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Diff for /imach/src/imach.c between versions 1.89 and 1.99

-version 1.89, 2003/06/24 12:30:52
+version 1.99, 2004/06/05 08:57:40
  Line 1
  /* $Id$
    $State$
    $Log$
+   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
+   Version 0.96d. Population forecasting command line is (temporarily)
+   suppressed.
+   Revision 1.96  2003/07/15 15:38:55  brouard
+   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+   rewritten within the same printf. Workaround: many printfs.
+   Revision 1.95  2003/07/08 07:54:34  brouard
+   * imach.c (Repository):
+   (Repository): Using imachwizard code to output a more meaningful covariance
+   matrix (cov(a12,c31) instead of numbers.
+   Revision 1.94  2003/06/27 13:00:02  brouard
+   Just cleaning
+   Revision 1.93  2003/06/25 16:33:55  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   (Module): Version 0.96b
+   Revision 1.92  2003/06/25 16:30:45  brouard
+   (Module): On windows (cygwin) function asctime_r doesn't
+   exist so I changed back to asctime which exists.
+   Revision 1.91  2003/06/25 15:30:29  brouard
+   * imach.c (Repository): Duplicated warning errors corrected.
+   (Repository): Elapsed time after each iteration is now output. It
+   helps to forecast when convergence will be reached. Elapsed time
+   is stamped in powell.  We created a new html file for the graphs
+   concerning matrix of covariance. It has extension -cov.htm.
+   Revision 1.90  2003/06/24 12:34:15  brouard
+   (Module): Some bugs corrected for windows. Also, when
+   mle=-1 a template is output in file "or"mypar.txt with the design
+   of the covariance matrix to be input.
    Revision 1.89  2003/06/24 12:30:52  brouard
    (Module): Some bugs corrected for windows. Also, when
    mle=-1 a template is output in file "or"mypar.txt with the design
- Line 137
+ Line 199
  #include <stdlib.h>
  #include <unistd.h>
- #include <sys/time.h>
+ /* #include <sys/time.h> */
  #include <time.h>
  #include "timeval.h"
+ /* #include <libintl.h> */
+ /* #define _(String) gettext (String) */
  #define MAXLINE 256
  #define GNUPLOTPROGRAM "gnuplot"
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- Line 161
+ Line 226
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
+ #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
  #ifdef unix
  #define DIRSEPARATOR '/'
  #define ODIRSEPARATOR '\\'
- Line 172
+ Line 238
  /* $Id$ */
  /* $State$ */
- char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
+ char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";
  char fullversion[]="$Revision$ $Date$";
- int erreur; /* Error number */
+ int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  int nvar;
  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
  int npar=NPARMAX;
- Line 202  int globpr; /* Global variable for print
+ Line 268  int globpr; /* Global variable for print
  double fretone; /* Only one call to likelihood */
  long ipmx; /* Number of contributions */
  double sw; /* Sum of weights */
+ char filerespow[FILENAMELENGTH];
  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
  FILE *ficresilk;
  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
  FILE *ficresprobmorprev;
- FILE *fichtm; /* Html File */
+ FILE *fichtm, *fichtmcov; /* Html File */
  FILE *ficreseij;
  char filerese[FILENAMELENGTH];
  FILE  *ficresvij;
- Line 216  char fileresvpl[FILENAMELENGTH];
+ Line 283  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
- char tmpout[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- char lfileres[FILENAMELENGTH];
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
  char fileregp[FILENAMELENGTH];
  char popfile[FILENAMELENGTH];
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ struct timezone tzp;
+ extern int gettimeofday();
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ long time_value;
+ extern long time();
+ char strcurr[80], strfor[80];
  #define NR_END 1
  #define FREE_ARG char*
- Line 256  static double maxarg1,maxarg2;
+ Line 331  static double maxarg1,maxarg2;
  static double sqrarg;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ int agegomp= AGEGOMP;
  int imx;
- int stepm;
+ int stepm=1;
  /* Stepm, step in month: minimum step interpolation*/
  int estepm;
- Line 266  int estepm;
+ Line 342  int estepm;
  int m,nb;
  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 **pmmij, ***probs;
+ double *ageexmed,*agecens;
  double dateintmean=0;
  double *weight;
- Line 282  double ftolhess; /* Tolerance for comput
+ Line 359  double ftolhess; /* Tolerance for comput
  /**************** split *************************/
  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 */
    int   l1, l2;                         /* length counters */
- Line 313  static int split( char *path, char *dirc
+ Line 393  static int split( char *path, char *dirc
  #endif
    */
    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 */
  }
- Line 533  void free_ma3x(double ***m, long nrl, lo
+ Line 615  void free_ma3x(double ***m, long nrl, lo
    free((FREE_ARG)(m+nrl-NR_END));
  }
+ /*************** function subdirf ***********/
+ char *subdirf(char fileres[])
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/"); /* Add to the right */
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf2 ***********/
+ char *subdirf2(char fileres[], char *preop)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
+ /*************** function subdirf3 ***********/
+ char *subdirf3(char fileres[], char *preop, char *preop2)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,preop2);
+   strcat(tmpout,fileres);
+   return tmpout;
+ }
  /***************** f1dim *************************/
  extern int ncom;
  extern double *pcom,*xicom;
- Line 708  void linmin(double p[], double xi[], int
+ Line 825  void linmin(double p[], double xi[], int
    free_vector(pcom,1,n);
  }
+ char *asc_diff_time(long time_sec, char ascdiff[])
+ {
+   long sec_left, days, hours, minutes;
+   days = (time_sec) / (60*60*24);
+   sec_left = (time_sec) % (60*60*24);
+   hours = (sec_left) / (60*60) ;
+   sec_left = (sec_left) %(60*60);
+   minutes = (sec_left) /60;
+   sec_left = (sec_left) % (60);
+   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   return ascdiff;
+ }
  /*************** powell ************************/
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
- Line 718  void powell(double p[], double **xi, int
+ Line 848  void powell(double p[], double **xi, int
    double del,t,*pt,*ptt,*xit;
    double fp,fptt;
    double *xits;
+   int niterf, itmp;
    pt=vector(1,n);
    ptt=vector(1,n);
    xit=vector(1,n);
- Line 728  void powell(double p[], double **xi, int
+ Line 860  void powell(double p[], double **xi, int
      fp=(*fret);
      ibig=0;
      del=0.0;
-     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     last_time=curr_time;
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     (void) gettimeofday(&curr_time,&tzp);
-     fprintf(ficrespow,"%d %.12f",*iter,*fret);
+     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);
-     for (i=1;i<=n;i++) {
+     /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
+     */
+    for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
-     fprintf(ficrespow,"\n");
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     if(*iter <=3){
+       tm = *localtime(&curr_time.tv_sec);
+       strcpy(strcurr,asctime(&tmf));
+ /*       asctime_r(&tm,strcurr); */
+       forecast_time=curr_time;
+       itmp = strlen(strcurr);
+       if(strcurr[itmp-1]=='\n')
+         strcurr[itmp-1]='\0';
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       for(niterf=10;niterf<=30;niterf+=10){
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         tmf = *localtime(&forecast_time.tv_sec);
+ /*      asctime_r(&tmf,strfor); */
+         strcpy(strfor,asctime(&tmf));
+         itmp = strlen(strfor);
+         if(strfor[itmp-1]=='\n')
+         strfor[itmp-1]='\0';
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+       }
+     }
      for (i=1;i<=n;i++) {
        for (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
- Line 901  double **pmij(double **ps, double *cov,
+ Line 1058  double **pmij(double **ps, double *cov,
    int i,j,j1, nc, ii, jj;
      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;*/
-   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;
  }
- Line 1151  double func( double *x)
+ Line 1308  double func( double *x)
            oldm=newm;
          } /* end mult */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-          * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
-          */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
-          * is higher than the multiple of stepm and negative otherwise.
-          */
          lli= (savm[s1][s2]>(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]>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.-+bh)*out[s1][s2])); */ /* exponential interpolation */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         /*if(lli ==000.0)*/
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- Line 1202  double func( double *x)
+ Line 1338  double func( double *x)
            oldm=newm;
          } /* end mult */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         /* But now since version 0.9 we anticipate for bias and large stepm.
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-          * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
-          */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias is positive if real duration
-          * is higher than the multiple of stepm and negative otherwise.
-          */
-         /* lli= (savm[s1][s2]>(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]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         /*if(lli ==000.0)*/
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- Line 1391  double funcone( double *x)
+ Line 1507  double funcone( double *x)
    return -l;
  }
- char *subdirf(char fileres[])
- {
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/"); /* Add to the right */
-   strcat(tmpout,fileres);
-   return tmpout;
- }
- char *subdirf2(char fileres[], char *preop)
- {
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
-   strcat(tmpout,preop);
-   strcat(tmpout,fileres);
-   return tmpout;
- }
- char *subdirf3(char fileres[], char *preop, char *preop2)
- {
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
-   strcat(tmpout,preop);
-   strcat(tmpout,preop2);
-   strcat(tmpout,fileres);
-   return tmpout;
- }
+ /*************** function likelione ***********/
  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
  {
    /* This routine should help understanding what is done with
- Line 1462  void mlikeli(FILE *ficres,double p[], in
+ Line 1551  void mlikeli(FILE *ficres,double p[], in
    double **xi;
    double fret;
    double fretone; /* Only one call to likelihood */
-   char filerespow[FILENAMELENGTH];
+   /*  char filerespow[FILENAMELENGTH];*/
    xi=matrix(1,npar,1,npar);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
- Line 1497  void hesscov(double **matcov, double p[]
+ Line 1586  void hesscov(double **matcov, double p[]
    int i, j,jk;
    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 ludcmp(double **a, int npar, int *indx, double *d) ;
+   double gompertz(double p[]);
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
- Line 1509  void hesscov(double **matcov, double p[]
+ Line 1598  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
      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++) {
- Line 1519  void hesscov(double **matcov, double p[]
+ Line 1610  void hesscov(double **matcov, double p[]
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
          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];
          /*printf(" %lf ",hess[i][j]);*/
        }
- Line 1590  void hesscov(double **matcov, double p[]
+ Line 1682  void hesscov(double **matcov, double p[]
  }
  /*************** 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 l=1, lmax=20;
    double k1,k2;
    double p2[NPARMAX+1];
    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;
    int k=0,kmax=10;
    double l1;
- Line 1637  double hessii( double x[], double delta,
+ Line 1729  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 l=1, l1, lmax=20;
- Line 2031  void  concatwav(int wav[], int **dh, int
+ Line 2123  void  concatwav(int wav[], int **dh, int
      wav[i]=mi;
      if(mi==0){
+       nbwarn++;
        if(first==0){
          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
          first=1;
- Line 2051  void  concatwav(int wav[], int **dh, int
+ Line 2144  void  concatwav(int wav[], int **dh, int
              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
              if(j==0) j=1;  /* Survives at least one month after exam */
              else if(j<0){
+               nberr++;
                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-               j=1; /* Careful 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("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);
              }
              k=k+1;
- Line 2074  void  concatwav(int wav[], int **dh, int
+ Line 2168  void  concatwav(int wav[], int **dh, int
            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
            if(j<0){
+             nberr++;
              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
            }
- Line 2250  void evsij(char fileres[], double ***eij
+ Line 2345  void evsij(char fileres[], double ***eij
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     /* Computing Variances of health expectancies */
+     /* Computing  Variances of health expectancies */
       for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){
- Line 2804  void varprob(char optionfilefiname[], do
+ Line 2899  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");
-   fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-   fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
+   file %s<br>\n",optionfilehtmcov);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+ and drawn. It helps understanding how is the covariance between two incidences.\
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+ standard deviations wide on each axis. <br>\
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    cov[1]=1;
    tj=cptcoveff;
- Line 2828  void varprob(char optionfilefiname[], do
+ Line 2933  void varprob(char optionfilefiname[], do
          fprintf(ficgp, "**********\n#\n");
-         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
          fprintf(ficresprobcor, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 2988  void varprob(char optionfilefiname[], do
+ Line 3093  void varprob(char optionfilefiname[], do
                      fprintf(ficgp,"\nset parametric;unset label");
                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                     fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
- Line 3003  void varprob(char optionfilefiname[], do
+ Line 3108  void varprob(char optionfilefiname[], do
                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                    }else{
                      first=0;
-                     fprintf(fichtm," %d (%.3f),",(int) age, c12);
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- Line 3026  void varprob(char optionfilefiname[], do
+ Line 3131  void varprob(char optionfilefiname[], do
    fclose(ficresprob);
    fclose(ficresprobcov);
    fclose(ficresprobcor);
-   /*  fclose(ficgp);*/
+   fflush(ficgp);
+   fflush(fichtmcov);
  }
- Line 3038  void printinghtml(char fileres[], char t
+ Line 3144  void printinghtml(char fileres[], char t
                    double jprev1, double mprev1,double anprev1, \
                    double jprev2, double mprev2,double anprev2){
    int jj1, k1, i1, cpt;
-   /*char optionfilehtm[FILENAMELENGTH];*/
- /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
- /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
- /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
- /*   } */
     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
-  - 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 ",
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
+    fprintf(fichtm,"\
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+    fprintf(fichtm,"\
+  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+    fprintf(fichtm,"\
   - Life expectancies by age and initial health status (estepm=%2d months): \
-    <a href=\"%s\">%s</a> <br>\n</li>", \
+    <a href=\"%s\">%s</a> <br>\n</li>",
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
- Line 3086  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 3190  fprintf(fichtm," \n<ul><li><b>Graphs</b>
          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
- health expectancies in states (1) and (2): %s%d.png<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     } /* end i1 */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
-  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
+  fprintf(fichtm,"\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
+ \n<br><li><h4> Result files (second order: variances)</h4>\n\
-  - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
-  - Correlation matrix 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",
-  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
+  fprintf(fichtm,"\
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+  fprintf(fichtm,"\
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+  fprintf(fichtm,"\
+  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  fprintf(fichtm,"\
+  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+  fprintf(fichtm,"\
   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
-          rfileres,rfileres,\
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
- Line 3116  health expectancies in states (1) and (2
+ Line 3224  health expectancies in states (1) and (2
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
- fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  fflush(fichtm);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   m=cptcoveff;
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- Line 3132  fprintf(fichtm," <ul><li><b>Graphs</b></
+ Line 3241  fprintf(fichtm," <ul><li><b>Graphs</b></
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- interval) in state (%d): %s%d%d.png <br>\
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"vr"),cpt,jj1,subdirf2(optionfilefiname,"vr"),cpt,jj1);
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
       }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+ health expectancies in states (1) and (2): %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     } /* end i1 */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
- Line 3669  int fileappend(FILE *fichier, char *opti
+ Line 3781  int fileappend(FILE *fichier, char *opti
    fflush(fichier);
    return (1);
  }
+ /**************** function prwizard **********************/
  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
  {
+   /* Wizard to print covariance matrix template */
    char ca[32], cb[32], cc[32];
    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
    int numlinepar;
- Line 3785  void prwizard(int ncovmodel, int nlstate
+ Line 3902  void prwizard(int ncovmodel, int nlstate
          } /* end k*/
        } /*end j */
      } /* end i */
-   }
+   } /* end itimes */
  } /* end of prwizard */
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
+ {
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
+   for (i=0;i<=imx-1 ; i++) {
+     sump=sump+weight[i];
+     sump=sump+1;
+     num=num+1;
+   }
+   /* for (i=1; 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=0;i<=imx-1 ; i++)
+     {
+       if (cens[i]==1 & wav[i]>1)
+         A=-x[1]/(x[2])*
+           (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
+       if (cens[i]==0 & wav[i]>1)
+         A=-x[1]/(x[2])*
+              (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
+           +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+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){
+   int i;
+   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>");
+   fflush(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   char dirfileres[132],optfileres[132];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     /*#endif */
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+   fprintf(ficgp, "set ter png small\n set log y\n");
+   fprintf(ficgp, "set size 0.65,0.65\n");
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+ }
  /***********************************************/
  /**************** Main Program *****************/
- Line 3797  int main(int argc, char *argv[])
+ Line 3991  int main(int argc, char *argv[])
  {
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   int jj, imk;
+   int jj, ll, li, lj, lk, imk;
    int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
+   int NDIM=2;
+   char ca[32], cb[32], cc[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
    double agedeb, agefin,hf;
- Line 3813  int main(int argc, char *argv[])
+ Line 4011  int main(int argc, char *argv[])
    int *indx;
    char line[MAXLINE], linepar[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 sdeb, sfin; /* Status at beginning and end */
    int c,  h , cpt,l;
- Line 3840  int main(int argc, char *argv[])
+ Line 4038  int main(int argc, char *argv[])
    double *epj, vepp;
    double kk1, kk2;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4];
+   int *dcwave;
    char z[1]="c", occ;
- Line 3852  int main(int argc, char *argv[])
+ Line 4050  int main(int argc, char *argv[])
    int lstra;
    long total_usecs;
-   struct timeval start_time, end_time, curr_time;
-   struct timezone tzp;
-   extern int gettimeofday();
-   struct tm tmg, tm, *gmtime(), *localtime();
-   long time_value;
-   extern long time();
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
    (void) gettimeofday(&start_time,&tzp);
+   curr_time=start_time;
    tm = *localtime(&start_time.tv_sec);
    tmg = *gmtime(&start_time.tv_sec);
    strcpy(strstart,asctime(&tm));
- Line 3881  int main(int argc, char *argv[])
+ Line 4080  int main(int argc, char *argv[])
  *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
  */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
    getcwd(pathcd, size);
    printf("\n%s\n%s",version,fullversion);
- Line 3896  int main(int argc, char *argv[])
+ Line 4097  int main(int argc, char *argv[])
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
    /* cutv(path,optionfile,pathtot,'\\');*/
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  /*   strcpy(pathimach,argv[0]); */
    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);
    strcpy(command,"mkdir ");
    strcat(command,optionfilefiname);
- Line 3922  int main(int argc, char *argv[])
+ Line 4125  int main(int argc, char *argv[])
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
    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\
   optionfile=%s\n\
   optionfilext=%s\n\
-  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("Localtime (at start):%s",strstart);
+   printf("Local time (at start):%s",strstart);
-   fprintf(ficlog,"Localtime (at start): %s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
    fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
    /* */
    strcpy(fileres,"r");
- Line 3993  int main(int argc, char *argv[])
+ Line 4198  int main(int argc, char *argv[])
    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
      printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
      fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      fclose (ficparo);
      fclose (ficlog);
      exit(0);
    }
-   /* 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 */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       puts(line);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
+       j=0;
+       for(jj=1; jj <=nlstate+ndeath; jj++){
+         if(jj==i) continue;
+         j++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1 != i) && (j1 != j)){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         if(mle==1)
+           printf("%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
+           if(mle==1){
+             printf(" %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         if(mle==1)
+           printf("\n");
+         fprintf(ficlog,"\n");
+         fprintf(ficparo,"\n");
+       }
+     }
+     fflush(ficlog);
-   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   for(i=1; i <=nlstate; i++){
+     p=param[1][1];
-     j=0;
-     for(jj=1; jj <=nlstate+ndeath; jj++){
+     /* Reads comments: lines beginning with '#' */
-       if(jj==i) continue;
+     while((c=getc(ficpar))=='#' && c!= EOF){
-       j++;
+       ungetc(c,ficpar);
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
+       fgets(line, MAXLINE, ficpar);
-       if ((i1 != i) && (j1 != j)){
+       numlinepar++;
-         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+       puts(line);
-         exit(1);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1-i)*(j1-j)!=0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
+         }
+         printf("%1d%1d",i,j);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
+         fscanf(ficpar,"\n");
+         numlinepar++;
+         printf("\n");
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
        }
-       fprintf(ficparo,"%1d%1d",i1,j1);
+     }
+     fflush(ficlog);
+     delti=delti3[1][1];
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
+       puts(line);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+     }
+     ungetc(c,ficpar);
+     matcov=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",&str);
        if(mle==1)
-         printf("%1d%1d",i,j);
+         printf("%s",str);
-       fprintf(ficlog,"%1d%1d",i,j);
+       fprintf(ficlog,"%s",str);
-       for(k=1; k<=ncovmodel;k++){
+       fprintf(ficparo,"%s",str);
-         fscanf(ficpar," %lf",&param[i][j][k]);
+       for(j=1; j <=i; j++){
+         fscanf(ficpar," %le",&matcov[i][j]);
          if(mle==1){
-           printf(" %lf",param[i][j][k]);
+           printf(" %.5le",matcov[i][j]);
-           fprintf(ficlog," %lf",param[i][j][k]);
          }
-         else
+         fprintf(ficlog," %.5le",matcov[i][j]);
-           fprintf(ficlog," %lf",param[i][j][k]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
-         fprintf(ficparo," %lf",param[i][j][k]);
        }
        fscanf(ficpar,"\n");
        numlinepar++;
- Line 4046  int main(int argc, char *argv[])
+ Line 4344  int main(int argc, char *argv[])
        fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
-   }
+     for(i=1; i <=npar; i++)
-   fflush(ficlog);
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
+     fflush(ficlog);
+     /*-------- Rewriting parameter file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   p=param[1][1];
-   /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
-     puts(line);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
-   for(i=1; i <=nlstate; i++){
-     for(j=1; j <=nlstate+ndeath-1; j++){
-       fscanf(ficpar,"%1d%1d",&i1,&j1);
-       if ((i1-i)*(j1-j)!=0){
-         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-         exit(1);
-       }
-       printf("%1d%1d",i,j);
-       fprintf(ficparo,"%1d%1d",i1,j1);
-       fprintf(ficlog,"%1d%1d",i1,j1);
-       for(k=1; k<=ncovmodel;k++){
-         fscanf(ficpar,"%le",&delti3[i][j][k]);
-         printf(" %le",delti3[i][j][k]);
-         fprintf(ficparo," %le",delti3[i][j][k]);
-         fprintf(ficlog," %le",delti3[i][j][k]);
-       }
-       fscanf(ficpar,"\n");
-       numlinepar++;
-       printf("\n");
-       fprintf(ficparo,"\n");
-       fprintf(ficlog,"\n");
-     }
-   }
-   fflush(ficlog);
-   delti=delti3[1][1];
-   /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-   /* Reads comments: lines beginning with '#' */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
-     puts(line);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
-   matcov=matrix(1,npar,1,npar);
-   for(i=1; i <=npar; i++){
-     fscanf(ficpar,"%s",&str);
-     if(mle==1)
-       printf("%s",str);
-     fprintf(ficlog,"%s",str);
-     fprintf(ficparo,"%s",str);
-     for(j=1; j <=i; j++){
-       fscanf(ficpar," %le",&matcov[i][j]);
-       if(mle==1){
-         printf(" %.5le",matcov[i][j]);
-       }
-       fprintf(ficlog," %.5le",matcov[i][j]);
-       fprintf(ficparo," %.5le",matcov[i][j]);
-     }
-     fscanf(ficpar,"\n");
-     numlinepar++;
-     if(mle==1)
-       printf("\n");
-     fprintf(ficlog,"\n");
-     fprintf(ficparo,"\n");
-   }
-   for(i=1; i <=npar; i++)
-     for(j=i+1;j<=npar;j++)
-       matcov[i][j]=matcov[j][i];
-   if(mle==1)
-     printf("\n");
-   fprintf(ficlog,"\n");
-   fflush(ficlog);
-   /*-------- Rewriting 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);
    /*-------- data file ----------*/
    if((fic=fopen(datafile,"r"))==NULL)    {
      printf("Problem with datafile: %s\n", datafile);goto end;
- Line 4323  int main(int argc, char *argv[])
+ Line 4539  int main(int argc, char *argv[])
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+         nberr++;
          printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
          fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         nberr++;
          printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
          fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
          s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
- Line 4346  int main(int argc, char *argv[])
+ Line 4564  int main(int argc, char *argv[])
            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
              else {
                if ((int)andc[i]!=9999){
+                 nbwarn++;
                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                  fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                  agev[m][i]=-1;
- Line 4382  int main(int argc, char *argv[])
+ Line 4601  int main(int argc, char *argv[])
    for (i=1; i<=imx; i++)  {
      for(m=firstpass; (m<=lastpass); m++){
        if (s[m][i] > (nlstate+ndeath)) {
+         nberr++;
          printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
          fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
          goto end;
- Line 4396  int main(int argc, char *argv[])
+ Line 4616  int main(int argc, char *argv[])
  }*/
    printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   agegomp=(int)agemin;
    free_vector(severity,1,maxwav);
    free_imatrix(outcome,1,maxwav+1,1,n);
    free_vector(moisnais,1,n);
- Line 4452  int main(int argc, char *argv[])
+ Line 4674  int main(int argc, char *argv[])
    /*------------ gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
    strcat(optionfilegnuplot,".gp");
    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
      printf("Problem with file %s",optionfilegnuplot);
    }
- Line 4464  int main(int argc, char *argv[])
+ Line 4689  int main(int argc, char *argv[])
    /*  fclose(ficgp);*/
    /*--------- index.htm --------*/
-   strcpy(optionfilehtm,optionfilefiname);
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
      printf("Problem with %s \n",optionfilehtm), exit(0);
    }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
+   else{
+   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
    fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
- Line 4480  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4719  Title=%s <br>Datafile=%s Firstpass=%d La
   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
   - Date and time at start: %s</ul>\n",\
-           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
+           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-           model,fileres,fileres,\
+           fileres,fileres,\
            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-   /*fclose(fichtm);*/
    fflush(fichtm);
    strcpy(pathr,path);
    strcat(pathr,optionfilefiname);
    chdir(optionfilefiname); /* Move to directory named optionfile */
-   strcpy(lfileres,fileres);
-   strcat(lfileres,"/");
-   strcat(lfileres,optionfilefiname);
    /* Calculates basic frequencies. Computes observed prevalence at single age
       and prints on file fileres'p'. */
- Line 4514  Interval (in months) between two waves:
+ Line 4749  Interval (in months) between two waves:
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
    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;
+         }
+     }
+     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);
    }
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   /*  for (i=1;i<=nlstate;i++)
+     for(j=1;j<=nlstate+ndeath;j++)
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   */
+   fprintf(ficrespow,"\n");
+     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     fclose(ficrespow);
-   /*--------- results files --------------*/
+     hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
-   fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
-   jk=1;
+     for(i=1; i <=NDIM; i++)
-   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       for(j=i+1;j<=NDIM;j++)
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+         matcov[i][j]=matcov[j][i];
-   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   for(i=1,jk=1; i <=nlstate; i++){
+     printf("\nCovariance matrix\n ");
-     for(k=1; k <=(nlstate+ndeath); k++){
+     for(i=1; i <=NDIM; i++) {
-       if (k != i)
+       for(j=1;j<=NDIM;j++){
-         {
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     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);
+   } /* 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);
- Line 4554  Interval (in months) between two waves:
+ Line 4870  Interval (in months) between two waves:
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
          }
+       }
      }
-   }
+     if(mle!=0){
-   if(mle!=0){
+       /* Computing hessian and covariance matrix */
-     /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
-     ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
-     hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
-   }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
-   printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
-   for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
-       if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
-         fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
-         printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
-         fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
-         for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
-           printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
-           fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
-           fprintf(ficres," %.5e",delti[jk]);
+             jk++;
-           jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
          }
-         printf("\n");
-         fprintf(ficlog,"\n");
-         fprintf(ficres,"\n");
        }
      }
-   }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-   fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
-   if(mle==1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
-   for(i=1,k=1;i<=npar;i++){
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     /*  if (k>nlstate) k=1;
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-         i1=(i-1)/(ncovmodel*nlstate)+1;
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-         printf("%s%d%d",alph[k],i1,tab[i]);
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
      */
-     fprintf(ficres,"%3d",i);
+     for(itimes=1;itimes<=2;itimes++){
-     if(mle==1)
+       jj=0;
-       printf("%3d",i);
+       for(i=1; i <=nlstate; i++){
-     fprintf(ficlog,"%3d",i);
+         for(j=1; j <=nlstate+ndeath; j++){
-     for(j=1; j<=i;j++){
+           if(j==i) continue;
-       fprintf(ficres," %.5e",matcov[i][j]);
+           for(k=1; k<=ncovmodel;k++){
-       if(mle==1)
+             jj++;
-         printf(" %.5e",matcov[i][j]);
+             ca[0]= k+'a'-1;ca[1]='\0';
-       fprintf(ficlog," %.5e",matcov[i][j]);
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
+       fputs(line,ficparo);
      }
-     fprintf(ficres,"\n");
-     if(mle==1)
-       printf("\n");
-     fprintf(ficlog,"\n");
-     k++;
-   }
-   while((c=getc(ficpar))=='#' && c!= EOF){
      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;
-   estepm=0;
+       fage = agemaxpar;
-   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) {
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     bage = ageminpar;
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-     fage = agemaxpar;
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   }
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+       ungetc(c,ficpar);
-   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       fgets(line, MAXLINE, ficpar);
-   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       puts(line);
+       fputs(line,ficparo);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     }
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
+     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);
-     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);
-     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,"#Stable prevalence \n");
-   fprintf(ficrespl,"#Age ");
+     fprintf(ficrespl,"#Age ");
-   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-   fprintf(ficrespl,"\n");
+     fprintf(ficrespl,"\n");
-   prlim=matrix(1,nlstate,1,nlstate);
+     prlim=matrix(1,nlstate,1,nlstate);
-   agebase=ageminpar;
+     agebase=ageminpar;
-   agelim=agemaxpar;
+     agelim=agemaxpar;
-   ftolpl=1.e-10;
+     ftolpl=1.e-10;
-   i1=cptcoveff;
+     i1=cptcoveff;
-   if (cptcovn < 1){i1=1;}
+     if (cptcovn < 1){i1=1;}
-   for(cptcov=1,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;
-       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-       fprintf(ficrespl,"\n#******");
+         fprintf(ficrespl,"\n#******");
-       printf("\n#******");
+         printf("\n#******");
-       fprintf(ficlog,"\n#******");
+         fprintf(ficlog,"\n#******");
-       for(j=1;j<=cptcoveff;j++) {
+         for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
+         }
-       fprintf(ficrespl,"******\n");
+         fprintf(ficrespl,"******\n");
-       printf("******\n");
+         printf("******\n");
-       fprintf(ficlog,"******\n");
+         fprintf(ficlog,"******\n");
-       for (age=agebase; age<=agelim; age++){
+         for (age=agebase; age<=agelim; age++){
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         fprintf(ficrespl,"%.0f ",age );
+           fprintf(ficrespl,"%.0f ",age );
-         for(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*/
+     /* 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 ");
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-       k=k+1;
+         k=k+1;
-       fprintf(ficrespij,"\n#****** ");
+         fprintf(ficrespij,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrespij,"******\n");
+         fprintf(ficrespij,"******\n");
-       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         oldm=oldms;savm=savms;
+           oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-         fprintf(ficrespij,"# 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(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");
          }
-         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);
-   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     fclose(ficrespij);
-   /*---------- 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);
        /* (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);
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         oldm=oldms;savm=savms;
-       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
+         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);
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
+         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);
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
-       if(popbased==1){
+         if(popbased==1){
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
-       }
+         }
-       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
-       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-       fprintf(ficrest,"\n");
+         fprintf(ficrest,"\n");
-       epj=vector(1,nlstate+1);
+         epj=vector(1,nlstate+1);
-       for(age=bage; age <=fage ;age++){
+         for(age=bage; age <=fage ;age++){
-         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         if (popbased==1) {
+           if (popbased==1) {
-           if(mobilav ==0){
+             if(mobilav ==0){
-             for(i=1; i<=nlstate;i++)
+               for(i=1; i<=nlstate;i++)
-               prlim[i][i]=probs[(int)age][i][k];
+                 prlim[i][i]=probs[(int)age][i][k];
-           }else{ /* mobilav */
+             }else{ /* mobilav */
-             for(i=1; i<=nlstate;i++)
+               for(i=1; i<=nlstate;i++)
-               prlim[i][i]=mobaverage[(int)age][i][k];
+                 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);
-       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(ficgp);
-   if(erreur >0){
+   if((nberr >0) || (nbwarn>0)){
-     printf("End of Imach with error or warning %d\n",erreur);
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
-     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
    }else{
-    printf("End of Imach\n");
+     printf("End of Imach\n");
-    fprintf(ficlog,"End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
    }
    printf("See log file on %s\n",filelog);
-   fclose(ficlog);
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
    (void) gettimeofday(&end_time,&tzp);
    tm = *localtime(&end_time.tv_sec);
    tmg = *gmtime(&end_time.tv_sec);
    strcpy(strtend,asctime(&tm));
-   printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend);
+   printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend);
-   fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
-   /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
+   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-   printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
+   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
-   fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
    /*  printf("Total time was %d uSec.\n", total_usecs);*/
  /*   if(fileappend(fichtm,optionfilehtm)){ */
    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
    fclose(fichtm);
+   fclose(fichtmcov);
    fclose(ficgp);
+   fclose(ficlog);
    /*------ End -----------*/
-   end:
- #ifdef windows
-   /* chdir(pathcd);*/
- #endif
    chdir(path);
-  /*system("wgnuplot graph.plt");*/
+   strcpy(plotcmd,"\"");
-  /*system("../gp37mgw/wgnuplot graph.plt");*/
+   strcat(plotcmd,pathimach);
-  /*system("cd ../gp37mgw");*/
+   strcat(plotcmd,GNUPLOTPROGRAM);
-  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
+   strcat(plotcmd,"\"");
-   strcpy(plotcmd,GNUPLOTPROGRAM);
    strcat(plotcmd," ");
    strcat(plotcmd,optionfilegnuplot);
    printf("Starting graphs with: %s",plotcmd);fflush(stdout);
-   system(plotcmd);
+   if((outcmd=system(plotcmd)) != 0){
+     printf(" Problem with gnuplot\n");
+   }
    printf(" Wait...");
-  /*#ifdef windows*/
    while (z[0] != 'q') {
      /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+     printf("\nType e to edit output files, g to graph again and q for exiting: ");
      scanf("%s",z);
-     if (z[0] == 'c') system("./imach");
+ /*     if (z[0] == 'c') system("./imach"); */
-     else 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] == 'q') exit(0);
    }
-   /*#endif */
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
  }

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