imach/src/imach.c - diff

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Diff for /imach/src/imach.c between versions 1.25 and 1.41.2.1

-version 1.25, 2002/02/26 17:11:54
+version 1.41.2.1, 2003/06/12 10:43:20
  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,*ficresprob,*ficpop;
  FILE *ficreseij;
    char filerese[FILENAMELENGTH];
- 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 1176  void lubksb(double **a, int n, int *indx
+ Line 1180  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 1200  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 1339  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 1390  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 1453  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 1461  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 1507  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 1524  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 1535  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 1733  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 1770  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 1782  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 1808  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 1835  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 1926  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 1943  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 ***********/
- 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[] ){
+ 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];*/
- Line 1891  void printinghtml(char fileres[], char t
+ Line 2073  void printinghtml(char fileres[], char t
      printf("Problem with %s \n",optionfilehtm), exit(0);
    }
-  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
+  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
+ \n
- Total number of observations=%d <br>
+ Total number of observations=%d <br>\n
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
  <hr  size=\"2\" color=\"#EC5E5E\">
- <li>Outputs files<br><br>\n
+  <ul><li>Outputs files<br>\n
-         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n
-         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
+  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
-         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
+  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n
-         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
+  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n
-         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
+  - 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);
-         - 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>
+  fprintf(fichtm,"\n
-         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
+  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
-         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
+   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
-         <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);
+  - 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>");
   m=cptcoveff;
- Line 1950  fclose(fichtm);
+ Line 2140  fclose(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){
+ void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
    strcpy(optionfilegnuplot,optionfilefiname);
-   strcat(optionfilegnuplot,".plt");
+   strcat(optionfilegnuplot,".gp.txt");
    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
      printf("Problem with file %s",optionfilegnuplot);
    }
- Line 1969  m=pow(2,cptcoveff);
+ Line 2159  m=pow(2,cptcoveff);
    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",ageminpar,fage,fileres,k1-1,k1-1);
-     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)");
- Line 1991  for (i=1; i<= nlstate ; i ++) {
+ Line 2176  for (i=1; i<= nlstate ; i ++) {
    else fprintf(ficgp," \%%*lf (\%%*lf)");
  }
       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
- #ifdef unix
- fprintf(ficgp,"\nset ter gif small size 400,300");
- #endif
  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
     }
    }
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);
      for (i=1; i<= nlstate+1 ; i ++) {
        k=2*i;
- Line 2032  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
+ Line 2215  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
-       k=2+nlstate*(cpt-1);
+       k=2+nlstate*(2*cpt-2);
-       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);
+       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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+i,cpt,i+1);
+         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);
      }
- Line 2045  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
+ Line 2237  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
      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);
+       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);
- Line 2077  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
+ Line 2269  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
      }
      for(jk=1; jk <=m; jk++) {
-   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
+   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;
- Line 2122  ij=1;
+ Line 2314  ij=1;
  /*************** Moving average **************/
- void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){
+ void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
    int i, cpt, cptcod;
-     for (agedeb=agemin; agedeb<=fage; agedeb++)
+     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=agemin+4; agedeb<=fage; agedeb++){
+     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++){
- Line 2143  void movingaverage(double agedeb, double
+ Line 2335  void movingaverage(double agedeb, double
  }
- /***********************************************/
- /**************** Main Program *****************/
- /***********************************************/
- int main(int argc, char *argv[])
+ /************** 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];
-   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+  agelim=AGESUP;
-   double agedeb, agefin,hf;
+ calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
-   double agemin=1.e20, agemax=-1.e20;
-   double fret;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
-   double **xi,tmp,delta;
+   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);
-   double dum; /* Dummy variable */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   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], fileresf[FILENAMELENGTH];
-   char filerest[FILENAMELENGTH];
+   if (mobilav==1) {
-   char fileregp[FILENAMELENGTH];
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   char popfile[FILENAMELENGTH];
+     movingaverage(agedeb, fage, ageminpar, mobaverage);
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
+   }
-   int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
-   int c,  h , cpt,l;
-   int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
-   int mobilav=0,popforecast=0;
-   int hstepm, nhstepm;
-   int *popage;/*boolprev=0 if date and zero if wave*/
-   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
-   double bage, fage, age, agelim, agebase;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   double ftolpl=FTOL;
+   if (stepm<=12) stepsize=1;
-   double **prlim;
-   double *severity;
+   agelim=AGESUP;
-   double ***param; /* Matrix of parameters */
-   double  *p;
+   hstepm=1;
-   double **matcov; /* Matrix of covariance */
+   hstepm=hstepm/stepm;
-   double ***delti3; /* Scale */
+   yp1=modf(dateintmean,&yp);
-   double *delti; /* Scale */
+   anprojmean=yp;
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
+   if(mprojmean==0) jprojmean=1;
+   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
+   for(cptcov=1;cptcov<=i2;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficresf,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficresf,"******\n");
+       fprintf(ficresf,"# StartingAge FinalAge");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
+         fprintf(ficresf,"\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
+               if (h==(int)(calagedate+12*cpt)){
+                 fprintf(ficresf," %.3f", kk1);
+               }
+             }
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+     }
+   }
+   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresf);
+ }
+ /************** Forecasting ******************/
+ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   int *popage;
+   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat,***tabpop,***tabpopprev;
+   char filerespop[FILENAMELENGTH];
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   agelim=AGESUP;
+   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   strcpy(filerespop,"pop");
+   strcat(filerespop,fileres);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", filerespop);
+   }
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav==1) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     movingaverage(agedeb, fage, ageminpar, mobaverage);
+   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   agelim=AGESUP;
+   hstepm=1;
+   hstepm=hstepm/stepm;
+   if (popforecast==1) {
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
+     }
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
+     popcount=vector(0,AGESUP);
+     i=1;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   }
+   for(cptcov=1;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficrespop,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
+               if (h==(int)(calagedate+12*cpt)){
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
+             }
+             for(i=1; i<=nlstate;i++){
+               kk1=0.;
+                 for(j=1; j<=nlstate;j++){
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+                 }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+             }
+             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+   /******/
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+               }
+               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+             }
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+    }
+   }
+   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if (popforecast==1) {
+     free_ivector(popage,0,AGESUP);
+     free_vector(popeffectif,0,AGESUP);
+     free_vector(popcount,0,AGESUP);
+   }
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficrespop);
+ }
+ /***********************************************/
+ /**************** Main Program *****************/
+ /***********************************************/
+ int main(int argc, char *argv[])
+ {
+   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+   double agedeb, agefin,hf;
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double fret;
+   double **xi,tmp,delta;
+   double dum; /* Dummy variable */
+   double ***p3mat;
+   int *indx;
+   char line[MAXLINE], linepar[MAXLINE];
+   char title[MAXLINE];
+   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+   char filerest[FILENAMELENGTH];
+   char fileregp[FILENAMELENGTH];
+   char popfile[FILENAMELENGTH];
+   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
+   int firstobs=1, lastobs=10;
+   int sdeb, sfin; /* Status at beginning and end */
+   int c,  h , cpt,l;
+   int ju,jl, mi;
+   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+   int mobilav=0,popforecast=0;
+   int hstepm, nhstepm;
+   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
+   double bage, fage, age, agelim, agebase;
+   double ftolpl=FTOL;
+   double **prlim;
+   double *severity;
+   double ***param; /* Matrix of parameters */
+   double  *p;
+   double **matcov; /* Matrix of covariance */
+   double ***delti3; /* Scale */
+   double *delti; /* Scale */
    double ***eij, ***vareij;
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
    double kk1, kk2;
-   double *popeffectif,*popcount;
+   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
-   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
-   double yp,yp1,yp2;
-   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";
+   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";
    char *alph[]={"a","a","b","c","d","e"}, str[4];
- Line 2212  int main(int argc, char *argv[])
+ Line 2658  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 2260  int main(int argc, char *argv[])
+ Line 2706  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 2367  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2813  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 2414  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2865  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 2433  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2884  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 2452  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2904  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 2483  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2934  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 2491  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2942  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 2508  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2959  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 2520  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 2971  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 2610  printf("Total number of individuals= %d,
+ Line 3065  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 2645  printf("Total number of individuals= %d,
+ Line 3101  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 2672  printf("Total number of individuals= %d,
+ Line 3128  printf("Total number of individuals= %d,
      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) {
- Line 2691  printf("Total number of individuals= %d,
+ Line 3147  printf("Total number of individuals= %d,
       }
      k=1;
-     fprintf(ficres,"# Covariance\n");
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     printf("# Covariance\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;
- Line 2716  printf("Total number of individuals= %d,
+ Line 3172  printf("Total number of individuals= %d,
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
+     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
+     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 = agemin;
+       bage = ageminpar;
-       fage = agemax;
+       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\n",agemin,agemax,bage,fage);
+     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\n",agemin,agemax,bage,fage);
+     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);
- Line 2753  printf("Total number of individuals= %d,
+ Line 3209  printf("Total number of individuals= %d,
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
    fscanf(ficpar,"pop_based=%d\n",&popbased);
-    fprintf(ficparo,"pop_based=%d\n",popbased);
+   fprintf(ficparo,"pop_based=%d\n",popbased);
-    fprintf(ficres,"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);
- Line 2763  printf("Total number of individuals= %d,
+ Line 3219  printf("Total number of individuals= %d,
      fputs(line,ficparo);
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mob_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
- fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
- fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
-  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);
+   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
+ fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+ fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+ while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
+   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
  /*------------ gnuplot -------------*/
-  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);
+  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
  /*------------ free_vector  -------------*/
   chdir(path);
- Line 2783  fprintf(ficres,"popforecast=%d popfile=%
+ Line 3253  fprintf(ficres,"popforecast=%d popfile=%
   /*free_matrix(covar,1,NCOVMAX,1,n);*/
   fclose(ficparo);
   fclose(ficres);
-   /* Reads comments: lines beginning with '#' */
-   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);
-   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 --------*/
-   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);
+   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);
    /*--------------- Prevalence limit --------------*/
- Line 2821  fprintf(ficres,"popforecast=%d popfile=%
+ Line 3279  fprintf(ficres,"popforecast=%d popfile=%
    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 2882  fprintf(ficres,"popforecast=%d popfile=%
+ Line 3340  fprintf(ficres,"popforecast=%d popfile=%
              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;
+   /*---------- Forecasting ------------------*/
+   if((stepm == 1) && (strcmp(model,".")==0)){
-   if (mobilav==1) {
+     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
-     movingaverage(agedeb, fage, agemin, mobaverage);
+   }
-   }
-   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<=(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>=(agemin-((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 ",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 (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
-             }
-             if (h==(int)(calagedate+12*cpt)){
-               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 ------------*/
    strcpy(filerest,"t");
- Line 3058  fprintf(ficres,"popforecast=%d popfile=%
+ Line 3392  fprintf(ficres,"popforecast=%d popfile=%
      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 3070  fprintf(ficres,"popforecast=%d popfile=%
+ Line 3406  fprintf(ficres,"popforecast=%d popfile=%
        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 3099  fprintf(ficres,"popforecast=%d popfile=%
+ Line 3436  fprintf(ficres,"popforecast=%d popfile=%
              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 3138  strcpy(fileresvpl,"vpl");
+ Line 3475  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 3169  strcpy(fileresvpl,"vpl");
+ Line 3506  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 3183  strcpy(fileresvpl,"vpl");
+ Line 3520  strcpy(fileresvpl,"vpl");
   end:
- #ifdef windows
    /* chdir(pathcd);*/
- #endif
   /*system("wgnuplot graph.plt");*/
   /*system("../gp37mgw/wgnuplot graph.plt");*/
   /*system("cd ../gp37mgw");*/
- Line 3195  strcpy(fileresvpl,"vpl");
+ Line 3530  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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