imach/src/imach.c - diff

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Diff for /imach/src/imach.c between versions 1.22 and 1.46

-version 1.22, 2002/02/22 17:54:20
+version 1.46, 2002/05/30 17:44:35
  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 82  int cptcovn, cptcovage=0, cptcoveff=0,cp
+ Line 83  int cptcovn, cptcovage=0, cptcoveff=0,cp
  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 95  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 *ficreseij;
    char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
- Line 123  FILE *ficreseij;
+ Line 124  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 136  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 686  double **prevalim(double **prlim, int nl
+ Line 690  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 1179  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 1199  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 1330  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 1454  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 1462  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 1508  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 1525  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 1536  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);
    }
+   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 1731  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 1768  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 1780  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 1806  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 1833  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 1855  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 1924  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 fileres[], 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, j1, z1;
-   int k=0, cptcode;
+   int k=0,l, cptcode;
    double **dnewm,**doldm;
    double *xp;
    double *gp, *gm;
- Line 1786  void varprob(char fileres[], double **ma
+ Line 1935  void varprob(char fileres[], double **ma
    double age,agelim, cov[NCOVMAX];
    int theta;
    char fileresprob[FILENAMELENGTH];
+   char fileresprobcov[FILENAMELENGTH];
+   char fileresprobcor[FILENAMELENGTH];
    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);
    doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
    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(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(ficresprobcor, "**********\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,1,9);
+         trgradg=matrix(1,9,1,npar);
+         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+         gm=vector(1,(nlstate+ndeath)*(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+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];
+             }
+           }
-       pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           for(i=1; i<= (nlstate+ndeath)*(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(theta=1; theta <=npar; theta++)
-       trgradg[j][theta]=gradg[theta][j];
-      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
-      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
-      pmij(pmmij,cov,ncovmodel,x,nlstate);
+         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
+           for(theta=1; theta <=npar; theta++)
-      k=0;
+             trgradg[j][theta]=gradg[theta][j];
-      for(i=1; i<=(nlstate+ndeath); i++){
-        for(j=1; j<=(nlstate+ndeath);j++){
+         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
-          k=k+1;
+         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
-          gm[k]=pmmij[i][j];
+         pmij(pmmij,cov,ncovmodel,x,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];
+           }
          }
-      }
-      /*printf("\n%d ",(int)age);
+         /*printf("\n%d ",(int)age);
       for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);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+ndeath)*(nlstate+ndeath-1);i++)
-   }
+           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           fprintf(ficresprobcov,"%12.3e ",gm[i]);
+           fprintf(ficresprobcor,"%12.3e ",gm[i]);
+         }
+         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," %12.3e",doldm[i][j]);
+               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));
+             }
+           }
+         }
+       }
+     }
      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   }
+   free_vector(xp,1,npar);
+   fclose(ficresprob);
+   fclose(ficresprobcov);
+   fclose(ficresprobcor);
  }
-  free_vector(xp,1,npar);
- fclose(ficresprob);
-  exit(0);
- }
- /***********************************************/
- /**************** Main Program *****************/
- /***********************************************/
- int main(int argc, char *argv[])
- {
-   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+ /******************* Printing html file ***********/
-   double agedeb, agefin,hf;
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-   double agemin=1.e20, agemax=-1.e20;
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
+                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
+                   char version[], int popforecast, int estepm ,\
+                   double jprev1, double mprev1,double anprev1, \
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
+   FILE *fichtm;
+   /*char optionfilehtm[FILENAMELENGTH];*/
-   double fret;
+   strcpy(optionfilehtm,optionfile);
-   double **xi,tmp,delta;
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
-   double dum; /* Dummy variable */
+   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
-   double ***p3mat;
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
-   int *indx;
+ \n
-   char line[MAXLINE], linepar[MAXLINE];
+ Total number of observations=%d <br>\n
-   char title[MAXLINE];
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
-   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+ <hr  size=\"2\" color=\"#EC5E5E\">
-   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+  <ul><li>Parameter files<br>\n
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
-   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;
+  - 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);
+    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>");
-   char filerest[FILENAMELENGTH];
+  m=cptcoveff;
-   char fileregp[FILENAMELENGTH];
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   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 */
-   int c,  h , cpt,l;
-   int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**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;
-   double bage, fage, age, agelim, agebase;
+  jj1=0;
-   double ftolpl=FTOL;
+  for(k1=1; k1<=m;k1++){
-   double **prlim;
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   double *severity;
+      jj1++;
-   double ***param; /* Matrix of parameters */
+      if (cptcovn > 0) {
-   double  *p;
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   double **matcov; /* Matrix of covariance */
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-   double ***delti3; /* Scale */
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   double *delti; /* Scale */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   double ***eij, ***vareij;
+      }
-   double **varpl; /* Variances of prevalence limits by age */
+      /* 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);
+ fprintf(fichtm,"\n</body>");
+    }
+  }
+ fclose(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   strcpy(optionfilegnuplot,optionfilefiname);
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==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];
+   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[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 */
+   int c,  h , cpt,l;
+   int ju,jl, mi;
+   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+   int mobilav=0,popforecast=0;
+   int hstepm, nhstepm;
+   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
+   double bage, fage, age, agelim, agebase;
+   double ftolpl=FTOL;
+   double **prlim;
+   double *severity;
+   double ***param; /* Matrix of parameters */
+   double  *p;
+   double **matcov; /* Matrix of covariance */
+   double ***delti3; /* Scale */
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
+   double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
    double kk1, kk2;
-   double *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 version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";
    char *alph[]={"a","a","b","c","d","e"}, str[4];
- Line 1948  int main(int argc, char *argv[])
+ Line 2728  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 2776  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 2883  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 2935  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 2954  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 2974  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 3004  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 3012  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 3029  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 3041  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 3135  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 3171  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 3273  chdir(path);
      fputs(line,ficparo);
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
-   printf("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);
- /*--------- index.htm --------*/
-   strcpy(optionfilehtm,optionfile);
+    dateprev1=anprev1+mprev1/12.+jprev1/365.;
-   strcat(optionfilehtm,".htm");
+    dateprev2=anprev2+mprev2/12.+jprev2/365.;
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm);goto end;
+   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);
-  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
+   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);
- Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
+ 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);
- Total number of observations=%d <br>
+ 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);
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
- <hr  size=\"2\" color=\"#EC5E5E\">
- <li>Outputs files<br><br>\n
-         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
- - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
-         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
-         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
-         - 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>
-         - 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>
-         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
-         - 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);
-  fprintf(fichtm," <li>Graphs</li><p>");
-  m=cptcoveff;
+ while((c=getc(ficpar))=='#' && c!= EOF){
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
-  j1=0;
+   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
-  for(k1=1; k1<=m;k1++){
+   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-        j1++;
-        if (cptcovn > 0) {
+  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
-          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-          for (cpt=1; cpt<=cptcoveff;cpt++)
+ /*------------ gnuplot -------------*/
-            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
+  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
-          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-        }
+ /*------------ free_vector  -------------*/
-        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
+  chdir(path);
- <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
-        for(cpt=1; cpt<nlstate;cpt++){
+  free_ivector(wav,1,imx);
-          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
+  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
- <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
+  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-        }
+  free_ivector(num,1,n);
-     for(cpt=1; cpt<=nlstate;cpt++) {
+  free_vector(agedc,1,n);
-        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+  /*free_matrix(covar,1,NCOVMAX,1,n);*/
- interval) in state (%d): v%s%d%d.gif <br>
+  fclose(ficparo);
- <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
+  fclose(ficres);
-      }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+ /*--------- index.htm --------*/
-         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);
+  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    /*--------------- Prevalence limit --------------*/
    strcpy(filerespl,"pl");
- Line 2786  fclose(fichtm);
+ Line 3349  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 3410  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(fileres, 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 3462  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 3476  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 3506  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 3545  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 3576  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);
    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 3604  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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