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Diff for /imach/src/imach.c between versions 1.22 and 1.41.2.2

-version 1.22, 2002/02/22 17:54:20
+version 1.41.2.2, 2003/06/13 07:45:28
  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 "wgnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
  #define FILENAMELENGTH 80
  /*#define DEBUG*/
- #define windows
+ /*#define windows*/
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- Line 82  int cptcovn, cptcovage=0, cptcoveff=0,cp
+ Line 84  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 96  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;
  FILE *ficreseij;
    char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
- Line 123  FILE *ficreseij;
+ Line 125  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 137  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 691  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 866  double func( double *x)
+ Line 870  double func( double *x)
    double **out;
    double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
+   int s1, s2;
    long ipmx;
    /*extern weight */
    /* We are differentiating ll according to initial status */
- Line 880  double func( double *x)
+ Line 885  double func( double *x)
      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      for(mi=1; mi<= wav[i]-1; mi++){
        for (ii=1;ii<=nlstate+ndeath;ii++)
-         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         for (j=1;j<=nlstate+ndeath;j++){
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
        for(d=0; d<dh[mi][i]; d++){
          newm=savm;
          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- Line 896  double func( double *x)
+ Line 904  double func( double *x)
        } /* end mult */
-       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
+       s1=s[mw[mi][i]][i];
-       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
+       s2=s[mw[mi+1][i]][i];
+       if( s2 > nlstate){
+         /* i.e. if s2 is a death state and if the date of death is known then the contribution
+            to the likelihood is the probability to die between last step unit time and current
+            step unit time, which is also the differences between probability to die before dh
+            and probability to die before dh-stepm .
+            In version up to 0.92 likelihood was computed
+            as if date of death was unknown. Death was treated as any other
+            health state: the date of the interview describes the actual state
+            and not the date of a change in health state. The former idea was
+            to consider that at each interview the state was recorded
+            (healthy, disable or death) and IMaCh was corrected; but when we
+            introduced the exact date of death then we should have modified
+            the contribution of an exact death to the likelihood. This new
+            contribution is smaller and very dependent of the step unit
+            stepm. It is no more the probability to die between last interview
+            and month of death but the probability to survive from last
+            interview up to one month before death multiplied by the
+            probability to die within a month. Thanks to Chris
+            Jackson for correcting this bug.  Former versions increased
+            mortality artificially. The bad side is that we add another loop
+            which slows down the processing. The difference can be up to 10%
+            lower mortality.
+         */
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       }else{
+         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */
+         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
+       }
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/
      } /* end of wave */
    } /* end of individual */
    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   /*exit(0);*/
    return -l;
  }
- Line 1176  void lubksb(double **a, int n, int *indx
+ Line 1214  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 1234  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 1329  void prevalence(int agemin, int agemax,
+ Line 1373  void prevalence(int agemin, int agemax,
          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(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
- Line 1378  void prevalence(int agemin, int agemax,
+ Line 1424  void prevalence(int agemin, int agemax,
          }
      }
    }
    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 1487  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 1495  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 1541  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 1558  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 1569  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.;
+     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");
- Line 1597  void varevsij(char fileres[], double ***
+ Line 1767  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 1804  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 1816  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 1842  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 1869  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 1775  void varprevlim(char fileres[], double *
+ Line 1960  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;
    double **dnewm,**doldm;
    double *xp;
- Line 1792  void varprob(char fileres[], double **ma
+ Line 1977  void varprob(char fileres[], double **ma
    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);
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+ fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");
+   fprintf(ficresprob,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++)
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   fprintf(ficresprob,"\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);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       fprintf(ficresprob, "**********\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);
       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);
-   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
-     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,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));
+       }
+     }
      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);
+   free_vector(xp,1,npar);
- fclose(ficresprob);
+   fclose(ficresprob);
-  exit(0);
  }
- /***********************************************/
+ /******************* Printing html file ***********/
- /**************** Main Program *****************/
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
- /***********************************************/
+  int lastpass, int stepm, int weightopt, char model[],\
+  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
+  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
+  char version[], int popforecast, int estepm ){
+   int jj1, k1, i1, cpt;
+   FILE *fichtm;
+   /*char optionfilehtm[FILENAMELENGTH];*/
- int main(int argc, char *argv[])
+   strcpy(optionfilehtm,optionfile);
- {
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
-   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
-   double agedeb, agefin,hf;
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
-   double agemin=1.e20, agemax=-1.e20;
+ \n
+ Total number of observations=%d <br>\n
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
+ <hr  size=\"2\" color=\"#EC5E5E\">
+  <ul><li>Outputs files<br>\n
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n
+  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n
+  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n
+  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+  fprintf(fichtm,"\n
+  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
+   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+  - Variances 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: <a href=\"t%s\">t%s</a> <br>\n
+  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,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>");
-   double fret;
+  m=cptcoveff;
-   double **xi,tmp,delta;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   double dum; /* Dummy variable */
+  jj1=0;
-   double ***p3mat;
+  for(k1=1; k1<=m;k1++){
-   int *indx;
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   char line[MAXLINE], linepar[MAXLINE];
+        jj1++;
-   char title[MAXLINE];
+        if (cptcovn > 0) {
-   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+          for (cpt=1; cpt<=cptcoveff;cpt++)
+            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;
+          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        }
+        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
+ <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+        for(cpt=1; cpt<nlstate;cpt++){
+          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
+ <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,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.gif <br>
+ <img src=\"v%s%d%d.gif\">",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.gif <br>
+ <img src=\"exp%s%d%d.gif\">",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.gif<br>
+ <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ fprintf(fichtm,"\n</body>");
+    }
+    }
+ fclose(fichtm);
+ }
-   char filerest[FILENAMELENGTH];
+ /******************* Gnuplot file **************/
-   char fileregp[FILENAMELENGTH];
+ void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   char popfile[FILENAMELENGTH];
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-   int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
+   strcpy(optionfilegnuplot,optionfilefiname);
-   int c,  h , cpt,l;
+   strcat(optionfilegnuplot,".gp.txt");
-   int ju,jl, mi;
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+     printf("Problem with file %s",optionfilegnuplot);
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+   }
+ #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 ++) {
+      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",ageminpar,fage,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\"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));
+ 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] ",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+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       else fprintf(ficgp,"\" t\"\" w l 0,");
+     }
+     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
+   }
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       k=2+nlstate*(2*cpt-2);
+       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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);
+       }
+       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       for (i=1; i< nlstate ; i ++)
+         fprintf(ficgp,"+$%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);
+       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,"p%d=%f ",jk,p[jk]);
+           jk++;
+           fprintf(ficgp,"\n");
+         }
+       }
+     }
+     }
+     for(jk=1; jk <=m; jk++) {
+   fprintf(ficgp,"\nset ter gif small size 400,300\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){
+         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;
+        }
+      }
+    }
+    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
+    }
+   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;
-   int *popage;/*boolprev=0 if date and zero if wave*/
+   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
-   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
    double bage, fage, age, agelim, agebase;
    double ftolpl=FTOL;
- Line 1931  int main(int argc, char *argv[])
+ Line 2676  int main(int argc, char *argv[])
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
    double kk1, kk2;
-   double *popeffectif,*popcount;
+   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
-   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
-   double yp,yp1,yp2;
-   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";
+   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";
    char *alph[]={"a","a","b","c","d","e"}, str[4];
- Line 1948  int main(int argc, char *argv[])
+ Line 2692  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 2740  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 2847  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 2899  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 2918  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 2938  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 2968  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 2976  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 2993  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 3005  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 3099  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 3135  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)
- Line 2400  printf("Total number of individuals= %d,
+ Line 3154  printf("Total number of individuals= %d,
             }
             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");
-         }
-       }
-     }
-     }
-   for(jk=1; jk <=m; jk++) {
-   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
-    i=1;
-    for(k2=1; k2<=nlstate; k2++) {
-      k3=i;
-      for(k=1; k<=(nlstate+ndeath); k++) {
-        if (k != k2){
-         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,")");
+           printf("\n");
+           fprintf(ficres,"\n");
          }
-         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);
+     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);
+     estepm=0;
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
+     if (fage <= 2) {
+       bage = ageminpar;
+       fage = agemaxpar;
+     }
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
    }
+   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 3237  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);
+   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);
-      }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and
- health expectancies in states (1) and (2): e%s%d.gif<br>
- <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
- fprintf(fichtm,"\n</body>");
-    }
-  }
- fclose(fichtm);
    /*--------------- Prevalence limit --------------*/
    strcpy(filerespl,"pl");
- Line 2786  fclose(fichtm);
+ Line 3313  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 3374  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 3426  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 3440  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 3470  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 3509  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 3540  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 3159  strcpy(fileresvpl,"vpl");
+ Line 3554  strcpy(fileresvpl,"vpl");
   end:
- #ifdef windows
    /* chdir(pathcd);*/
- #endif
   /*system("wgnuplot graph.plt");*/
   /*system("../gp37mgw/wgnuplot graph.plt");*/
   /*system("cd ../gp37mgw");*/
- Line 3171  strcpy(fileresvpl,"vpl");
+ Line 3564  strcpy(fileresvpl,"vpl");
   strcat(plotcmd,optionfilegnuplot);
   system(plotcmd);
- #ifdef windows
+  /*#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
+   /*#endif */
  }

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