imach/src/imach.c - diff

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Diff for /imach/src/imach.c between versions 1.22 and 1.47

-version 1.22, 2002/02/22 17:54:20
+version 1.47, 2002/06/10 13:12:01
  Line 1
  /* $Id$
-    Interpolate Markov Chain
+    Interpolated Markov Chain
    Short summary of the programme:
  Line 14
    model. More health states you consider, more time is necessary to reach the
    Maximum Likelihood of the parameters involved in the model.  The
    simplest model is the multinomial logistic model where pij is the
-   probabibility to be observed in state j at the second wave
+   probability to be observed in state j at the second wave
    conditional to be observed in state i at the first wave. Therefore
    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    'age' is age and 'sex' is a covariate. If you want to have a more
  Line 56
  #include <unistd.h>
  #define MAXLINE 256
- #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"
+ #define GNUPLOTPROGRAM "gnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
  #define FILENAMELENGTH 80
  /*#define DEBUG*/
  #define windows
- Line 74
+ Line 75
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
+ #ifdef windows
+ #define DIRSEPARATOR '\\'
+ #else
+ #define DIRSEPARATOR '/'
+ #endif
+ char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";
  int erreur; /* Error number */
  int nvar;
  int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- Line 94  int **dh; /* dh[mi][i] is number of step
+ Line 100  int **dh; /* dh[mi][i] is number of step
  double jmean; /* Mean space between 2 waves */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;
+ FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficgp, *fichtm,*ficresprob,*ficpop;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ FILE *fichtm; /* Html File */
  FILE *ficreseij;
-   char filerese[FILENAMELENGTH];
+ char filerese[FILENAMELENGTH];
-  FILE  *ficresvij;
+ FILE  *ficresvij;
-   char fileresv[FILENAMELENGTH];
+ char fileresv[FILENAMELENGTH];
-  FILE  *ficresvpl;
+ FILE  *ficresvpl;
-   char fileresvpl[FILENAMELENGTH];
+ char fileresvpl[FILENAMELENGTH];
+ char title[MAXLINE];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char filerest[FILENAMELENGTH];
+ char fileregp[FILENAMELENGTH];
+ char popfile[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
  #define NR_END 1
  #define FREE_ARG char*
- Line 123  FILE *ficreseij;
+ Line 141  FILE *ficreseij;
  static double maxarg1,maxarg2;
  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  #define rint(a) floor(a+0.5)
- Line 135  int imx;
+ Line 153  int imx;
  int stepm;
  /* Stepm, step in month: minimum step interpolation*/
+ int estepm;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  int m,nb;
  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- Line 157  static int split( char *path, char *dirc
+ Line 178  static int split( char *path, char *dirc
     l1 = strlen( path );                 /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- #ifdef windows
+    s = strrchr( path,  DIRSEPARATOR );          /* find last / */
-    s = strrchr( path, '\\' );           /* find last / */
- #else
-    s = strrchr( path, '/' );            /* find last / */
- #endif
     if ( s == NULL ) {                   /* no directory, so use current */
  #if     defined(__bsd__)                /* get current working directory */
        extern char       *getwd( );
- Line 686  double **prevalim(double **prlim, int nl
+ Line 703  double **prevalim(double **prlim, int nl
        for (k=1; k<=cptcovn;k++) {
          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/
+         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
        }
-       for (k=1; k<=cptcovage;k++)
+       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        for (k=1; k<=cptcovprod;k++)
          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      savm=oldm;
- Line 1176  void lubksb(double **a, int n, int *indx
+ Line 1192  void lubksb(double **a, int n, int *indx
  }
  /************ Frequencies ********************/
- void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)
+ void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
  {  /* Some frequencies */
    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
    double ***freq; /* Frequencies */
    double *pp;
    double pos, k2, dateintsum=0,k2cpt=0;
    FILE *ficresp;
    char fileresp[FILENAMELENGTH];
    pp=vector(1,nlstate);
    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    strcpy(fileresp,"p");
- Line 1196  void  freqsummary(char fileres[], int ag
+ Line 1212  void  freqsummary(char fileres[], int ag
    }
    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
    j1=0;
    j=cptcoveff;
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    for(k1=1; k1<=j;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+     for(i1=1; i1<=ncodemax[k1];i1++){
-        j1++;
+       j1++;
-        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-          scanf("%d", i);*/
+         scanf("%d", i);*/
-         for (i=-1; i<=nlstate+ndeath; i++)
+       for (i=-1; i<=nlstate+ndeath; i++)
-          for (jk=-1; jk<=nlstate+ndeath; jk++)
+         for (jk=-1; jk<=nlstate+ndeath; jk++)
-            for(m=agemin; m <= agemax+3; m++)
+           for(m=agemin; m <= agemax+3; m++)
-              freq[i][jk][m]=0;
+             freq[i][jk][m]=0;
-         dateintsum=0;
+       dateintsum=0;
-         k2cpt=0;
+       k2cpt=0;
-        for (i=1; i<=imx; i++) {
+       for (i=1; i<=imx; i++) {
-          bool=1;
+         bool=1;
-          if  (cptcovn>0) {
+         if  (cptcovn>0) {
-            for (z1=1; z1<=cptcoveff; z1++)
+           for (z1=1; z1<=cptcoveff; z1++)
-              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-                bool=0;
+               bool=0;
-          }
+         }
-          if (bool==1) {
+         if (bool==1) {
-            for(m=firstpass; m<=lastpass; m++){
+           for(m=firstpass; m<=lastpass; m++){
-              k2=anint[m][i]+(mint[m][i]/12.);
+             k2=anint[m][i]+(mint[m][i]/12.);
-              if ((k2>=dateprev1) && (k2<=dateprev2)) {
+             if ((k2>=dateprev1) && (k2<=dateprev2)) {
-                if(agev[m][i]==0) agev[m][i]=agemax+1;
+               if(agev[m][i]==0) agev[m][i]=agemax+1;
-                if(agev[m][i]==1) agev[m][i]=agemax+2;
+               if(agev[m][i]==1) agev[m][i]=agemax+2;
-                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+               if (m<lastpass) {
-                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
+                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
-                  dateintsum=dateintsum+k2;
+               }
-                  k2cpt++;
-                }
+               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
+                 dateintsum=dateintsum+k2;
-              }
+                 k2cpt++;
-            }
+               }
-          }
+             }
-        }
+           }
-         if  (cptcovn>0) {
+         }
-          fprintf(ficresp, "\n#********** Variable ");
+       }
-          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-        fprintf(ficresp, "**********\n#");
-         }
-        for(i=1; i<=nlstate;i++)
-          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-        fprintf(ficresp, "\n");
-   for(i=(int)agemin; i <= (int)agemax+3; i++){
+       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
-     if(i==(int)agemax+3)
-       printf("Total");
-     else
-       printf("Age %d", i);
-     for(jk=1; jk <=nlstate ; jk++){
-       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-         pp[jk] += freq[jk][m][i];
-     }
-     for(jk=1; jk <=nlstate ; jk++){
-       for(m=-1, pos=0; m <=0 ; m++)
-         pos += freq[jk][m][i];
-       if(pp[jk]>=1.e-10)
-         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-       else
-         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-     }
-      for(jk=1; jk <=nlstate ; jk++){
+       if  (cptcovn>0) {
-       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+         fprintf(ficresp, "\n#********** Variable ");
-         pp[jk] += freq[jk][m][i];
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      }
+         fprintf(ficresp, "**********\n#");
+       }
+       for(i=1; i<=nlstate;i++)
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresp, "\n");
+       for(i=(int)agemin; i <= (int)agemax+3; i++){
+         if(i==(int)agemax+3)
+           printf("Total");
+         else
+           printf("Age %d", i);
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
+         }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
+             pos += freq[jk][m][i];
+           if(pp[jk]>=1.e-10)
+             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           else
+             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+         }
-     for(jk=1,pos=0; jk <=nlstate ; jk++)
+         for(jk=1; jk <=nlstate ; jk++){
-       pos += pp[jk];
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-     for(jk=1; jk <=nlstate ; jk++){
+             pp[jk] += freq[jk][m][i];
-       if(pos>=1.e-5)
-         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-       else
-         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-       if( i <= (int) agemax){
-         if(pos>=1.e-5){
-           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
-           probs[i][jk][j1]= pp[jk]/pos;
-           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
          }
-       else
-           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+         for(jk=1,pos=0; jk <=nlstate ; jk++)
+           pos += pp[jk];
+         for(jk=1; jk <=nlstate ; jk++){
+           if(pos>=1.e-5)
+             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           else
+             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           if( i <= (int) agemax){
+             if(pos>=1.e-5){
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+               probs[i][jk][j1]= pp[jk]/pos;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+             }
+             else
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+           }
+         }
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
+           for(m=-1; m <=nlstate+ndeath; m++)
+             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+         if(i <= (int) agemax)
+           fprintf(ficresp,"\n");
+         printf("\n");
        }
      }
-     for(jk=-1; jk <=nlstate+ndeath; jk++)
+   }
-       for(m=-1; m <=nlstate+ndeath; m++)
-         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-     if(i <= (int) agemax)
-       fprintf(ficresp,"\n");
-     printf("\n");
-     }
-     }
-  }
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
    free_vector(pp,1,nlstate);
    /* End of Freq */
  }
  /************ Prevalence ********************/
- void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
+ void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
  {  /* Some frequencies */
    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
- Line 1321  void prevalence(int agemin, int agemax,
+ Line 1343  void prevalence(int agemin, int agemax,
    j=cptcoveff;
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-  for(k1=1; k1<=j;k1++){
+   for(k1=1; k1<=j;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;
        for (i=-1; i<=nlstate+ndeath; i++)
          for (jk=-1; jk<=nlstate+ndeath; jk++)
            for(m=agemin; m <= agemax+3; m++)
              freq[i][jk][m]=0;
        for (i=1; i<=imx; i++) {
          bool=1;
          if  (cptcovn>0) {
            for (z1=1; z1<=cptcoveff; z1++)
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                bool=0;
          }
          if (bool==1) {
            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                if(agev[m][i]==0) agev[m][i]=agemax+1;
                if(agev[m][i]==1) agev[m][i]=agemax+2;
-               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+               if (m<lastpass) {
-               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];
+                 if (calagedate>0)
+                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+                 else
+                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
+               }
              }
            }
          }
        }
+       for(i=(int)agemin; i <= (int)agemax+3; i++){
-         for(i=(int)agemin; i <= (int)agemax+3; i++){
+         for(jk=1; jk <=nlstate ; jk++){
-           for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
-               pp[jk] += freq[jk][m][i];
+         }
-           }
+         for(jk=1; jk <=nlstate ; jk++){
-           for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
-             for(m=-1, pos=0; m <=0 ; m++)
              pos += freq[jk][m][i];
          }
-          for(jk=1; jk <=nlstate ; jk++){
+         for(jk=1; jk <=nlstate ; jk++){
-            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-              pp[jk] += freq[jk][m][i];
+             pp[jk] += freq[jk][m][i];
-          }
-          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
-          for(jk=1; jk <=nlstate ; jk++){
-            if( i <= (int) agemax){
-              if(pos>=1.e-5){
-                probs[i][jk][j1]= pp[jk]/pos;
-              }
-            }
-          }
          }
+         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <= (int) agemax){
+             if(pos>=1.e-5){
+               probs[i][jk][j1]= pp[jk]/pos;
+             }
+           }
+         }
+       }
      }
    }
    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
    free_vector(pp,1,nlstate);
- Line 1441  void  concatwav(int wav[], int **dh, int
+ Line 1467  void  concatwav(int wav[], int **dh, int
            if (j >= jmax) jmax=j;
            if (j <= jmin) jmin=j;
            sum=sum+j;
-           /* if (j<10) printf("j=%d num=%d ",j,i); */
+           /*if (j<0) printf("j=%d num=%d \n",j,i); */
            }
          }
          else{
- Line 1449  void  concatwav(int wav[], int **dh, int
+ Line 1475  void  concatwav(int wav[], int **dh, int
            k=k+1;
            if (j >= jmax) jmax=j;
            else if (j <= jmin)jmin=j;
-           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
            sum=sum+j;
          }
          jk= j/stepm;
- Line 1495  void tricode(int *Tvar, int **nbcode, in
+ Line 1521  void tricode(int *Tvar, int **nbcode, in
        for (k=0; k<=19; k++) {
          if (Ndum[k] != 0) {
            nbcode[Tvar[j]][ij]=k;
            ij++;
          }
          if (ij > ncodemax[j]) break;
- Line 1511  void tricode(int *Tvar, int **nbcode, in
+ Line 1538  void tricode(int *Tvar, int **nbcode, in
   ij=1;
   for (i=1; i<=10; i++) {
-    if((Ndum[i]!=0) && (i<=ncov)){
+    if((Ndum[i]!=0) && (i<=ncovcol)){
       Tvaraff[ij]=i;
       ij++;
     }
- Line 1522  void tricode(int *Tvar, int **nbcode, in
+ Line 1549  void tricode(int *Tvar, int **nbcode, in
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
+ void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
  {
    /* Health expectancies */
-   int i, j, nhstepm, hstepm, h;
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
-   double age, agelim,hf;
+   double age, agelim, hf;
-   double ***p3mat;
+   double ***p3mat,***varhe;
+   double **dnewm,**doldm;
+   double *xp;
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
+   int theta;
+   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
+   xp=vector(1,npar);
+   dnewm=matrix(1,nlstate*2,1,npar);
+   doldm=matrix(1,nlstate*2,1,nlstate*2);
    fprintf(ficreseij,"# Health expectancies\n");
    fprintf(ficreseij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
-       fprintf(ficreseij," %1d-%1d",i,j);
+       fprintf(ficreseij," %1d-%1d (SE)",i,j);
    fprintf(ficreseij,"\n");
-   hstepm=1*YEARM; /*  Every j years of age (in month) */
+   if(estepm < stepm){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
+    * if stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression inbetween and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
    agelim=AGESUP;
    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      /* nhstepm age range expressed in number of stepm */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm);
+     nstepm=(int) rint((agelim-age)*YEARM/stepm);
-     /* Typically if 20 years = 20*12/6=40 stepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     if (stepm >= YEARM) hstepm=1;
+     /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
+     gp=matrix(0,nhstepm,1,nlstate*2);
+     gm=matrix(0,nhstepm,1,nlstate*2);
      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     /* Computing Variances of health expectancies */
+      for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       cptj=0;
+       for(j=1; j<= nlstate; j++){
+         for(i=1; i<=nlstate; i++){
+           cptj=cptj+1;
+           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+           }
+         }
+       }
+       for(i=1; i<=npar; i++)
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       cptj=0;
+       for(j=1; j<= nlstate; j++){
+         for(i=1;i<=nlstate;i++){
+           cptj=cptj+1;
+           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
+             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+           }
+         }
+       }
+       for(j=1; j<= nlstate*2; j++)
+         for(h=0; h<=nhstepm-1; h++){
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         }
+      }
+ /* End theta */
+      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
+      for(h=0; h<=nhstepm-1; h++)
+       for(j=1; j<=nlstate*2;j++)
+         for(theta=1; theta <=npar; theta++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
+      for(i=1;i<=nlstate*2;i++)
+       for(j=1;j<=nlstate*2;j++)
+         varhe[i][j][(int)age] =0.;
+      printf("%d|",(int)age);fflush(stdout);
+      for(h=0;h<=nhstepm-1;h++){
+       for(k=0;k<=nhstepm-1;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
+         for(i=1;i<=nlstate*2;i++)
+           for(j=1;j<=nlstate*2;j++)
+             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+       }
+     }
+     /* Computing expectancies */
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-           eij[i][j][(int)age] +=p3mat[i][j][h];
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+ /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
-     hf=1;
+     fprintf(ficreseij,"%3.0f",age );
-     if (stepm >= YEARM) hf=stepm/YEARM;
+     cptj=0;
-     fprintf(ficreseij,"%.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
+         cptj++;
+         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
        }
      fprintf(ficreseij,"\n");
+     free_matrix(gm,0,nhstepm,1,nlstate*2);
+     free_matrix(gp,0,nhstepm,1,nlstate*2);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }
+   printf("\n");
+   free_vector(xp,1,npar);
+   free_matrix(dnewm,1,nlstate*2,1,npar);
+   free_matrix(doldm,1,nlstate*2,1,nlstate*2);
+   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
  }
  /************ Variance ******************/
- void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+ void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    double **newm;
    double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm, h;
+   int i, j, nhstepm, hstepm, h, nstepm ;
    int k, cptcode;
    double *xp;
    double **gp, **gm;
    double ***gradg, ***trgradg;
    double ***p3mat;
-   double age,agelim;
+   double age,agelim, hf;
    int theta;
-    fprintf(ficresvij,"# Covariances of life expectancies\n");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
    fprintf(ficresvij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
- Line 1597  void varevsij(char fileres[], double ***
+ Line 1744  void varevsij(char fileres[], double ***
    dnewm=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
-   hstepm=1*YEARM; /* Every year of age */
+   if(estepm < stepm){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like k years */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
    agelim = AGESUP;
    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     if (stepm >= YEARM) hstepm=1;
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
      gp=matrix(0,nhstepm,1,nlstate);
- Line 1620  void varevsij(char fileres[], double ***
+ Line 1781  void varevsij(char fileres[], double ***
          for(i=1; i<=nlstate;i++)
            prlim[i][i]=probs[(int)age][i][ij];
        }
        for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
- Line 1632  void varevsij(char fileres[], double ***
+ Line 1793  void varevsij(char fileres[], double ***
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        if (popbased==1) {
          for(i=1; i<=nlstate;i++)
            prlim[i][i]=probs[(int)age][i][ij];
- Line 1658  void varevsij(char fileres[], double ***
+ Line 1819  void varevsij(char fileres[], double ***
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)
          vareij[i][j][(int)age] =0.;
      for(h=0;h<=nhstepm;h++){
        for(k=0;k<=nhstepm;k++){
          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
          for(i=1;i<=nlstate;i++)
            for(j=1;j<=nlstate;j++)
-             vareij[i][j][(int)age] += doldm[i][j];
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        }
      }
-     h=1;
-     if (stepm >= YEARM) h=stepm/YEARM;
      fprintf(ficresvij,"%.0f ",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
        }
      fprintf(ficresvij,"\n");
      free_matrix(gp,0,nhstepm,1,nlstate);
- Line 1684  void varevsij(char fileres[], double ***
+ Line 1846  void varevsij(char fileres[], double ***
      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    } /* End age */
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,npar);
    free_matrix(dnewm,1,nlstate,1,nlstate);
- Line 1706  void varprevlim(char fileres[], double *
+ Line 1868  void varprevlim(char fileres[], double *
    double age,agelim;
    int theta;
-   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
+   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
    fprintf(ficresvpl,"# Age");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
- Line 1775  void varprevlim(char fileres[], double *
+ Line 1937  void varprevlim(char fileres[], double *
  }
  /************ Variance of one-step probabilities  ******************/
- void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
  {
-   int i, j;
+   int i, j,  i1, k1, l1;
-   int k=0, cptcode;
+   int k2, l2, j1,  z1;
+   int k=0,l, cptcode;
+   int first=1;
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
    double **dnewm,**doldm;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
+   double **mu;
    double age,agelim, cov[NCOVMAX];
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    int theta;
    char fileresprob[FILENAMELENGTH];
+   char fileresprobcov[FILENAMELENGTH];
+   char fileresprobcor[FILENAMELENGTH];
+   double ***varpij;
    strcpy(fileresprob,"prob");
    strcat(fileresprob,fileres);
    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprob);
    }
-   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
+   strcpy(fileresprobcov,"probcov");
+   strcat(fileresprobcov,fileres);
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcov);
+   }
+   strcpy(fileresprobcor,"probcor");
+   strcat(fileresprobcor,fileres);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcor);
+   }
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   fprintf(ficresprob,"# Age");
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   fprintf(ficresprobcov,"# Age");
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcov,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     }
+   fprintf(ficresprob,"\n");
+   fprintf(ficresprobcov,"\n");
+   fprintf(ficresprobcor,"\n");
    xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   first=1;
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+     exit(0);
+   }
+   else{
+     fprintf(ficgp,"\n# Routine varprob");
+   }
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+     printf("Problem with html file: %s\n", optionfilehtm);
+     exit(0);
+   }
+   else{
+     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");
+     fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
+   }
    cov[1]=1;
-   for (age=bage; age<=fage; age ++){
+   j=cptcoveff;
-     cov[2]=age;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-     gradg=matrix(1,npar,1,9);
+   j1=0;
-     trgradg=matrix(1,9,1,npar);
+   for(k1=1; k1<=1;k1++){
-     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+     for(i1=1; i1<=ncodemax[k1];i1++){
-     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+     j1++;
-     for(theta=1; theta <=npar; theta++){
+     if  (cptcovn>0) {
-       for(i=1; i<=npar; i++)
+       fprintf(ficresprob, "\n#********** Variable ");
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       fprintf(ficresprobcov, "\n#********** Variable ");
+       fprintf(ficgp, "\n#********** Variable ");
+       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");
+       fprintf(ficresprobcor, "\n#********** Variable ");
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       fprintf(ficresprob, "**********\n#");
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       fprintf(ficresprobcov, "**********\n#");
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       fprintf(ficgp, "**********\n#");
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       fprintf(ficgp, "**********\n#");
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       fprintf(fichtm, "**********\n#");
+     }
+       for (age=bage; age<=fage; age ++){
+         cov[2]=age;
+         for (k=1; k<=cptcovn;k++) {
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+         }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+         for (k=1; k<=cptcovprod;k++)
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         gp=vector(1,(nlstate)*(nlstate+ndeath));
+         gm=vector(1,(nlstate)*(nlstate+ndeath));
+         for(theta=1; theta <=npar; theta++){
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<= (nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gp[k]=pmmij[i][j];
+             }
+           }
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] - (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<=(nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gm[k]=pmmij[i][j];
+             }
+           }
-       pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
-       k=0;
-       for(i=1; i<= (nlstate+ndeath); i++){
-         for(j=1; j<=(nlstate+ndeath);j++){
-            k=k+1;
-           gp[k]=pmmij[i][j];
-         }
-       }
-       for(i=1; i<=npar; i++)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       pmij(pmmij,cov,ncovmodel,xp,nlstate);
-       k=0;
-       for(i=1; i<=(nlstate+ndeath); i++){
-         for(j=1; j<=(nlstate+ndeath);j++){
-           k=k+1;
-           gm[k]=pmmij[i][j];
          }
-       }
-        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
-            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
-     }
-      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-       for(theta=1; theta <=npar; theta++)
+           for(theta=1; theta <=npar; theta++)
-       trgradg[j][theta]=gradg[theta][j];
+             trgradg[j][theta]=gradg[theta][j];
-      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-      pmij(pmmij,cov,ncovmodel,x,nlstate);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-      k=0;
+         k=0;
-      for(i=1; i<=(nlstate+ndeath); i++){
+         for(i=1; i<=(nlstate); i++){
-        for(j=1; j<=(nlstate+ndeath);j++){
+           for(j=1; j<=(nlstate+ndeath);j++){
-          k=k+1;
+             k=k+1;
-          gm[k]=pmmij[i][j];
+             mu[k][(int) age]=pmmij[i][j];
+           }
          }
-      }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-      /*printf("\n%d ",(int)age);
+             varpij[i][j][(int)age] = doldm[i][j];
-      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+         /*printf("\n%d ",(int)age);
+      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       }*/
-   fprintf(ficresprob,"\n%d ",(int)age);
+         fprintf(ficresprob,"\n%d ",(int)age);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
- if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-   }
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+         }
+         i=0;
+         for (k=1; k<=(nlstate);k++){
+           for (l=1; l<=(nlstate+ndeath);l++){
+             i=i++;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+             for (j=1; j<=i;j++){
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+             }
+           }
+         }/* end of loop for state */
+       } /* end of loop for age */
+         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       for (k1=1; k1<=(nlstate);k1++){
+         for (l1=1; l1<=(nlstate+ndeath);l1++){
+           if(l1==k1) continue;
+           i=(k1-1)*(nlstate+ndeath)+l1;
+           for (k2=1; k2<=(nlstate);k2++){
+             for (l2=1; l2<=(nlstate+ndeath);l2++){
+               if(l2==k2) continue;
+               j=(k2-1)*(nlstate+ndeath)+l2;
+               if(j<=i) continue;
+               for (age=bage; age<=fage; age ++){
+                 if ((int)age %5==0){
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
+                   /* Computing eigen value of matrix of covariance */
+                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
+                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
+                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
+                   /* Eigen vectors */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                   v21=sqrt(1.-v11*v11);
+                   v12=-v21;
+                   v22=v11;
+                   /*printf(fignu*/
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
+                   if(first==1){
+                     first=0;
+                     fprintf(ficgp,"\nset parametric;set nolabel");
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
+                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);
+                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);
+                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
+                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
+                   }else{
+                     first=0;
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
+                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
+                   }/* if first */
+                 } /* age mod 5 */
+               } /* end loop age */
+               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);
+               first=1;
+             } /*l12 */
+           } /* k12 */
+         } /*l1 */
+       }/* k1 */
+     } /* loop covariates */
+     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
- }
+   }
-  free_vector(xp,1,npar);
+   free_vector(xp,1,npar);
- fclose(ficresprob);
+   fclose(ficresprob);
-  exit(0);
+   fclose(ficresprobcov);
+   fclose(ficresprobcor);
+   fclose(ficgp);
+   fclose(fichtm);
  }
- /***********************************************/
- /**************** Main Program *****************/
- /***********************************************/
- int main(int argc, char *argv[])
+ /******************* Printing html file ***********/
- {
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+                   int popforecast, int estepm ,\
+                   double jprev1, double mprev1,double anprev1, \
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
+   /*char optionfilehtm[FILENAMELENGTH];*/
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
+    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+  - Life expectancies by age and initial health status (estepm=%2d months):
+    <a href=\"e%s\">e%s</a> <br>\n</li>", \
+   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
+  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
+  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+  if(popforecast==1) fprintf(fichtm,"\n
+  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
+  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
+         <br>",fileres,fileres,fileres,fileres);
+  else
+    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
+ fprintf(fichtm," <li>Graphs</li><p>");
-   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+  m=cptcoveff;
-   double agedeb, agefin,hf;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   double agemin=1.e20, agemax=-1.e20;
-   double fret;
+  jj1=0;
-   double **xi,tmp,delta;
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
+      /* Pij */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
+ <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+      /* Quasi-incidences */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+ <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+        /* Stable prevalence in each health state */
+        for(cpt=1; cpt<nlstate;cpt++){
+          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+ <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+        }
+     for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+ interval) in state (%d): v%s%d%d.png <br>
+ <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
+         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+ <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and
+ health expectancies in states (1) and (2): e%s%d.png<br>
+ <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+    }
+  }
+ fclose(fichtm);
+ }
-   double dum; /* Dummy variable */
+ /******************* Gnuplot file **************/
-   double ***p3mat;
+ void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+ #ifdef windows
+     fprintf(ficgp,"cd \"%s\" \n",pathc);
+ #endif
+ m=pow(2,cptcoveff);
+  /* 1eme*/
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
+    for (k1=1; k1<= m ; k1 ++) {
+ #ifdef windows
+      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+ #endif
+ #ifdef unix
+ fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
+ #endif
+ for (i=1; i<= nlstate ; i ++) {
+   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
+     for (i=1; i<= nlstate ; i ++) {
+   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
+   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+ #ifdef unix
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
+ #endif
+    }
+   }
+   /*2 eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+     for (i=1; i<= nlstate+1 ; i ++) {
+       k=2*i;
+       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       fprintf(ficgp,"\" t\"\" w l 0,");
+      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       else fprintf(ficgp,"\" t\"\" w l 0,");
+     }
+   }
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       k=2+nlstate*(2*cpt-2);
+       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ */
+       for (i=1; i< nlstate ; i ++) {
+         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+       }
+     }
+   }
+   /* CV preval stat */
+     for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<nlstate ; cpt ++) {
+       k=3;
+       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       for (i=1; i< nlstate ; i ++)
+         fprintf(ficgp,"+$%d",k+i+1);
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+       l=3+(nlstate+ndeath)*cpt;
+       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+       for (i=1; i< nlstate ; i ++) {
+         l=3+(nlstate+ndeath)*cpt;
+         fprintf(ficgp,"+$%d",l+i+1);
+       }
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+     }
+   }
+   /* proba elementaires */
+    for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         for(j=1; j <=ncovmodel; j++){
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
+           fprintf(ficgp,"\n");
+         }
+       }
+     }
+    }
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+      for(jk=1; jk <=m; jk++) {
+        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
+        if (ng==2)
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+        else
+          fprintf(ficgp,"\nset title \"Probability\"\n");
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+        i=1;
+        for(k2=1; k2<=nlstate; k2++) {
+          k3=i;
+          for(k=1; k<=(nlstate+ndeath); k++) {
+            if (k != k2){
+              if(ng==2)
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+              else
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+              ij=1;
+              for(j=3; j <=ncovmodel; j++) {
+                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                  ij++;
+                }
+                else
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+              }
+              fprintf(ficgp,")/(1");
+              for(k1=1; k1 <=nlstate; k1++){
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                ij=1;
+                for(j=3; j <=ncovmodel; j++){
+                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                    ij++;
+                  }
+                  else
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                }
+                fprintf(ficgp,")");
+              }
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+              i=i+ncovmodel;
+            }
+          }
+        }
+      }
+    }
+    fclose(ficgp);
+ }  /* end gnuplot */
+ /*************** Moving average **************/
+ void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
+   int i, cpt, cptcod;
+     for (agedeb=ageminpar; agedeb<=fage; agedeb++)
+       for (i=1; i<=nlstate;i++)
+         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
+           mobaverage[(int)agedeb][i][cptcod]=0.;
+     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
+       for (i=1; i<=nlstate;i++){
+         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+           for (cpt=0;cpt<=4;cpt++){
+             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
+           }
+           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
+         }
+       }
+     }
+ }
+ /************** Forecasting ******************/
+ prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   int *popage;
+   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat;
+   char fileresf[FILENAMELENGTH];
+  agelim=AGESUP;
+ calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   strcpy(fileresf,"f");
+   strcat(fileresf,fileres);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
+   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav==1) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     movingaverage(agedeb, fage, ageminpar, mobaverage);
+   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   agelim=AGESUP;
+   hstepm=1;
+   hstepm=hstepm/stepm;
+   yp1=modf(dateintmean,&yp);
+   anprojmean=yp;
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
+   if(mprojmean==0) jprojmean=1;
+   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
+   for(cptcov=1;cptcov<=i2;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficresf,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficresf,"******\n");
+       fprintf(ficresf,"# StartingAge FinalAge");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
+         fprintf(ficresf,"\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
+               if (h==(int)(calagedate+12*cpt)){
+                 fprintf(ficresf," %.3f", kk1);
+               }
+             }
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+     }
+   }
+   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresf);
+ }
+ /************** Forecasting ******************/
+ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   int *popage;
+   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat,***tabpop,***tabpopprev;
+   char filerespop[FILENAMELENGTH];
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   agelim=AGESUP;
+   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   strcpy(filerespop,"pop");
+   strcat(filerespop,fileres);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", filerespop);
+   }
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav==1) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     movingaverage(agedeb, fage, ageminpar, mobaverage);
+   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   agelim=AGESUP;
+   hstepm=1;
+   hstepm=hstepm/stepm;
+   if (popforecast==1) {
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
+     }
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
+     popcount=vector(0,AGESUP);
+     i=1;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   }
+   for(cptcov=1;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficrespop,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
+               if (h==(int)(calagedate+12*cpt)){
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
+             }
+             for(i=1; i<=nlstate;i++){
+               kk1=0.;
+                 for(j=1; j<=nlstate;j++){
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+                 }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+             }
+             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+   /******/
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+               }
+               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+             }
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+    }
+   }
+   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if (popforecast==1) {
+     free_ivector(popage,0,AGESUP);
+     free_vector(popeffectif,0,AGESUP);
+     free_vector(popcount,0,AGESUP);
+   }
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficrespop);
+ }
+ /***********************************************/
+ /**************** Main Program *****************/
+ /***********************************************/
+ int main(int argc, char *argv[])
+ {
+   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+   double agedeb, agefin,hf;
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double fret;
+   double **xi,tmp,delta;
+   double dum; /* Dummy variable */
+   double ***p3mat;
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
-   char title[MAXLINE];
-   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
-   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
-   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;
-   char filerest[FILENAMELENGTH];
-   char fileregp[FILENAMELENGTH];
-   char popfile[FILENAMELENGTH];
    char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
    int firstobs=1, lastobs=10;
    int sdeb, sfin; /* Status at beginning and end */
- Line 1915  int main(int argc, char *argv[])
+ Line 2782  int main(int argc, char *argv[])
    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
-   int *popage;/*boolprev=0 if date and zero if wave*/
+   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
-   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
    double bage, fage, age, agelim, agebase;
    double ftolpl=FTOL;
- Line 1931  int main(int argc, char *argv[])
+ Line 2797  int main(int argc, char *argv[])
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
    double kk1, kk2;
-   double *popeffectif,*popcount;
+   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
-   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
-   double yp,yp1,yp2;
-   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";
    char *alph[]={"a","a","b","c","d","e"}, str[4];
- Line 1948  int main(int argc, char *argv[])
+ Line 2812  int main(int argc, char *argv[])
    struct timeval start_time, end_time;
    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   getcwd(pathcd, size);
    printf("\n%s",version);
    if(argc <=1){
- Line 1996  int main(int argc, char *argv[])
+ Line 2860  int main(int argc, char *argv[])
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
  while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
- Line 2103  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2967  while((c=getc(ficpar))=='#' && c!= EOF){
    printf("\n");
-     /*-------- data file ----------*/
+     /*-------- Rewriting paramater file ----------*/
-     if((ficres =fopen(fileres,"w"))==NULL) {
+      strcpy(rfileres,"r");    /* "Rparameterfile */
-       printf("Problem with resultfile: %s\n", fileres);goto end;
+      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(ficres,"#%s\n",version);
+     /*-------- data file ----------*/
      if((fic=fopen(datafile,"r"))==NULL)    {
        printf("Problem with datafile: %s\n", datafile);goto end;
      }
- Line 2150  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3019  while((c=getc(ficpar))=='#' && c!= EOF){
          cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
          cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
-         for (j=ncov;j>=1;j--){
+         for (j=ncovcol;j>=1;j--){
            cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
          }
          num[i]=atol(stra);
- Line 2169  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3038  while((c=getc(ficpar))=='#' && c!= EOF){
      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
-     }
+     }*/
+    /*  for (i=1; i<=imx; i++){
-     for (i=1; i<=imx; i++)
+      if (s[4][i]==9)  s[4][i]=-1;
-     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/
+      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
    /* Calculation of the number of parameter from char model*/
    Tvar=ivector(1,15);
    Tprod=ivector(1,15);
- Line 2188  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3058  while((c=getc(ficpar))=='#' && c!= EOF){
      cptcovn=j+1;
      cptcovprod=j1;
      strcpy(modelsav,model);
      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
        printf("Error. Non available option model=%s ",model);
- Line 2219  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3088  while((c=getc(ficpar))=='#' && c!= EOF){
          }
          else {
            cutv(strb,stre,strc,'V');
-           Tvar[i]=ncov+k1;
+           Tvar[i]=ncovcol+k1;
            cutv(strb,strc,strd,'V');
            Tprod[k1]=i;
            Tvard[k1][1]=atoi(strc);
- Line 2227  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3096  while((c=getc(ficpar))=='#' && c!= EOF){
            Tvar[cptcovn+k2]=Tvard[k1][1];
            Tvar[cptcovn+k2+1]=Tvard[k1][2];
            for (k=1; k<=lastobs;k++)
-             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
            k1++;
            k2=k2+2;
          }
- Line 2244  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3113  while((c=getc(ficpar))=='#' && c!= EOF){
      }
  }
-   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
    printf("cptcovprod=%d ", cptcovprod);
    scanf("%d ",i);*/
      fclose(fic);
- Line 2256  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3125  while((c=getc(ficpar))=='#' && c!= EOF){
      /*-calculation of age at interview from date of interview and age at death -*/
      agev=matrix(1,maxwav,1,imx);
-    for (i=1; i<=imx; i++)
+     for (i=1; i<=imx; i++) {
-      for(m=2; (m<= maxwav); m++)
+       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
+      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
+       }
+     }
      for (i=1; i<=imx; i++)  {
        agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
        for(m=1; (m<= maxwav); m++){
          if(s[m][i] >0){
-           if (s[m][i] == nlstate+1) {
+           if (s[m][i] >= nlstate+1) {
              if(agedc[i]>0)
                if(moisdc[i]!=99 && andc[i]!=9999)
-               agev[m][i]=agedc[i];
+                 agev[m][i]=agedc[i];
-             else {
+             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+            else {
                if (andc[i]!=9999){
                printf("Warning negative age at death: %d line:%d\n",num[i],i);
                agev[m][i]=-1;
- Line 2346  printf("Total number of individuals= %d,
+ Line 3219  printf("Total number of individuals= %d,
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
-            if (h>m) h=1;codtab[h][k]=j;
+            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           }
         }
       }
     }
+    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+       codtab[1][2]=1;codtab[2][2]=2; */
-    /*for(i=1; i <=m ;i++){
+    /* for(i=1; i <=m ;i++){
-      for(k=1; k <=cptcovn; k++){
+       for(k=1; k <=cptcovn; k++){
-        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
+       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-      }
+       }
-      printf("\n");
+       printf("\n");
-    }
+       }
-    scanf("%d",i);*/
+       scanf("%d",i);*/
     /* Calculates basic frequencies. Computes observed prevalence at single age
         and prints on file fileres'p'. */
- Line 2381  printf("Total number of individuals= %d,
+ Line 3255  printf("Total number of individuals= %d,
      }
      /*--------- results files --------------*/
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     jk=1;
-    fprintf(ficres,"# Parameters\n");
+    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-    printf("# Parameters\n");
+    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i)
           {
             printf("%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficres,"\n");
           }
       }
     }
   if(mle==1){
      /* Computing hessian and covariance matrix */
      ftolhess=ftol; /* Usually correct */
      hesscov(matcov, p, npar, delti, ftolhess, func);
   }
-     fprintf(ficres,"# Scales\n");
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-     printf("# Scales\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath; j++){
          if (j!=i) {
            fprintf(ficres,"%1d%1d",i,j);
            printf("%1d%1d",i,j);
            for(k=1; k<=ncovmodel;k++){
              printf(" %.5e",delti[jk]);
              fprintf(ficres," %.5e",delti[jk]);
              jk++;
            }
            printf("\n");
            fprintf(ficres,"\n");
-         }
-       }
-      }
-     k=1;
-     fprintf(ficres,"# Covariance\n");
-     printf("# Covariance\n");
-     for(i=1;i<=npar;i++){
-       /*  if (k>nlstate) k=1;
-       i1=(i-1)/(ncovmodel*nlstate)+1;
-       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
-       printf("%s%d%d",alph[k],i1,tab[i]);*/
-       fprintf(ficres,"%3d",i);
-       printf("%3d",i);
-       for(j=1; j<=i;j++){
-         fprintf(ficres," %.5e",matcov[i][j]);
-         printf(" %.5e",matcov[i][j]);
-       }
-       fprintf(ficres,"\n");
-       printf("\n");
-       k++;
-     }
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
-       fputs(line,ficparo);
-     }
-     ungetc(c,ficpar);
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
-     if (fage <= 2) {
-       bage = agemin;
-       fage = agemax;
-     }
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
-     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 mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-    dateprev1=anprev1+mprev1/12.+jprev1/365.;
-    dateprev2=anprev2+mprev2/12.+jprev2/365.;
-   fscanf(ficpar,"pop_based=%d\n",&popbased);
-    fprintf(ficparo,"pop_based=%d\n",popbased);
-    fprintf(ficres,"pop_based=%d\n",popbased);
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
-     puts(line);
-     fputs(line,ficparo);
-   }
-   ungetc(c,ficpar);
-   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
- fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
- fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
-  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);
-     /*------------ gnuplot -------------*/
-     /*chdir(pathcd);*/
-     strcpy(optionfilegnuplot,optionfilefiname);
-     strcat(optionfilegnuplot,".plt");
-     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-       printf("Problem with file %s",optionfilegnuplot);goto end;
-     }
- #ifdef windows
-     fprintf(ficgp,"cd \"%s\" \n",pathc);
- #endif
- m=pow(2,cptcoveff);
-  /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
-    for (k1=1; k1<= m ; k1 ++) {
- #ifdef windows
-     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);
- #endif
- #ifdef unix
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
- #endif
- for (i=1; i<= nlstate ; i ++) {
-   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
-     for (i=1; i<= nlstate ; i ++) {
-   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
-      for (i=1; i<= nlstate ; i ++) {
-   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
- #ifdef unix
- fprintf(ficgp,"\nset ter gif small size 400,300");
- #endif
- fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-    }
-   }
-   /*2 eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
-     for (i=1; i<= nlstate+1 ; i ++) {
-       k=2*i;
-       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
-       for (j=1; j<= nlstate+1 ; j ++) {
-   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-       fprintf(ficgp,"\" t\"\" w l 0,");
-      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
-       for (j=1; j<= nlstate+1 ; j ++) {
-   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-   else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
-       else fprintf(ficgp,"\" t\"\" w l 0,");
-     }
-     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
-   }
-   /*3eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(cpt-1);
-       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);
-       for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);
-       }
-       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-     }
-   }
-   /* CV preval stat */
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<nlstate ; cpt ++) {
-       k=3;
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
-       for (i=1; i< nlstate ; i ++)
-         fprintf(ficgp,"+$%d",k+i+1);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-       l=3+(nlstate+ndeath)*cpt;
-       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
-       for (i=1; i< nlstate ; i ++) {
-         l=3+(nlstate+ndeath)*cpt;
-         fprintf(ficgp,"+$%d",l+i+1);
-       }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-     }
-   }
-   /* proba elementaires */
-    for(i=1,jk=1; i <=nlstate; i++){
-     for(k=1; k <=(nlstate+ndeath); k++){
-       if (k != i) {
-         for(j=1; j <=ncovmodel; j++){
-           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
-           /*fprintf(ficgp,"%s",alph[1]);*/
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-           jk++;
-           fprintf(ficgp,"\n");
          }
        }
+      }
+     k=1;
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     for(i=1;i<=npar;i++){
+       /*  if (k>nlstate) k=1;
+       i1=(i-1)/(ncovmodel*nlstate)+1;
+       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+       printf("%s%d%d",alph[k],i1,tab[i]);*/
+       fprintf(ficres,"%3d",i);
+       printf("%3d",i);
+       for(j=1; j<=i;j++){
+         fprintf(ficres," %.5e",matcov[i][j]);
+         printf(" %.5e",matcov[i][j]);
+       }
+       fprintf(ficres,"\n");
+       printf("\n");
+       k++;
      }
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       puts(line);
+       fputs(line,ficparo);
      }
+     ungetc(c,ficpar);
-   for(jk=1; jk <=m; jk++) {
+     estepm=0;
-   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-    i=1;
+     if (estepm==0 || estepm < stepm) estepm=stepm;
-    for(k2=1; k2<=nlstate; k2++) {
+     if (fage <= 2) {
-      k3=i;
+       bage = ageminpar;
-      for(k=1; k<=(nlstate+ndeath); k++) {
+       fage = agemaxpar;
-        if (k != k2){
+     }
-         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
- ij=1;
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-         for(j=3; j <=ncovmodel; j++) {
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-             ij++;
+     while((c=getc(ficpar))=='#' && c!= EOF){
-           }
+     ungetc(c,ficpar);
-           else
+     fgets(line, MAXLINE, ficpar);
-           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+     puts(line);
-         }
+     fputs(line,ficparo);
-           fprintf(ficgp,")/(1");
-         for(k1=1; k1 <=nlstate; k1++){
-           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
- ij=1;
-           for(j=3; j <=ncovmodel; j++){
-           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-             ij++;
-           }
-           else
-             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-           }
-           fprintf(ficgp,")");
-         }
-         fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-         i=i+ncovmodel;
-        }
-      }
-    }
-    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
    }
+   ungetc(c,ficpar);
-   fclose(ficgp);
-   /* end gnuplot */
- chdir(path);
-     free_ivector(wav,1,imx);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-     free_ivector(num,1,n);
-     free_vector(agedc,1,n);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-     fclose(ficparo);
-     fclose(ficres);
-     /*  }*/
-    /*________fin mle=1_________*/
-     /* No more information from the sample is required now */
+   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
-   /* Reads comments: lines beginning with '#' */
+   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
- Line 2698  chdir(path);
+ Line 3357  chdir(path);
      fputs(line,ficparo);
    }
    ungetc(c,ficpar);
+    dateprev1=anprev1+mprev1/12.+jprev1/365.;
+    dateprev2=anprev2+mprev2/12.+jprev2/365.;
+   fscanf(ficpar,"pop_based=%d\n",&popbased);
+   fprintf(ficparo,"pop_based=%d\n",popbased);
+   fprintf(ficres,"pop_based=%d\n",popbased);
-   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
+     ungetc(c,ficpar);
-   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
+   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
+ fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+ fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+ while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
+   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+ /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   fclose(ficgp);
+  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
  /*--------- index.htm --------*/
    strcpy(optionfilehtm,optionfile);
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm);goto end;
+     printf("Problem with %s \n",optionfilehtm), exit(0);
    }
-  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
+   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
- Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
- Total number of observations=%d <br>
+ \n
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
+ Total number of observations=%d <br>\n
- <hr  size=\"2\" color=\"#EC5E5E\">
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
- <li>Outputs files<br><br>\n
+ <hr  size=\"2\" color=\"#EC5E5E\">
-         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+  <ul><li>Parameter files<br>\n
- - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
-         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
+  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
-         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
+   fclose(fichtm);
-         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
-         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
+  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
-         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
+ /*------------ free_vector  -------------*/
-         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
+  chdir(path);
-         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
- <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
+  free_ivector(wav,1,imx);
+  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-  fprintf(fichtm," <li>Graphs</li><p>");
+  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+  free_ivector(num,1,n);
-  m=cptcoveff;
+  free_vector(agedc,1,n);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  /*free_matrix(covar,1,NCOVMAX,1,n);*/
+  fclose(ficparo);
+  fclose(ficres);
-  j1=0;
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
-        j1++;
-        if (cptcovn > 0) {
-          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-          for (cpt=1; cpt<=cptcoveff;cpt++)
-            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
-          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-        }
-        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
- <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
-        for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
- <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-        }
-     for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
- interval) in state (%d): v%s%d%d.gif <br>
- <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-      }
-      for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
- <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-      }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and
- health expectancies in states (1) and (2): e%s%d.gif<br>
- <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
- fprintf(fichtm,"\n</body>");
-    }
-  }
- fclose(fichtm);
    /*--------------- Prevalence limit --------------*/
- Line 2786  fclose(fichtm);
+ Line 3455  fclose(fichtm);
    savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
    oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
    k=0;
-   agebase=agemin;
+   agebase=ageminpar;
-   agelim=agemax;
+   agelim=agemaxpar;
    ftolpl=1.e-10;
    i1=cptcoveff;
    if (cptcovn < 1){i1=1;}
- Line 2847  fclose(fichtm);
+ Line 3516  fclose(fichtm);
              for(j=1; j<=nlstate+ndeath;j++)
                fprintf(ficrespij," %1d-%1d",i,j);
            fprintf(ficrespij,"\n");
-           for (h=0; h<=nhstepm; h++){
+            for (h=0; h<=nhstepm; h++){
              fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
              for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate+ndeath;j++)
                  fprintf(ficrespij," %.5f", p3mat[i][j][h]);
              fprintf(ficrespij,"\n");
-           }
+              }
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            fprintf(ficrespij,"\n");
          }
      }
    }
-   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
+   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
    fclose(ficrespij);
-   if(stepm == 1) {
-   /*---------- Forecasting ------------------*/
-   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
-   /*printf("calage= %f", calagedate);*/
-   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
-   strcpy(fileresf,"f");
-   strcat(fileresf,fileres);
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
-     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
-   }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   free_matrix(mint,1,maxwav,1,n);
-   free_matrix(anint,1,maxwav,1,n);
-   free_matrix(agev,1,maxwav,1,imx);
-   /* Mobile average */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (mobilav==1) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
-       for (i=1; i<=nlstate;i++)
-         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
-           mobaverage[(int)agedeb][i][cptcod]=0.;
-     for (agedeb=bage+4; agedeb<=fage; agedeb++){
-       for (i=1; i<=nlstate;i++){
-         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-           for (cpt=0;cpt<=4;cpt++){
-             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
-           }
-           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
-         }
-       }
-     }
-   }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (stepm<=12) stepsize=1;
-   agelim=AGESUP;
-   /*hstepm=stepsize*YEARM; *//* Every year of age */
-   hstepm=1;
-   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */
-   yp1=modf(dateintmean,&yp);
-   anprojmean=yp;
-   yp2=modf((yp1*12),&yp);
-   mprojmean=yp;
-   yp1=modf((yp2*30.5),&yp);
-   jprojmean=yp;
-   if(jprojmean==0) jprojmean=1;
-   if(mprojmean==0) jprojmean=1;
-   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
-   if (popforecast==1) {
-     if((ficpop=fopen(popfile,"r"))==NULL)    {
-       printf("Problem with population file : %s\n",popfile);goto end;
-     }
-     popage=ivector(0,AGESUP);
-     popeffectif=vector(0,AGESUP);
-     popcount=vector(0,AGESUP);
-     i=1;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
-       {
-         i=i+1;
-       }
-     imx=i;
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   }
-   for(cptcov=1;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       k=k+1;
-       fprintf(ficresf,"\n#******");
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
-       fprintf(ficresf,"******\n");
-       fprintf(ficresf,"# StartingAge FinalAge");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
-       if (popforecast==1)  fprintf(ficresf," [Population]");
-       for (cpt=0; cpt<4;cpt++) {
-         fprintf(ficresf,"\n");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
-         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */
-         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-         nhstepm = nhstepm/hstepm;
-         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-         for (h=0; h<=nhstepm; h++){
-           if (h==(int) (calagedate+YEARM*cpt)) {
-             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
-           }
-           for(j=1; j<=nlstate+ndeath;j++) {
-             kk1=0.;kk2=0;
-             for(i=1; i<=nlstate;i++) {
-               if (mobilav==1)
-                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-               else {
-                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/
-               }
-               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
+   /*---------- Forecasting ------------------*/
-             }
+   if((stepm == 1) && (strcmp(model,".")==0)){
+     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
-             if (h==(int)(calagedate+12*cpt)){
+     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
-               fprintf(ficresf," %.3f", kk1);
+   }
-               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
-             }
-           }
-         }
-         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       }
-       }
-     }
-   }
-   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if (popforecast==1) {
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
-     free_vector(popcount,0,AGESUP);
-   }
-   free_imatrix(s,1,maxwav+1,1,n);
-   free_vector(weight,1,n);
-   fclose(ficresf);
-   }/* End forecasting */
    else{
      erreur=108;
-     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);
+     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);
    }
    /*---------- Health expectancies and variances ------------*/
- Line 3034  fclose(fichtm);
+ Line 3568  fclose(fichtm);
      printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
    }
    printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   calagedate=-1;
+ prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    k=0;
    for(cptcov=1;cptcov<=i1;cptcov++){
- Line 3046  fclose(fichtm);
+ Line 3582  fclose(fichtm);
        fprintf(ficreseij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
-         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
+         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        fprintf(ficreseij,"******\n");
        fprintf(ficresvij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        fprintf(ficresvij,"******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);
+       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
        fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
        for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
        fprintf(ficrest,"\n");
-       hf=1;
-       if (stepm >= YEARM) hf=stepm/YEARM;
        epj=vector(1,nlstate+1);
        for(age=bage; age <=fage ;age++){
          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
- Line 3075  fclose(fichtm);
+ Line 3612  fclose(fichtm);
              prlim[i][i]=probs[(int)age][i][k];
          }
-         fprintf(ficrest," %.0f",age);
+         fprintf(ficrest," %4.0f",age);
          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
            for(i=1, epj[j]=0.;i <=nlstate;i++) {
-             epj[j] += prlim[i][i]*hf*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]);*/
            }
            epj[nlstate+1] +=epj[j];
          }
          for(i=1, vepp=0.;i <=nlstate;i++)
            for(j=1;j <=nlstate;j++)
              vepp += vareij[i][j][(int)age];
-         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
+         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
          for(j=1;j <=nlstate;j++){
-           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
+           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
          }
          fprintf(ficrest,"\n");
        }
      }
    }
+ free_matrix(mint,1,maxwav,1,n);
+     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
+     free_vector(weight,1,n);
+   fclose(ficreseij);
-  fclose(ficreseij);
+   fclose(ficresvij);
-  fclose(ficresvij);
    fclose(ficrest);
    fclose(ficpar);
    free_vector(epj,1,nlstate+1);
-   /*  scanf("%d ",i); */
    /*------- Variance limit prevalence------*/
- strcpy(fileresvpl,"vpl");
+   strcpy(fileresvpl,"vpl");
    strcat(fileresvpl,fileres);
    if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
      printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
- Line 3114  strcpy(fileresvpl,"vpl");
+ Line 3651  strcpy(fileresvpl,"vpl");
    }
    printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
-  k=0;
+   k=0;
-  for(cptcov=1;cptcov<=i1;cptcov++){
+   for(cptcov=1;cptcov<=i1;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-      k=k+1;
+       k=k+1;
-      fprintf(ficresvpl,"\n#****** ");
+       fprintf(ficresvpl,"\n#****** ");
-      for(j=1;j<=cptcoveff;j++)
+       for(j=1;j<=cptcoveff;j++)
-        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      fprintf(ficresvpl,"******\n");
+       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);
-    }
+     }
   }
    fclose(ficresvpl);
- Line 3145  strcpy(fileresvpl,"vpl");
+ Line 3682  strcpy(fileresvpl,"vpl");
    free_matrix(matcov,1,npar,1,npar);
    free_vector(delti,1,npar);
+   free_matrix(agev,1,maxwav,1,imx);
    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   fprintf(fichtm,"\n</body>");
+   fclose(fichtm);
+   fclose(ficgp);
    if(erreur >0)
-     printf("End of Imach with error %d\n",erreur);
+     printf("End of Imach with error or warning %d\n",erreur);
    else   printf("End of Imach\n");
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
- Line 3173  strcpy(fileresvpl,"vpl");
+ Line 3715  strcpy(fileresvpl,"vpl");
  #ifdef windows
    while (z[0] != 'q') {
-     chdir(path);
+     /* chdir(path); */
-     printf("\nType e to edit output files, c to start again, and q for exiting: ");
+     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
      scanf("%s",z);
      if (z[0] == 'c') system("./imach");
-     else if (z[0] == 'e') {
+     else if (z[0] == 'e') system(optionfilehtm);
-       chdir(path);
+     else if (z[0] == 'g') system(plotcmd);
-       system(optionfilehtm);
-     }
      else if (z[0] == 'q') exit(0);
    }
  #endif

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