1;j<=NDIM;j++)
         for(k=1; k<=ncovmodel;k++){          matcov[i][j]=matcov[j][i];
           printf(" %.5e",delti[jk]);      
           fprintf(ficlog," %.5e",delti[jk]);      printf("\nCovariance matrix\n ");
           fprintf(ficres," %.5e",delti[jk]);      for(i=1; i <=NDIM; i++) {
           jk++;        for(j=1;j<=NDIM;j++){ 
         }          printf("%f ",matcov[i][j]);
         printf("\n");  
         fprintf(ficlog,"\n");  
         fprintf(ficres,"\n");  
       }        }
         printf("\n ");
     }      }
   }      
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
         
   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");       for (k=agegomp;k<=AGESUP;k++) {
   if(mle>=1)        agemortsup=k;
     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");        if (p[1]*exp(p[2]*(k-agegomp))>1) break;
   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      }
 /* # 121 Var(a12)\n\ */     
 /* # 122 Cov(b12,a12) Var(b12)\n\ */        for (k=agegomp;k<agemortsup;k++)
 /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */        lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
 /* # 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" */  
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
 /* Just to have a covariance matrix which will be more understandable   tpop[agegomp]=sumlpop;
    even is we still don't want to manage dictionary of variables      for (k=agegomp;k<(agemortsup-3);k++){
 */        /*  tpop[k+1]=2;*/
   for(itimes=1;itimes<=2;itimes++){        tpop[k+1]=tpop[k]-lpop[k];
     jj=0;         }
     for(i=1; i <=nlstate; i++){     
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){        for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;          if (j!=i) {
         for(k=1; k<=ncovmodel;k++){            fprintf(ficres,"%1d%1d",i,j);
           jj++;            printf("%1d%1d",i,j);
           ca[0]= k+'a'-1;ca[1]='\0';            fprintf(ficlog,"%1d%1d",i,j);
           if(itimes==1){            for(k=1; k<=ncovmodel;k++){
             if(mle>=1)              printf(" %.5e",delti[jk]);
               printf("#%1d%1d%d",i,j,k);              fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficlog,"#%1d%1d%d",i,j,k);              fprintf(ficres," %.5e",delti[jk]);
             fprintf(ficres,"#%1d%1d%d",i,j,k);              jk++;
           }else{  
             if(mle>=1)  
               printf("%1d%1d%d",i,j,k);  
             fprintf(ficlog,"%1d%1d%d",i,j,k);  
             fprintf(ficres,"%1d%1d%d",i,j,k);  
           }            }
           ll=0;            printf("\n");
           for(li=1;li <=nlstate; li++){            fprintf(ficlog,"\n");
             for(lj=1;lj <=nlstate+ndeath; lj++){            fprintf(ficres,"\n");
               if(lj==li) continue;          }
               for(lk=1;lk<=ncovmodel;lk++){        }
                 ll++;      }
                 if(ll<=jj){      
                   cb[0]= lk +'a'-1;cb[1]='\0';      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(ll<jj){      if(mle>=1)
                     if(itimes==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");
                       if(mle>=1)      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");
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);      /* # 121 Var(a12)\n\ */
                       fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);      /* # 122 Cov(b12,a12) Var(b12)\n\ */
                       fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);      /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                     }else{      /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                       if(mle>=1)      /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                         printf(" %.5e",matcov[jj][ll]);       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                       fprintf(ficlog," %.5e",matcov[jj][ll]);       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                       fprintf(ficres," %.5e",matcov[jj][ll]);       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                     }      
                   }else{      
                     if(itimes==1){      /* Just to have a covariance matrix which will be more understandable
                       if(mle>=1)         even is we still don't want to manage dictionary of variables
                         printf(" Var(%s%1d%1d)",ca,i,j);      */
                       fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);      for(itimes=1;itimes<=2;itimes++){
                       fprintf(ficres," Var(%s%1d%1d)",ca,i,j);        jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                     }else{                      }else{
                       if(mle>=1)                        if(itimes==1){
                         printf(" %.5e",matcov[jj][ll]);                           if(mle>=1)
                       fprintf(ficlog," %.5e",matcov[jj][ll]);                             printf(" Var(%s%1d%1d)",ca,i,j);
                       fprintf(ficres," %.5e",matcov[jj][ll]);                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                     }                      }
                   }                    }
                 }                  } /* end lk */
               } /* end lk */                } /* end lj */
             } /* end lj */              } /* end li */
           } /* end li */              if(mle>=1)
           if(mle>=1)                printf("\n");
             printf("\n");              fprintf(ficlog,"\n");
           fprintf(ficlog,"\n");              fprintf(ficres,"\n");
           fprintf(ficres,"\n");              numlinepar++;
           numlinepar++;            } /* end k*/
         } /* end k*/          } /*end j */
       } /*end j */        } /* end i */
     } /* end i */      } /* end itimes */
   } /* end itimes */      
       fflush(ficlog);
   fflush(ficlog);      fflush(ficres);
   fflush(ficres);      
       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);  
   
   estepm=0;  
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);  
   if (estepm==0 || estepm < stepm) estepm=stepm;  
   if (fage <= 2) {  
     bage = ageminpar;  
     fage = agemaxpar;  
   }  
      
   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  
   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
      
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      estepm=0;
     fputs(line,ficparo);      fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
   }      if (estepm==0 || estepm < stepm) estepm=stepm;
   ungetc(c,ficpar);      if (fage <= 2) {
           bage = ageminpar;
   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);        fage = agemaxpar;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      }
   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      
   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
   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);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
          fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   while((c=getc(ficpar))=='#' && c!= EOF){      
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      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);
     fputs(line,ficparo);      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);
   ungetc(c,ficpar);      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);
       
   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;      while((c=getc(ficpar))=='#' && c!= EOF){
   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;        ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
   fscanf(ficpar,"pop_based=%d\n",&popbased);        puts(line);
   fprintf(ficparo,"pop_based=%d\n",popbased);           fputs(line,ficparo);
   fprintf(ficres,"pop_based=%d\n",popbased);         }
     
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      
     fputs(line,ficparo);      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
   }      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   ungetc(c,ficpar);      
       fscanf(ficpar,"pop_based=%d\n",&popbased);
   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,"pop_based=%d\n",popbased);   
   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,"pop_based=%d\n",popbased);   
   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);      while((c=getc(ficpar))=='#' && c!= EOF){
   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);        ungetc(c,ficpar);
   /* day and month of proj2 are not used but only year anproj2.*/        fgets(line, MAXLINE, ficpar);
         puts(line);
   while((c=getc(ficpar))=='#' && c!= EOF){        fputs(line,ficparo);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      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);
     fputs(line,ficparo);      fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
   }      printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
   ungetc(c,ficpar);      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);
   /*  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      /* day and month of proj2 are not used but only year anproj2.*/
   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);*/      
       
   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/      /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/      /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
   replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
   printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\      printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\                   model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                   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(bh,1,lastpass-firstpass+1,1,imx);      free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
   free_lvector(num,1,n);      free_lvector(num,1,n);
   free_vector(agedc,1,n);      free_vector(agedc,1,n);
   /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
   /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
   fclose(ficparo);      fclose(ficparo);
   fclose(ficres);      fclose(ficres);
   
   
   /*--------------- Prevalence limit  (stable prevalence) --------------*/      /*--------------- Prevalence limit  (stable prevalence) --------------*/
       
   strcpy(filerespl,"pl");      strcpy(filerespl,"pl");
   strcat(filerespl,fileres);      strcat(filerespl,fileres);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;        printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;        fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
   }      }
   printf("Computing stable prevalence: result on file '%s' \n", filerespl);      printf("Computing stable prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);      fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
   fprintf(ficrespl,"#Stable prevalence \n");      fprintf(ficrespl, "#Local time at start: %s", strstart);
   fprintf(ficrespl,"#Age ");      fprintf(ficrespl,"#Stable prevalence \n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      fprintf(ficrespl,"#Age ");
   fprintf(ficrespl,"\n");      for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
         fprintf(ficrespl,"\n");
   prlim=matrix(1,nlstate,1,nlstate);    
       prlim=matrix(1,nlstate,1,nlstate);
   agebase=ageminpar;  
   agelim=agemaxpar;      agebase=ageminpar;
   ftolpl=1.e-10;      agelim=agemaxpar;
   i1=cptcoveff;      ftolpl=1.e-10;
   if (cptcovn < 1){i1=1;}      i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       k=k+1;        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          k=k+1;
       fprintf(ficrespl,"\n#******");          /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
       printf("\n#******");          fprintf(ficrespl,"\n#******");
       fprintf(ficlog,"\n#******");          printf("\n#******");
       for(j=1;j<=cptcoveff;j++) {          fprintf(ficlog,"\n#******");
         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(j=1;j<=cptcoveff;j++) {
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }            fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficrespl,"******\n");          }
       printf("******\n");          fprintf(ficrespl,"******\n");
       fprintf(ficlog,"******\n");          printf("******\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(j=1;j<=cptcoveff;j++)            for(j=1;j<=cptcoveff;j++)
           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         for(i=1; i<=nlstate;i++)            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 ------------*/
       
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      strcpy(filerespij,"pij");  strcat(filerespij,fileres);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      if((ficrespij=fopen(filerespij,"w"))==NULL) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
   }      }
   printf("Computing pij: result on file '%s' \n", filerespij);      printf("Computing pij: result on file '%s' \n", filerespij);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);      fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
       
   stepsize=(int) (stepm+YEARM-1)/YEARM;      stepsize=(int) (stepm+YEARM-1)/YEARM;
   /*if (stepm<=24) stepsize=2;*/      /*if (stepm<=24) stepsize=2;*/
   
   agelim=AGESUP;      agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */      hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
   /* hstepm=1;   aff par mois*/  
   
   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      /* hstepm=1;   aff par mois*/
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){      fprintf(ficrespij, "#Local time at start: %s", strstart);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       k=k+1;      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       fprintf(ficrespij,"\n#****** ");        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       for(j=1;j<=cptcoveff;j++)           k=k+1;
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespij,"\n#****** ");
       fprintf(ficrespij,"******\n");          for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
                   
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          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,"# Cov Agex agex+h hpijx with i,j=");            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," %.5f", p3mat[i][j][h]);                fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");            fprintf(ficrespij,"\n");
         }          }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespij,"\n");  
       }        }
     }      }
   }  
   
   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);  
   
   fclose(ficrespij);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      fclose(ficrespij);
   for(i=1;i<=AGESUP;i++)  
     for(j=1;j<=NCOVMAX;j++)  
       for(k=1;k<=NCOVMAX;k++)  
         probs[i][j][k]=0.;  
   
   /*---------- Forecasting ------------------*/      probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*if((stepm == 1) && (strcmp(model,".")==0)){*/      for(i=1;i<=AGESUP;i++)
   if(prevfcast==1){        for(j=1;j<=NCOVMAX;j++)
     /*    if(stepm ==1){*/          for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
 /*      }  */        /*      }  */
 /*      else{ */        /*      else{ */
 /*        erreur=108; */        /*        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); */        /*        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); */        /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
 /*      } */        /*      } */
   }      }
       
   
   /*---------- Health expectancies and variances ------------*/      /*---------- Health expectancies and variances ------------*/
   
   strcpy(filerest,"t");      strcpy(filerest,"t");
   strcat(filerest,fileres);      strcat(filerest,fileres);
   if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
   }      }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
   strcpy(filerese,"e");      strcpy(filerese,"e");
   strcat(filerese,fileres);      strcat(filerese,fileres);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
   }      }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Health Expectancies: result on file '%s' \n", filerese);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
   strcpy(fileresv,"v");      strcpy(fileresv,"v");
   strcat(fileresv,fileres);      strcat(fileresv,fileres);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      if((ficresvij=fopen(fileresv,"w"))==NULL) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
   }      }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      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);
   
   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      /* 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);      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",\      /*  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);          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){
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       printf(" Error in movingaverage mobilav=%d\n",mobilav);          printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
     }      }
   }  
   
   for(cptcov=1,k=0;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(ficrest,"\n#****** ");          fprintf(ficrest,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficrest,"******\n");          fprintf(ficrest,"******\n");
   
       fprintf(ficreseij,"\n#****** ");          fprintf(ficreseij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficreseij,"******\n");          fprintf(ficreseij,"******\n");
   
       fprintf(ficresvij,"\n#****** ");          fprintf(ficresvij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficresvij,"******\n");          fprintf(ficresvij,"******\n");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);  
       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);  
       }  
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
     
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          oldm=oldms;savm=savms;
       fprintf(ficrest,"\n");          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
       epj=vector(1,nlstate+1);            varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {  
           if(mobilav ==0){  
             for(i=1; i<=nlstate;i++)  
               prlim[i][i]=probs[(int)age][i][k];  
           }else{ /* mobilav */   
             for(i=1; i<=nlstate;i++)  
               prlim[i][i]=mobaverage[(int)age][i][k];  
           }  
         }          }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
                   
         fprintf(ficrest," %4.0f",age);            fprintf(ficrest," %4.0f",age);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              for(i=1, epj[j]=0.;i <=nlstate;i++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                epj[j] += prlim[i][i]*eij[i][j][(int)age];
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
           }            }
           epj[nlstate+1] +=epj[j];  
         }  
   
         for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1, vepp=0.;i <=nlstate;i++)
           for(j=1;j <=nlstate;j++)              for(j=1;j <=nlstate;j++)
             vepp += vareij[i][j][(int)age];                vepp += vareij[i][j][(int)age];
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
         for(j=1;j <=nlstate;j++){            for(j=1;j <=nlstate;j++){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             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_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          free_vector(epj,1,nlstate+1);
       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
       free_vector(epj,1,nlstate+1);      }
     }      free_vector(weight,1,n);
   }      free_imatrix(Tvard,1,15,1,2);
   free_vector(weight,1,n);      free_imatrix(s,1,maxwav+1,1,n);
   free_imatrix(Tvard,1,15,1,2);      free_matrix(anint,1,maxwav,1,n); 
   free_imatrix(s,1,maxwav+1,1,n);      free_matrix(mint,1,maxwav,1,n);
   free_matrix(anint,1,maxwav,1,n);       free_ivector(cod,1,n);
   free_matrix(mint,1,maxwav,1,n);      free_ivector(tab,1,NCOVMAX);
   free_ivector(cod,1,n);      fclose(ficreseij);
   free_ivector(tab,1,NCOVMAX);      fclose(ficresvij);
   fclose(ficreseij);      fclose(ficrest);
   fclose(ficresvij);      fclose(ficpar);
   fclose(ficrest);    
   fclose(ficpar);      /*------- Variance of stable prevalence------*/   
     
   /*------- Variance of stable prevalence------*/         strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
   strcpy(fileresvpl,"vpl");      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
   strcat(fileresvpl,fileres);        printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        exit(0);
     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);      }
     exit(0);      printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   }  
   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){          k=k+1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresvpl,"\n#****** ");
       k=k+1;          for(j=1;j<=cptcoveff;j++) 
       fprintf(ficresvpl,"\n#****** ");            fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       for(j=1;j<=cptcoveff;j++)           fprintf(ficresvpl,"******\n");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\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,strstart);
       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
     }      }
   }  
   
   fclose(ficresvpl);      fclose(ficresvpl);
   
   /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    }  /* mle==-3 arrives here for freeing */
         free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(covar,0,NCOVMAX,1,n);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(matcov,1,npar,1,npar);      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   /*free_vector(delti,1,npar);*/      free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     
   free_matrix(agev,1,maxwav,1,imx);      free_matrix(covar,0,NCOVMAX,1,n);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_matrix(matcov,1,npar,1,npar);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*free_vector(delti,1,npar);*/
   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   free_ivector(ncodemax,1,8);  
   free_ivector(Tvar,1,15);  
   free_ivector(Tprod,1,15);  
   free_ivector(Tvaraff,1,15);  
   free_ivector(Tage,1,15);  
   free_ivector(Tcode,1,100);  
   
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
Line 5194  ageminpar, agemax, s[lastpass][imx], age Line 5513  ageminpar, agemax, s[lastpass][imx], age
   tm = *localtime(&end_time.tv_sec);    tm = *localtime(&end_time.tv_sec);
   tmg = *gmtime(&end_time.tv_sec);    tmg = *gmtime(&end_time.tv_sec);
   strcpy(strtend,asctime(&tm));    strcpy(strtend,asctime(&tm));
   printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend);     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);     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 used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
Line 5211  ageminpar, agemax, s[lastpass][imx], age Line 5530  ageminpar, agemax, s[lastpass][imx], age
   /*------ End -----------*/    /*------ End -----------*/
   
   chdir(path);    chdir(path);
   strcpy(plotcmd,GNUPLOTPROGRAM);    strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
   strcat(plotcmd," ");    strcat(plotcmd," ");
   strcat(plotcmd,optionfilegnuplot);    strcat(plotcmd,optionfilegnuplot);
   printf("Starting graphs with: %s",plotcmd);fflush(stdout);    printf("Starting graphs with: %s",plotcmd);fflush(stdout);
Line 5224  ageminpar, agemax, s[lastpass][imx], age Line 5546  ageminpar, agemax, s[lastpass][imx], age
     printf("\nType e to edit output files, g to graph 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"); */
     if (z[0] == 'e') system(optionfilehtm);      if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
Removed from v.1.97  
changed lines
  Added in v.1.106

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