imach/src/imach.c - diff

Return to imach.c CVS log

Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.24 and 1.51

-version 1.24, 2002/02/22 18:10:15
+version 1.51, 2002/07/19 12:22:25
  Line 14
    model. More health states you consider, more time is necessary to reach the
    Maximum Likelihood of the parameters involved in the model.  The
    simplest model is the multinomial logistic model where pij is the
-   probabibility to be observed in state j at the second wave
+   probability to be observed in state j at the second wave
    conditional to be observed in state i at the first wave. Therefore
    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    'age' is age and 'sex' is a covariate. If you want to have a more
  Line 56
  #include <unistd.h>
  #define MAXLINE 256
- #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"
+ #define GNUPLOTPROGRAM "gnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
  #define FILENAMELENGTH 80
  /*#define DEBUG*/
  #define windows
- Line 74
+ Line 75
  #define YEARM 12. /* Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
+ #ifdef windows
+ #define DIRSEPARATOR '\\'
+ #define ODIRSEPARATOR '/'
+ #else
+ #define DIRSEPARATOR '/'
+ #define ODIRSEPARATOR '\\'
+ #endif
+ char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";
  int erreur; /* Error number */
  int nvar;
- int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
+ int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- Line 94  int **dh; /* dh[mi][i] is number of step
+ Line 102  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 *ficlog;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ FILE *ficresprobmorprev;
+ FILE *fichtm; /* Html File */
  FILE *ficreseij;
-   char filerese[FILENAMELENGTH];
+ char filerese[FILENAMELENGTH];
-  FILE  *ficresvij;
+ FILE  *ficresvij;
-   char fileresv[FILENAMELENGTH];
+ char fileresv[FILENAMELENGTH];
-  FILE  *ficresvpl;
+ FILE  *ficresvpl;
-   char fileresvpl[FILENAMELENGTH];
+ char fileresvpl[FILENAMELENGTH];
+ char title[MAXLINE];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char filelog[FILENAMELENGTH]; /* Log file */
+ char filerest[FILENAMELENGTH];
+ char fileregp[FILENAMELENGTH];
+ char popfile[FILENAMELENGTH];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
  #define NR_END 1
  #define FREE_ARG char*
- Line 123  FILE *ficreseij;
+ Line 145  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 157  int imx;
  int stepm;
  /* Stepm, step in month: minimum step interpolation*/
+ int estepm;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  int m,nb;
  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- Line 157  static int split( char *path, char *dirc
+ Line 182  static int split( char *path, char *dirc
     l1 = strlen( path );                 /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- #ifdef windows
+    s= strrchr( path, DIRSEPARATOR );            /* find last / */
-    s = strrchr( path, '\\' );           /* find last / */
- #else
-    s = strrchr( path, '/' );            /* find last / */
- #endif
     if ( s == NULL ) {                   /* no directory, so use current */
+      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
  #if     defined(__bsd__)                /* get current working directory */
        extern char       *getwd( );
- Line 228  int nbocc(char *s, char occ)
+ Line 251  int nbocc(char *s, char occ)
  void cutv(char *u,char *v, char*t, char occ)
  {
+   /* cuts string t into u and v where u is ended by char occ excluding it
+      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+      gives u="abcedf" and v="ghi2j" */
    int i,lg,j,p=0;
    i=0;
    for(j=0; j<=strlen(t)-1; j++) {
- Line 424  double brent(double ax, double bx, doubl
+ Line 450  double brent(double ax, double bx, doubl
      tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      printf(".");fflush(stdout);
+     fprintf(ficlog,".");fflush(ficlog);
  #ifdef DEBUG
      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
  #endif
      if (fabs(x-xm) <= (tol2-0.5*(b-a))){
- Line 550  void linmin(double p[], double xi[], int
+ Line 578  void linmin(double p[], double xi[], int
    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
  #ifdef DEBUG
    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  #endif
    for (j=1;j<=n;j++) {
      xi[j] *= xmin;
- Line 580  void powell(double p[], double **xi, int
+ Line 609  void powell(double p[], double **xi, int
      ibig=0;
      del=0.0;
      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
      for (i=1;i<=n;i++)
        printf(" %d %.12f",i, p[i]);
+     fprintf(ficlog," %d %.12f",i, p[i]);
      printf("\n");
+     fprintf(ficlog,"\n");
      for (i=1;i<=n;i++) {
        for (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
  #ifdef DEBUG
        printf("fret=%lf \n",*fret);
+       fprintf(ficlog,"fret=%lf \n",*fret);
  #endif
        printf("%d",i);fflush(stdout);
+       fprintf(ficlog,"%d",i);fflush(ficlog);
        linmin(p,xit,n,fret,func);
        if (fabs(fptt-(*fret)) > del) {
          del=fabs(fptt-(*fret));
- Line 597  void powell(double p[], double **xi, int
+ Line 631  void powell(double p[], double **xi, int
        }
  #ifdef DEBUG
        printf("%d %.12e",i,(*fret));
+       fprintf(ficlog,"%d %.12e",i,(*fret));
        for (j=1;j<=n;j++) {
          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
          printf(" x(%d)=%.12e",j,xit[j]);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        }
-       for(j=1;j<=n;j++)
+       for(j=1;j<=n;j++) {
          printf(" p=%.12e",p[j]);
+         fprintf(ficlog," p=%.12e",p[j]);
+       }
        printf("\n");
+       fprintf(ficlog,"\n");
  #endif
      }
      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- Line 612  void powell(double p[], double **xi, int
+ Line 651  void powell(double p[], double **xi, int
        k[0]=1;
        k[1]=-1;
        printf("Max: %.12e",(*func)(p));
-       for (j=1;j<=n;j++)
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       for (j=1;j<=n;j++) {
          printf(" %.12e",p[j]);
+         fprintf(ficlog," %.12e",p[j]);
+       }
        printf("\n");
+       fprintf(ficlog,"\n");
        for(l=0;l<=1;l++) {
          for (j=1;j<=n;j++) {
            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
          }
          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        }
  #endif
- Line 648  void powell(double p[], double **xi, int
+ Line 693  void powell(double p[], double **xi, int
          }
  #ifdef DEBUG
          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         for(j=1;j<=n;j++)
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         for(j=1;j<=n;j++){
            printf(" %.12e",xit[j]);
+           fprintf(ficlog," %.12e",xit[j]);
+         }
          printf("\n");
+         fprintf(ficlog,"\n");
  #endif
        }
      }
- Line 686  double **prevalim(double **prlim, int nl
+ Line 735  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 922  void mlikeli(FILE *ficres,double p[], in
+ Line 970  void mlikeli(FILE *ficres,double p[], in
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
-   printf("Powell\n");
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
    powell(p,xi,npar,ftol,&iter,&fret,func);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  }
- Line 946  void hesscov(double **matcov, double p[]
+ Line 995  void hesscov(double **matcov, double p[]
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    for (i=1;i<=npar;i++){
      printf("%d",i);fflush(stdout);
+     fprintf(ficlog,"%d",i);fflush(ficlog);
      hess[i][i]=hessii(p,ftolhess,i,delti);
      /*printf(" %f ",p[i]);*/
      /*printf(" %lf ",hess[i][i]);*/
- Line 957  void hesscov(double **matcov, double p[]
+ Line 1008  void hesscov(double **matcov, double p[]
      for (j=1;j<=npar;j++)  {
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
          hess[i][j]=hessij(p,delti,i,j);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
- Line 964  void hesscov(double **matcov, double p[]
+ Line 1016  void hesscov(double **matcov, double p[]
      }
    }
    printf("\n");
+   fprintf(ficlog,"\n");
    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
    a=matrix(1,npar,1,npar);
    y=matrix(1,npar,1,npar);
- Line 985  void hesscov(double **matcov, double p[]
+ Line 1039  void hesscov(double **matcov, double p[]
    }
    printf("\n#Hessian matrix#\n");
+   fprintf(ficlog,"\n#Hessian matrix#\n");
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++) {
        printf("%.3e ",hess[i][j]);
+       fprintf(ficlog,"%.3e ",hess[i][j]);
      }
      printf("\n");
+     fprintf(ficlog,"\n");
    }
    /* Recompute Inverse */
- Line 1006  void hesscov(double **matcov, double p[]
+ Line 1063  void hesscov(double **matcov, double p[]
      for (i=1;i<=npar;i++){
        y[i][j]=x[i];
        printf("%.3e ",y[i][j]);
+       fprintf(ficlog,"%.3e ",y[i][j]);
      }
      printf("\n");
+     fprintf(ficlog,"\n");
    }
    */
- Line 1049  double hessii( double x[], double delta,
+ Line 1108  double hessii( double x[], double delta,
  #ifdef DEBUG
        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
  #endif
        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
- Line 1096  double hessij( double x[], double delti[
+ Line 1156  double hessij( double x[], double delti[
      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
  #ifdef DEBUG
      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
  #endif
    }
    return res;
- Line 1176  void lubksb(double **a, int n, int *indx
+ Line 1237  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;
+   int first;
    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");
    strcat(fileresp,fileres);
    if((ficresp=fopen(fileresp,"w"))==NULL) {
      printf("Problem with prevalence resultfile: %s\n", fileresp);
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
    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++){
+   first=1;
-    for(i1=1; i1<=ncodemax[k1];i1++){
-        j1++;
-        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-          scanf("%d", i);*/
-         for (i=-1; i<=nlstate+ndeath; i++)
-          for (jk=-1; jk<=nlstate+ndeath; jk++)
-            for(m=agemin; m <= agemax+3; m++)
-              freq[i][jk][m]=0;
-         dateintsum=0;
-         k2cpt=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]] += weight[i];
-                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
-                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
-                  dateintsum=dateintsum+k2;
-                  k2cpt++;
-                }
-              }
+   for(k1=1; k1<=j;k1++){
-            }
+     for(i1=1; i1<=ncodemax[k1];i1++){
-          }
+       j1++;
-        }
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-         if  (cptcovn>0) {
+         scanf("%d", i);*/
-          fprintf(ficresp, "\n#********** Variable ");
+       for (i=-1; i<=nlstate+ndeath; i++)
-          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (jk=-1; jk<=nlstate+ndeath; jk++)
-        fprintf(ficresp, "**********\n#");
+           for(m=agemin; m <= agemax+3; m++)
-         }
+             freq[i][jk][m]=0;
-        for(i=1; i<=nlstate;i++)
-          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       dateintsum=0;
-        fprintf(ficresp, "\n");
+       k2cpt=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;
+               if (m<lastpass) {
+                 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];
+               }
+               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
+                 dateintsum=dateintsum+k2;
+                 k2cpt++;
+               }
+             }
+           }
+         }
+       }
-   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){
+           fprintf(ficlog,"Total");
+         }else{
+           if(first==1){
+             first=0;
+             printf("See log file for details...\n");
+           }
+           fprintf(ficlog,"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){
+             if(first==1){
+             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+             }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %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
+         for(jk=1,pos=0; jk <=nlstate ; jk++)
-         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           pos += pp[jk];
-       if( i <= (int) agemax){
+         for(jk=1; jk <=nlstate ; jk++){
-         if(pos>=1.e-5){
+           if(pos>=1.e-5){
-           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+             if(first==1)
-           probs[i][jk][j1]= pp[jk]/pos;
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*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]);*/
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             fprintf(ficlog," %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);
+           }
          }
-       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 ) {
+             if(first==1)
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
+         if(i <= (int) agemax)
+           fprintf(ficresp,"\n");
+         if(first==1)
+           printf("Others in log...\n");
+         fprintf(ficlog,"\n");
        }
      }
-     for(jk=-1; jk <=nlstate+ndeath; jk++)
+   }
-       for(m=-1; m <=nlstate+ndeath; m++)
-         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-     if(i <= (int) agemax)
-       fprintf(ficresp,"\n");
-     printf("\n");
-     }
-     }
-  }
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
    free_vector(pp,1,nlstate);
    /* End of Freq */
  }
  /************ Prevalence ********************/
- void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
+ void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
  {  /* Some frequencies */
    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
- Line 1321  void prevalence(int agemin, int agemax,
+ Line 1414  void prevalence(int agemin, int agemax,
    j=cptcoveff;
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-  for(k1=1; k1<=j;k1++){
+   for(k1=1; k1<=j;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;
        for (i=-1; i<=nlstate+ndeath; i++)
          for (jk=-1; jk<=nlstate+ndeath; jk++)
            for(m=agemin; m <= agemax+3; m++)
              freq[i][jk][m]=0;
        for (i=1; i<=imx; i++) {
          bool=1;
          if  (cptcovn>0) {
            for (z1=1; z1<=cptcoveff; z1++)
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                bool=0;
          }
          if (bool==1) {
            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                if(agev[m][i]==0) agev[m][i]=agemax+1;
                if(agev[m][i]==1) agev[m][i]=agemax+2;
-               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+               if (m<lastpass) {
-               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];
+                 if (calagedate>0)
+                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+                 else
+                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
+               }
              }
            }
          }
        }
+       for(i=(int)agemin; i <= (int)agemax+3; i++){
-         for(i=(int)agemin; i <= (int)agemax+3; i++){
+         for(jk=1; jk <=nlstate ; jk++){
-           for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
-               pp[jk] += freq[jk][m][i];
+         }
-           }
+         for(jk=1; jk <=nlstate ; jk++){
-           for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
-             for(m=-1, pos=0; m <=0 ; m++)
              pos += freq[jk][m][i];
          }
-          for(jk=1; jk <=nlstate ; jk++){
+         for(jk=1; jk <=nlstate ; jk++){
-            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-              pp[jk] += freq[jk][m][i];
+             pp[jk] += freq[jk][m][i];
-          }
-          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
-          for(jk=1; jk <=nlstate ; jk++){
-            if( i <= (int) agemax){
-              if(pos>=1.e-5){
-                probs[i][jk][j1]= pp[jk]/pos;
-              }
-            }
-          }
          }
-     }
-   }
+         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <= (int) agemax){
+             if(pos>=1.e-5){
+               probs[i][jk][j1]= pp[jk]/pos;
+             }
+           }
+         }/* end jk */
+       }/* end i */
+     } /* end i1 */
+   } /* end k1 */
    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
    free_vector(pp,1,nlstate);
- Line 1399  void  concatwav(int wav[], int **dh, int
+ Line 1495  void  concatwav(int wav[], int **dh, int
    int i, mi, m;
    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       double sum=0., jmean=0.;*/
+   int first;
    int j, k=0,jk, ju, jl;
    double sum=0.;
+   first=0;
    jmin=1e+5;
    jmax=-1;
    jmean=0.;
- Line 1424  void  concatwav(int wav[], int **dh, int
+ Line 1521  void  concatwav(int wav[], int **dh, int
      }
      wav[i]=mi;
-     if(mi==0)
+     if(mi==0){
-       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
+       if(first==0){
+         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
+         first=1;
+       }
+       if(first==1){
+         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
+       }
+     } /* end mi==0 */
    }
    for(i=1; i<=imx; i++){
- Line 1441  void  concatwav(int wav[], int **dh, int
+ Line 1545  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 1553  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 1466  void  concatwav(int wav[], int **dh, int
+ Line 1570  void  concatwav(int wav[], int **dh, int
    }
    jmean=sum/k;
    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   }
  /*********** Tricode ****************************/
  void tricode(int *Tvar, int **nbcode, int imx)
  {
- Line 1495  void tricode(int *Tvar, int **nbcode, in
+ Line 1601  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 1505  void tricode(int *Tvar, int **nbcode, in
+ Line 1612  void tricode(int *Tvar, int **nbcode, in
   for (k=0; k<19; k++) Ndum[k]=0;
   for (i=1; i<=ncovmodel-2; i++) {
-       ij=Tvar[i];
+    ij=Tvar[i];
-       Ndum[ij]++;
+    Ndum[ij]++;
-     }
+  }
   ij=1;
   for (i=1; i<=10; i++) {
-    if((Ndum[i]!=0) && (i<=ncov)){
+    if((Ndum[i]!=0) && (i<=ncovcol)){
       Tvaraff[ij]=i;
       ij++;
     }
   }
-     cptcoveff=ij-1;
+  cptcoveff=ij-1;
  }
  /*********** Health Expectancies ****************/
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
+ void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
  {
    /* Health expectancies */
-   int i, j, nhstepm, hstepm, h;
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
-   double age, agelim,hf;
+   double age, agelim, hf;
-   double ***p3mat;
+   double ***p3mat,***varhe;
+   double **dnewm,**doldm;
+   double *xp;
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
+   int theta;
+   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
+   xp=vector(1,npar);
+   dnewm=matrix(1,nlstate*2,1,npar);
+   doldm=matrix(1,nlstate*2,1,nlstate*2);
    fprintf(ficreseij,"# Health expectancies\n");
    fprintf(ficreseij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
-       fprintf(ficreseij," %1d-%1d",i,j);
+       fprintf(ficreseij," %1d-%1d (SE)",i,j);
    fprintf(ficreseij,"\n");
-   hstepm=1*YEARM; /*  Every j years of age (in month) */
+   if(estepm < stepm){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
+    * if stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression inbetween and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
    agelim=AGESUP;
    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      /* nhstepm age range expressed in number of stepm */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm);
+     nstepm=(int) rint((agelim-age)*YEARM/stepm);
-     /* Typically if 20 years = 20*12/6=40 stepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     if (stepm >= YEARM) hstepm=1;
+     /* if (stepm >= YEARM) hstepm=1;*/
-     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
+     gp=matrix(0,nhstepm,1,nlstate*2);
+     gm=matrix(0,nhstepm,1,nlstate*2);
      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     /* Computing Variances of health expectancies */
+      for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       cptj=0;
+       for(j=1; j<= nlstate; j++){
+         for(i=1; i<=nlstate; i++){
+           cptj=cptj+1;
+           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+           }
+         }
+       }
+       for(i=1; i<=npar; i++)
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       cptj=0;
+       for(j=1; j<= nlstate; j++){
+         for(i=1;i<=nlstate;i++){
+           cptj=cptj+1;
+           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
+             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+           }
+         }
+       }
+       for(j=1; j<= nlstate*2; j++)
+         for(h=0; h<=nhstepm-1; h++){
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         }
+      }
+ /* End theta */
+      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
+      for(h=0; h<=nhstepm-1; h++)
+       for(j=1; j<=nlstate*2;j++)
+         for(theta=1; theta <=npar; theta++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
+      for(i=1;i<=nlstate*2;i++)
+       for(j=1;j<=nlstate*2;j++)
+         varhe[i][j][(int)age] =0.;
+      printf("%d|",(int)age);fflush(stdout);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+      for(h=0;h<=nhstepm-1;h++){
+       for(k=0;k<=nhstepm-1;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
+         for(i=1;i<=nlstate*2;i++)
+           for(j=1;j<=nlstate*2;j++)
+             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+       }
+     }
+     /* Computing expectancies */
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-           eij[i][j][(int)age] +=p3mat[i][j][h];
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+ /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
-     hf=1;
+     fprintf(ficreseij,"%3.0f",age );
-     if (stepm >= YEARM) hf=stepm/YEARM;
+     cptj=0;
-     fprintf(ficreseij,"%.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);
+         cptj++;
+         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
        }
      fprintf(ficreseij,"\n");
+     free_matrix(gm,0,nhstepm,1,nlstate*2);
+     free_matrix(gp,0,nhstepm,1,nlstate*2);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }
+   printf("\n");
+   fprintf(ficlog,"\n");
+   free_vector(xp,1,npar);
+   free_matrix(dnewm,1,nlstate*2,1,npar);
+   free_matrix(doldm,1,nlstate*2,1,nlstate*2);
+   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
  }
  /************ Variance ******************/
- void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+ void varevsij(char optionfilefiname[], 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, int cptcov, int cptcod, int popbased)
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   double **newm;
+   /* double **newm;*/
    double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm, h;
+   double **dnewmp,**doldmp;
+   int i, j, nhstepm, hstepm, h, nstepm ;
    int k, cptcode;
    double *xp;
-   double **gp, **gm;
+   double **gp, **gm;  /* for var eij */
-   double ***gradg, ***trgradg;
+   double ***gradg, ***trgradg; /*for var eij */
+   double **gradgp, **trgradgp; /* for var p point j */
+   double *gpp, *gmp; /* for var p point j */
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
    double ***p3mat;
-   double age,agelim;
+   double age,agelim, hf;
    int theta;
+   char digit[4];
+   char digitp[16];
+   char fileresprobmorprev[FILENAMELENGTH];
+   if(popbased==1)
+     strcpy(digitp,"-populbased-");
+   else
+     strcpy(digitp,"-stablbased-");
+   strcpy(fileresprobmorprev,"prmorprev");
+   sprintf(digit,"%-d",ij);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   strcat(fileresprobmorprev,digitp); /* Popbased or not */
+   strcat(fileresprobmorprev,fileres);
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   }
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     fprintf(ficresprobmorprev," p.%-d SE",j);
+     for(i=1; i<=nlstate;i++)
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   }
+   fprintf(ficresprobmorprev,"\n");
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+     exit(0);
+   }
+   else{
+     fprintf(ficgp,"\n# Routine varevsij");
+   }
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+     printf("Problem with html file: %s\n", optionfilehtm);
+     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+     exit(0);
+   }
+   else{
+     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+   }
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-    fprintf(ficresvij,"# Covariances of life expectancies\n");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
    fprintf(ficresvij,"# Age");
    for(i=1; i<=nlstate;i++)
      for(j=1; j<=nlstate;j++)
- Line 1596  void varevsij(char fileres[], double ***
+ Line 1876  void varevsij(char fileres[], double ***
    xp=vector(1,npar);
    dnewm=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   hstepm=1*YEARM; /* Every year of age */
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   gpp=vector(nlstate+1,nlstate+ndeath);
+   gmp=vector(nlstate+1,nlstate+ndeath);
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   if(estepm < stepm){
+     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);
      gm=matrix(0,nhstepm,1,nlstate);
      for(theta=1; theta <=npar; theta++){
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
- Line 1620  void varevsij(char fileres[], double ***
+ Line 1922  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++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
+       /* This for computing forces of mortality (h=1)as a weighted average */
+       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
+         for(i=1; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
+       /* end force of mortality */
        for(i=1; i<=npar; i++) /* Computes gradient */
          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 1644  void varevsij(char fileres[], double ***
+ Line 1952  void varevsij(char fileres[], double ***
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
+       /* This for computing force of mortality (h=1)as a weighted average */
+       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+         for(i=1; i<= nlstate; i++)
+           gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
+       /* end force of mortality */
-       for(j=1; j<= nlstate; j++)
+       for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+       }
      } /* End theta */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-     for(h=0; h<=nhstepm; h++)
+     for(h=0; h<=nhstepm; h++) /* veij */
        for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(theta=1; theta <=npar; theta++)
+         trgradgp[j][theta]=gradgp[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;
+     /* pptj */
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+         varppt[j][i]=doldmp[j][i];
+     /* end ppptj */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+     if (popbased==1) {
+       for(i=1; i<=nlstate;i++)
+         prlim[i][i]=probs[(int)age][i][ij];
+     }
+     /* This for computing force of mortality (h=1)as a weighted average */
+     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+       for(i=1; i<= nlstate; i++)
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+     }
+     /* end force of mortality */
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+       for(i=1; i<=nlstate;i++){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+       }
+     }
+     fprintf(ficresprobmorprev,"\n");
      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 2038  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(gpp,nlstate+1,nlstate+ndeath);
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
    free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(doldm,1,nlstate,1,nlstate);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   free_matrix(dnewm,1,nlstate,1,npar);
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   fclose(ficresprobmorprev);
+   fclose(ficgp);
+   fclose(fichtm);
  }
- Line 1706  void varprevlim(char fileres[], double *
+ Line 2079  void varprevlim(char fileres[], double *
    double age,agelim;
    int theta;
-   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
+   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
    fprintf(ficresvpl,"# Age");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
- Line 1775  void varprevlim(char fileres[], double *
+ Line 2148  void varprevlim(char fileres[], double *
  }
  /************ Variance of one-step probabilities  ******************/
- void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
  {
-   int i, j;
+   int i, j=0,  i1, k1, l1, t, tj;
-   int k=0, cptcode;
+   int k2, l2, j1,  z1;
+   int k=0,l, cptcode;
+   int first=1, first1;
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
    double **dnewm,**doldm;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
+   double **mu;
    double age,agelim, cov[NCOVMAX];
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    int theta;
    char fileresprob[FILENAMELENGTH];
+   char fileresprobcov[FILENAMELENGTH];
+   char fileresprobcor[FILENAMELENGTH];
+   double ***varpij;
    strcpy(fileresprob,"prob");
    strcat(fileresprob,fileres);
    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprob);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
    }
-   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
+   strcpy(fileresprobcov,"probcov");
+   strcat(fileresprobcov,fileres);
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcov);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
+   strcpy(fileresprobcor,"probcor");
+   strcat(fileresprobcor,fileres);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcor);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+   }
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   fprintf(ficresprob,"# Age");
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   fprintf(ficresprobcov,"# Age");
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcov,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     }
+   fprintf(ficresprob,"\n");
+   fprintf(ficresprobcov,"\n");
+   fprintf(ficresprobcor,"\n");
    xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   cov[1]=1;
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   for (age=bage; age<=fage; age ++){
+   first=1;
-     cov[2]=age;
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
-     gradg=matrix(1,npar,1,9);
+     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
-     trgradg=matrix(1,9,1,npar);
+     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
-     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+     exit(0);
-     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+   }
+   else{
-     for(theta=1; theta <=npar; theta++){
+     fprintf(ficgp,"\n# Routine varprob");
-       for(i=1; i<=npar; i++)
+   }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+     printf("Problem with html file: %s\n", optionfilehtm);
-       pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+     exit(0);
-       k=0;
+   }
-       for(i=1; i<= (nlstate+ndeath); i++){
+   else{
-         for(j=1; j<=(nlstate+ndeath);j++){
+     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-            k=k+1;
+     fprintf(fichtm,"\n");
-           gp[k]=pmmij[i][j];
-         }
-       }
-       for(i=1; i<=npar; i++)
+     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
-       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);
+   cov[1]=1;
-      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
+   tj=cptcoveff;
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   j1=0;
+   for(t=1; t<=tj;t++){
+     for(i1=1; i1<=ncodemax[t];i1++){
+       j1++;
+       if  (cptcovn>0) {
+         fprintf(ficresprob, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprob, "**********\n#");
+         fprintf(ficresprobcov, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobcov, "**********\n#");
+         fprintf(ficgp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficgp, "**********\n#");
+         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+         fprintf(ficresprobcor, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficgp, "**********\n#");
+       }
+       for (age=bage; age<=fage; age ++){
+         cov[2]=age;
+         for (k=1; k<=cptcovn;k++) {
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+         }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+         for (k=1; k<=cptcovprod;k++)
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         gp=vector(1,(nlstate)*(nlstate+ndeath));
+         gm=vector(1,(nlstate)*(nlstate+ndeath));
+         for(theta=1; theta <=npar; theta++){
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<= (nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gp[k]=pmmij[i][j];
+             }
+           }
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] - (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<=(nlstate); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gm[k]=pmmij[i][j];
+             }
+           }
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
+         }
-      pmij(pmmij,cov,ncovmodel,x,nlstate);
+         for(j=1; j<=(nlstate)*(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,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-          k=k+1;
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-          gm[k]=pmmij[i][j];
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
+         k=0;
+         for(i=1; i<=(nlstate); i++){
+           for(j=1; j<=(nlstate+ndeath);j++){
+             k=k+1;
+             mu[k][(int) age]=pmmij[i][j];
+           }
          }
-      }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-      /*printf("\n%d ",(int)age);
+             varpij[i][j][(int)age] = doldm[i][j];
-      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+         /*printf("\n%d ",(int)age);
+      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       }*/
-   fprintf(ficresprob,"\n%d ",(int)age);
+         fprintf(ficresprob,"\n%d ",(int)age);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
+         fprintf(ficresprobcor,"\n%d ",(int)age);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+         }
+         i=0;
+         for (k=1; k<=(nlstate);k++){
+           for (l=1; l<=(nlstate+ndeath);l++){
+             i=i++;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+             for (j=1; j<=i;j++){
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+             }
+           }
+         }/* end of loop for state */
+       } /* end of loop for age */
+       /* Confidence intervalle of pij  */
+       /*
+       fprintf(ficgp,"\nset noparametric;unset label");
+       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+       */
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       first1=1;
+       for (k2=1; k2<=(nlstate);k2++){
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
+           if(l2==k2) continue;
+           j=(k2-1)*(nlstate+ndeath)+l2;
+           for (k1=1; k1<=(nlstate);k1++){
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
+               if(l1==k1) continue;
+               i=(k1-1)*(nlstate+ndeath)+l1;
+               if(i<=j) continue;
+               for (age=bage; age<=fage; age ++){
+                 if ((int)age %5==0){
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
+                   c12=cv12/sqrt(v1*v2);
+                   /* Computing eigen value of matrix of covariance */
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                   /* Eigen vectors */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                   /*v21=sqrt(1.-v11*v11); *//* error */
+                   v21=(lc1-v1)/cv12*v11;
+                   v12=-v21;
+                   v22=v11;
+                   tnalp=v21/v11;
+                   if(first1==1){
+                     first1=0;
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   }
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   /*printf(fignu*/
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                   if(first==1){
+                     first=0;
+                     fprintf(ficgp,"\nset parametric;unset label");
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }else{
+                     first=0;
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }/* if first */
+                 } /* age mod 5 */
+               } /* end loop age */
+               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
+               first=1;
+             } /*l12 */
+           } /* k12 */
+         } /*l1 */
+       }/* k1 */
+     } /* loop covariates */
+     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   }
+   free_vector(xp,1,npar);
+   fclose(ficresprob);
+   fclose(ficresprobcov);
+   fclose(ficresprobcor);
+   fclose(ficgp);
+   fclose(fichtm);
+ }
+ /******************* Printing html file ***********/
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+                   int popforecast, int estepm ,\
+                   double jprev1, double mprev1,double anprev1, \
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
+   /*char optionfilehtm[FILENAMELENGTH];*/
+   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
+   }
+    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+  - Life expectancies by age and initial health status (estepm=%2d months):
+    <a href=\"e%s\">e%s</a> <br>\n</li>", \
+   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+  m=cptcoveff;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
+      /* Pij */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
+ <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+      /* Quasi-incidences */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+ <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+        /* Stable prevalence in each health state */
+        for(cpt=1; cpt<nlstate;cpt++){
+          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+ <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+        }
+      for(cpt=1; cpt<=nlstate;cpt++) {
+         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+ <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and
+ health expectancies in states (1) and (2): e%s%d.png<br>
+ <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+    } /* end i1 */
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
+  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
+  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
+  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+  if(popforecast==1) fprintf(fichtm,"\n
+  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
+  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
+         <br>",fileres,fileres,fileres,fileres);
+  else
+    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
+ fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+  m=cptcoveff;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+ interval) in state (%d): v%s%d%d.png <br>
+ <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+    } /* end i1 */
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
+ fclose(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   int ng;
+   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
+   }
+ #ifdef windows
+     fprintf(ficgp,"cd \"%s\" \n",pathc);
+ #endif
+ m=pow(2,cptcoveff);
+  /* 1eme*/
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
+    for (k1=1; k1<= m ; k1 ++) {
+ #ifdef windows
+      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+ #endif
+ #ifdef unix
+ fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
+ #endif
+ for (i=1; i<= nlstate ; i ++) {
+   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
+     for (i=1; i<= nlstate ; i ++) {
+   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
+   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+ #ifdef unix
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
+ #endif
+    }
+   }
+   /*2 eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+     for (i=1; i<= nlstate+1 ; i ++) {
+       k=2*i;
+       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       fprintf(ficgp,"\" t\"\" w l 0,");
+      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       else fprintf(ficgp,"\" t\"\" w l 0,");
+     }
+   }
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       k=2+nlstate*(2*cpt-2);
+       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ */
+       for (i=1; i< nlstate ; i ++) {
+         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+       }
+     }
+   }
+   /* CV preval stat */
+     for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<nlstate ; cpt ++) {
+       k=3;
+       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       for (i=1; i< nlstate ; i ++)
+         fprintf(ficgp,"+$%d",k+i+1);
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+       l=3+(nlstate+ndeath)*cpt;
+       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+       for (i=1; i< nlstate ; i ++) {
+         l=3+(nlstate+ndeath)*cpt;
+         fprintf(ficgp,"+$%d",l+i+1);
+       }
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+     }
+   }
+   /* proba elementaires */
+    for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         for(j=1; j <=ncovmodel; j++){
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
+           fprintf(ficgp,"\n");
+         }
+       }
+     }
+    }
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+      for(jk=1; jk <=m; jk++) {
+        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
+        if (ng==2)
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+        else
+          fprintf(ficgp,"\nset title \"Probability\"\n");
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+        i=1;
+        for(k2=1; k2<=nlstate; k2++) {
+          k3=i;
+          for(k=1; k<=(nlstate+ndeath); k++) {
+            if (k != k2){
+              if(ng==2)
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+              else
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+              ij=1;
+              for(j=3; j <=ncovmodel; j++) {
+                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                  ij++;
+                }
+                else
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+              }
+              fprintf(ficgp,")/(1");
+              for(k1=1; k1 <=nlstate; k1++){
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                ij=1;
+                for(j=3; j <=ncovmodel; j++){
+                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                    ij++;
+                  }
+                  else
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                }
+                fprintf(ficgp,")");
+              }
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+              i=i+ncovmodel;
+            }
+          } /* end k */
+        } /* end k2 */
+      } /* end jk */
+    } /* end ng */
+    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);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
- if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
+   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);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   }
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   fprintf(ficlog,"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);
+       fprintf(ficlog,"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);
-     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+   if (popforecast==1) {
-     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+     free_ivector(popage,0,AGESUP);
-     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+     free_vector(popeffectif,0,AGESUP);
-     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+     free_vector(popcount,0,AGESUP);
- }
+   }
-  free_vector(xp,1,npar);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- fclose(ficresprob);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  exit(0);
+   fclose(ficrespop);
  }
  /***********************************************/
- Line 1888  int main(int argc, char *argv[])
+ Line 3040  int main(int argc, char *argv[])
    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
    double agedeb, agefin,hf;
-   double agemin=1.e20, agemax=-1.e20;
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
    double fret;
    double **xi,tmp,delta;
- Line 1897  int main(int argc, char *argv[])
+ Line 3049  int main(int argc, char *argv[])
    double ***p3mat;
    int *indx;
    char line[MAXLINE], linepar[MAXLINE];
-   char title[MAXLINE];
+   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
-   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
-   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
-   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
-   char filerest[FILENAMELENGTH];
-   char fileregp[FILENAMELENGTH];
-   char popfile[FILENAMELENGTH];
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
    int firstobs=1, lastobs=10;
    int sdeb, sfin; /* Status at beginning and end */
    int c,  h , cpt,l;
- Line 1915  int main(int argc, char *argv[])
+ Line 3058  int main(int argc, char *argv[])
    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
    int mobilav=0,popforecast=0;
    int hstepm, nhstepm;
-   int *popage;/*boolprev=0 if date and zero if wave*/
+   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
-   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
    double bage, fage, age, agelim, agebase;
    double ftolpl=FTOL;
- Line 1931  int main(int argc, char *argv[])
+ Line 3073  int main(int argc, char *argv[])
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
    double kk1, kk2;
-   double *popeffectif,*popcount;
+   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
-   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
-   double yp,yp1,yp2;
-   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";
    char *alph[]={"a","a","b","c","d","e"}, str[4];
- Line 1948  int main(int argc, char *argv[])
+ Line 3088  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 1970  int main(int argc, char *argv[])
+ Line 3110  int main(int argc, char *argv[])
  /*-------- arguments in the command line --------*/
+   /* Log file */
+   strcat(filelog, optionfilefiname);
+   strcat(filelog,".log");    /* */
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
+   fprintf(ficlog,"\n%s",version);
+   fprintf(ficlog,"\nEnter the parameter file name: ");
+   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   fflush(ficlog);
+   /* */
    strcpy(fileres,"r");
    strcat(fileres, optionfilefiname);
    strcat(fileres,".txt");    /* Other files have txt extension */
- Line 1978  int main(int argc, char *argv[])
+ Line 3132  int main(int argc, char *argv[])
    if((ficpar=fopen(optionfile,"r"))==NULL)    {
      printf("Problem with optionfile %s\n",optionfile);
+     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
      goto end;
    }
    strcpy(filereso,"o");
    strcat(filereso,fileres);
    if((ficparo=fopen(filereso,"w"))==NULL) {
-     printf("Problem with Output resultfile: %s\n", filereso);goto end;
+     printf("Problem with Output resultfile: %s\n", filereso);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     goto end;
    }
    /* Reads comments: lines beginning with '#' */
- Line 1996  int main(int argc, char *argv[])
+ Line 3153  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 model=%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 2030  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3187  while((c=getc(ficpar))=='#' && c!= EOF){
      for(j=1; j <=nlstate+ndeath-1; j++){
        fscanf(ficpar,"%1d%1d",&i1,&j1);
        fprintf(ficparo,"%1d%1d",i1,j1);
-       printf("%1d%1d",i,j);
+       if(mle==1)
+         printf("%1d%1d",i,j);
+       fprintf(ficlog,"%1d%1d",i,j);
        for(k=1; k<=ncovmodel;k++){
          fscanf(ficpar," %lf",&param[i][j][k]);
-         printf(" %lf",param[i][j][k]);
+         if(mle==1){
+           printf(" %lf",param[i][j][k]);
+           fprintf(ficlog," %lf",param[i][j][k]);
+         }
+         else
+           fprintf(ficlog," %lf",param[i][j][k]);
          fprintf(ficparo," %lf",param[i][j][k]);
        }
        fscanf(ficpar,"\n");
-       printf("\n");
+       if(mle==1)
+         printf("\n");
+       fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
- Line 2085  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3251  while((c=getc(ficpar))=='#' && c!= EOF){
    matcov=matrix(1,npar,1,npar);
    for(i=1; i <=npar; i++){
      fscanf(ficpar,"%s",&str);
-     printf("%s",str);
+     if(mle==1)
+       printf("%s",str);
+     fprintf(ficlog,"%s",str);
      fprintf(ficparo,"%s",str);
      for(j=1; j <=i; j++){
        fscanf(ficpar," %le",&matcov[i][j]);
-       printf(" %.5le",matcov[i][j]);
+       if(mle==1){
+         printf(" %.5le",matcov[i][j]);
+         fprintf(ficlog," %.5le",matcov[i][j]);
+       }
+       else
+         fprintf(ficlog," %.5le",matcov[i][j]);
        fprintf(ficparo," %.5le",matcov[i][j]);
      }
      fscanf(ficpar,"\n");
-     printf("\n");
+     if(mle==1)
+       printf("\n");
+     fprintf(ficlog,"\n");
      fprintf(ficparo,"\n");
    }
    for(i=1; i <=npar; i++)
      for(j=i+1;j<=npar;j++)
        matcov[i][j]=matcov[j][i];
-   printf("\n");
+   if(mle==1)
+     printf("\n");
+   fprintf(ficlog,"\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(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
      }
      fprintf(ficres,"#%s\n",version);
+     /*-------- data file ----------*/
      if((fic=fopen(datafile,"r"))==NULL)    {
        printf("Problem with datafile: %s\n", datafile);goto end;
+       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
      }
      n= lastobs;
- Line 2150  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3334  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 3353  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);
+   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
    Tprod=ivector(1,15);
    Tvaraff=ivector(1,15);
    Tvard=imatrix(1,15,1,2);
- Line 2188  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3373  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);
+       fprintf(ficlog,"Error. Non available option model=%s ",model);
        goto end;
      }
      for(i=(j+1); i>=1;i--){
-       cutv(stra,strb,modelsav,'+');
+       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
        /*scanf("%d",i);*/
-       if (strchr(strb,'*')) {
+       if (strchr(strb,'*')) {  /* Model includes a product */
-         cutv(strd,strc,strb,'*');
+         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
-         if (strcmp(strc,"age")==0) {
+         if (strcmp(strc,"age")==0) { /* Vn*age */
            cptcovprod--;
            cutv(strb,stre,strd,'V');
-           Tvar[i]=atoi(stre);
+           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
            cptcovage++;
              Tage[cptcovage]=i;
              /*printf("stre=%s ", stre);*/
          }
-         else if (strcmp(strd,"age")==0) {
+         else if (strcmp(strd,"age")==0) { /* or age*Vn */
            cptcovprod--;
            cutv(strb,stre,strc,'V');
            Tvar[i]=atoi(stre);
            cptcovage++;
            Tage[cptcovage]=i;
          }
-         else {
+         else {  /* Age is not in the model */
-           cutv(strb,stre,strc,'V');
+           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncov+k1;
+           Tvar[i]=ncovcol+k1;
-           cutv(strb,strc,strd,'V');
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
            Tprod[k1]=i;
-           Tvard[k1][1]=atoi(strc);
+           Tvard[k1][1]=atoi(strc); /* m*/
-           Tvard[k1][2]=atoi(stre);
+           Tvard[k1][2]=atoi(stre); /* n */
            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;
          }
        }
-       else {
+       else { /* no more sum */
          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
         /*  scanf("%d",i);*/
        cutv(strd,strc,strb,'V');
- Line 2241  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3426  while((c=getc(ficpar))=='#' && c!= EOF){
        strcpy(modelsav,stra);
        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
          scanf("%d",i);*/
-     }
+     } /* end of loop + */
- }
+   } /* end model */
-   /*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);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
    scanf("%d ",i);*/
      fclose(fic);
- Line 2256  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3442  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);
+               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                agev[m][i]=-1;
                }
              }
- Line 2306  while((c=getc(ficpar))=='#' && c!= EOF){
+ Line 3497  while((c=getc(ficpar))=='#' && c!= EOF){
      for (i=1; i<=imx; i++)  {
        for(m=1; (m<= maxwav); m++){
          if (s[m][i] > (nlstate+ndeath)) {
-           printf("Error: Wrong value in nlstate or ndeath\n");
+           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
            goto end;
          }
        }
      }
  printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
      free_vector(severity,1,maxwav);
      free_imatrix(outcome,1,maxwav+1,1,n);
- Line 2329  printf("Total number of individuals= %d,
+ Line 3522  printf("Total number of individuals= %d,
      mw=imatrix(1,lastpass-firstpass+1,1,imx);
      /* Concatenates waves */
        concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-       Tcode=ivector(1,100);
-       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-       ncodemax[1]=1;
-       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-    codtab=imatrix(1,100,1,10);
-    h=0;
-    m=pow(2,cptcoveff);
-    for(k=1;k<=cptcoveff; k++){
-      for(i=1; i <=(m/pow(2,k));i++){
-        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;
-          }
-        }
-      }
-    }
-    /*for(i=1; i <=m ;i++){
-      for(k=1; k <=cptcovn; k++){
-        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
-      }
-      printf("\n");
-    }
-    scanf("%d",i);*/
-    /* Calculates basic frequencies. Computes observed prevalence at single age
-        and prints on file fileres'p'. */
-     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     /* For Powell, parameters are in a vector p[] starting at p[1]
-        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-     if(mle==1){
-     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     }
-     /*--------- results files --------------*/
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d 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);
-    jk=1;
-    fprintf(ficres,"# Parameters\n");
-    printf("# Parameters\n");
-    for(i=1,jk=1; i <=nlstate; i++){
-      for(k=1; k <=(nlstate+ndeath); k++){
-        if (k != i)
-          {
-            printf("%d%d ",i,k);
-            fprintf(ficres,"%1d%1d ",i,k);
-            for(j=1; j <=ncovmodel; j++){
-              printf("%f ",p[jk]);
-              fprintf(ficres,"%f ",p[jk]);
-              jk++;
-            }
-            printf("\n");
-            fprintf(ficres,"\n");
-          }
-      }
-    }
-  if(mle==1){
-     /* Computing hessian and covariance matrix */
-     ftolhess=ftol; /* Usually correct */
-     hesscov(matcov, p, npar, delti, ftolhess, func);
-  }
-     fprintf(ficres,"# Scales\n");
-     printf("# Scales\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++){
+       Tcode=ivector(1,100);
-     for(k=1; k <=(nlstate+ndeath); k++){
+       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-       if (k != i) {
+       ncodemax[1]=1;
-         for(j=1; j <=ncovmodel; j++){
+       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
-           /*fprintf(ficgp,"%s",alph[1]);*/
+    codtab=imatrix(1,100,1,10);
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+    h=0;
-           jk++;
+    m=pow(2,cptcoveff);
-           fprintf(ficgp,"\n");
-         }
+    for(k=1;k<=cptcoveff; k++){
+      for(i=1; i <=(m/pow(2,k));i++){
+        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;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(k=1; k <=cptcovn; k++){
+       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
+       printf("\n");
+       }
+       scanf("%d",i);*/
+    /* Calculates basic frequencies. Computes observed prevalence at single age
+        and prints on file fileres'p'. */
+     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+     /* For Powell, parameters are in a vector p[] starting at p[1]
+        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+     if(mle==1){
+     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
      }
-     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
-   for(jk=1; jk <=m; jk++) {
+    jk=1;
-   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
+    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-    i=1;
+    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-    for(k2=1; k2<=nlstate; k2++) {
+    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-      k3=i;
+    for(i=1,jk=1; i <=nlstate; i++){
-      for(k=1; k<=(nlstate+ndeath); k++) {
+      for(k=1; k <=(nlstate+ndeath); k++){
-        if (k != k2){
+        if (k != i)
-         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+          {
- ij=1;
+            printf("%d%d ",i,k);
-         for(j=3; j <=ncovmodel; j++) {
+            fprintf(ficlog,"%d%d ",i,k);
-           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+            fprintf(ficres,"%1d%1d ",i,k);
-             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+            for(j=1; j <=ncovmodel; j++){
-             ij++;
+              printf("%f ",p[jk]);
-           }
+              fprintf(ficlog,"%f ",p[jk]);
-           else
+              fprintf(ficres,"%f ",p[jk]);
-           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+              jk++;
-         }
+            }
-           fprintf(ficgp,")/(1");
+            printf("\n");
+            fprintf(ficlog,"\n");
-         for(k1=1; k1 <=nlstate; k1++){
+            fprintf(ficres,"\n");
-           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)) {
+    if(mle==1){
-             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+      /* Computing hessian and covariance matrix */
-             ij++;
+      ftolhess=ftol; /* Usually correct */
-           }
+      hesscov(matcov, p, npar, delti, ftolhess, func);
-           else
+    }
-             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-           }
+    printf("# Scales (for hessian or gradient estimation)\n");
-           fprintf(ficgp,")");
+    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-         }
+    for(i=1,jk=1; i <=nlstate; i++){
-         fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+      for(j=1; j <=nlstate+ndeath; j++){
-         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+        if (j!=i) {
-         i=i+ncovmodel;
+          fprintf(ficres,"%1d%1d",i,j);
+          printf("%1d%1d",i,j);
+          fprintf(ficlog,"%1d%1d",i,j);
+          for(k=1; k<=ncovmodel;k++){
+            printf(" %.5e",delti[jk]);
+            fprintf(ficlog," %.5e",delti[jk]);
+            fprintf(ficres," %.5e",delti[jk]);
+            jk++;
+          }
+          printf("\n");
+          fprintf(ficlog,"\n");
+          fprintf(ficres,"\n");
         }
       }
     }
-    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
-   }
-   fclose(ficgp);
+    k=1;
-   /* end gnuplot */
+    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+    if(mle==1)
+      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+    fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+    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);
+      if(mle==1)
+        printf("%3d",i);
+      fprintf(ficlog,"%3d",i);
+      for(j=1; j<=i;j++){
+        fprintf(ficres," %.5e",matcov[i][j]);
+        if(mle==1)
+          printf(" %.5e",matcov[i][j]);
+        fprintf(ficlog," %.5e",matcov[i][j]);
+      }
+      fprintf(ficres,"\n");
+      if(mle==1)
+        printf("\n");
+      fprintf(ficlog,"\n");
+      k++;
+    }
- chdir(path);
+    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;
+    }
-     free_ivector(wav,1,imx);
+    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-     free_ivector(num,1,n);
-     free_vector(agedc,1,n);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-     fclose(ficparo);
-     fclose(ficres);
-     /*  }*/
-    /*________fin mle=1_________*/
+    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\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
+    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);
+      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);
-     /* No more information from the sample is required now */
-   /* Reads comments: lines beginning with '#' */
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
- Line 2698  chdir(path);
+ Line 3709  chdir(path);
      fputs(line,ficparo);
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
+   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);
-   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
+ 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(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
+ fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+ while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
+   }
+   ungetc(c,ficpar);
+   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+ /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
+   strcat(optionfilegnuplot,".gp");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+   fclose(ficgp);
+  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
  /*--------- index.htm --------*/
    strcpy(optionfilehtm,optionfile);
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtm);goto end;
+     printf("Problem with %s \n",optionfilehtm), exit(0);
    }
-  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
+   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
- Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
- Total number of observations=%d <br>
+ \n
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
+ Total number of observations=%d <br>\n
- <hr  size=\"2\" color=\"#EC5E5E\">
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
- <li>Outputs files<br><br>\n
+ <hr  size=\"2\" color=\"#EC5E5E\">
-         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+  <ul><li><h4>Parameter files</h4>\n
- - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
-         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n
-         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
+  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
-         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
+   fclose(fichtm);
-         - 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>
+  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-         - 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>
+ /*------------ free_vector  -------------*/
-         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
+  chdir(path);
- <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
+  free_ivector(wav,1,imx);
-  fprintf(fichtm," <li>Graphs</li><p>");
+  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-  m=cptcoveff;
+  free_ivector(num,1,n);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  free_vector(agedc,1,n);
+  /*free_matrix(covar,1,NCOVMAX,1,n);*/
+  fclose(ficparo);
+  fclose(ficres);
-  j1=0;
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
-        j1++;
-        if (cptcovn > 0) {
-          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-          for (cpt=1; cpt<=cptcoveff;cpt++)
-            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
-          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-        }
-        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
- <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
-        for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
- <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-        }
-     for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
- interval) in state (%d): v%s%d%d.gif <br>
- <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-      }
-      for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
- <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-      }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and
- health expectancies in states (1) and (2): e%s%d.gif<br>
- <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
- fprintf(fichtm,"\n</body>");
-    }
-  }
- fclose(fichtm);
    /*--------------- Prevalence limit --------------*/
- Line 2772  fclose(fichtm);
+ Line 3778  fclose(fichtm);
    strcat(filerespl,fileres);
    if((ficrespl=fopen(filerespl,"w"))==NULL) {
      printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
+     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
    }
    printf("Computing prevalence limit: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
    fprintf(ficrespl,"#Prevalence limit\n");
    fprintf(ficrespl,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
- Line 2786  fclose(fichtm);
+ Line 3794  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 2797  fclose(fichtm);
+ Line 3805  fclose(fichtm);
          k=k+1;
          /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
          fprintf(ficrespl,"\n#******");
-         for(j=1;j<=cptcoveff;j++)
+         printf("\n#******");
+         fprintf(ficlog,"\n#******");
+         for(j=1;j<=cptcoveff;j++) {
            fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
          fprintf(ficrespl,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
          for (age=agebase; age<=agelim; age++){
            prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
- Line 2817  fclose(fichtm);
+ Line 3832  fclose(fichtm);
    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
    if((ficrespij=fopen(filerespij,"w"))==NULL) {
      printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
    }
    printf("Computing pij: result on file '%s' \n", filerespij);
+   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
    stepsize=(int) (stepm+YEARM-1)/YEARM;
    /*if (stepm<=24) stepsize=2;*/
- Line 2826  fclose(fichtm);
+ Line 3843  fclose(fichtm);
    agelim=AGESUP;
    hstepm=stepsize*YEARM; /* Every year of age */
    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+   /* hstepm=1;   aff par mois*/
    k=0;
    for(cptcov=1;cptcov<=i1;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- Line 2839  fclose(fichtm);
+ Line 3858  fclose(fichtm);
          for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
            nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
            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);
- Line 2847  fclose(fichtm);
+ Line 3869  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 );
+             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
              for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate+ndeath;j++)
                  fprintf(ficrespij," %.5f", p3mat[i][j][h]);
              fprintf(ficrespij,"\n");
-           }
+              }
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            fprintf(ficrespij,"\n");
          }
      }
    }
-   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
+   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
    fclose(ficrespij);
-   if(stepm == 1) {
-   /*---------- Forecasting ------------------*/
-   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
-   /*printf("calage= %f", calagedate);*/
-   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
-   strcpy(fileresf,"f");
-   strcat(fileresf,fileres);
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
-     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
-   }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   free_matrix(mint,1,maxwav,1,n);
-   free_matrix(anint,1,maxwav,1,n);
-   free_matrix(agev,1,maxwav,1,imx);
-   /* Mobile average */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (mobilav==1) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
-       for (i=1; i<=nlstate;i++)
-         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
-           mobaverage[(int)agedeb][i][cptcod]=0.;
-     for (agedeb=bage+4; agedeb<=fage; agedeb++){
-       for (i=1; i<=nlstate;i++){
-         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-           for (cpt=0;cpt<=4;cpt++){
-             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
-           }
-           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
-         }
-       }
-     }
-   }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (stepm<=12) stepsize=1;
-   agelim=AGESUP;
-   /*hstepm=stepsize*YEARM; *//* Every year of age */
-   hstepm=1;
-   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */
-   yp1=modf(dateintmean,&yp);
-   anprojmean=yp;
-   yp2=modf((yp1*12),&yp);
-   mprojmean=yp;
-   yp1=modf((yp2*30.5),&yp);
-   jprojmean=yp;
-   if(jprojmean==0) jprojmean=1;
-   if(mprojmean==0) jprojmean=1;
-   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
-   if (popforecast==1) {
-     if((ficpop=fopen(popfile,"r"))==NULL)    {
-       printf("Problem with population file : %s\n",popfile);goto end;
-     }
-     popage=ivector(0,AGESUP);
-     popeffectif=vector(0,AGESUP);
-     popcount=vector(0,AGESUP);
-     i=1;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
-       {
-         i=i+1;
-       }
-     imx=i;
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   }
-   for(cptcov=1;cptcov<=i1;cptcov++){
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       k=k+1;
-       fprintf(ficresf,"\n#******");
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
-       fprintf(ficresf,"******\n");
-       fprintf(ficresf,"# StartingAge FinalAge");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
-       if (popforecast==1)  fprintf(ficresf," [Population]");
-       for (cpt=0; cpt<4;cpt++) {
-         fprintf(ficresf,"\n");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
-         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */
-         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-         nhstepm = nhstepm/hstepm;
-         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-         for (h=0; h<=nhstepm; h++){
-           if (h==(int) (calagedate+YEARM*cpt)) {
-             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
-           }
-           for(j=1; j<=nlstate+ndeath;j++) {
-             kk1=0.;kk2=0;
-             for(i=1; i<=nlstate;i++) {
-               if (mobilav==1)
-                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-               else {
-                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/
-               }
-               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
+   /*---------- Forecasting ------------------*/
-             }
+   if((stepm == 1) && (strcmp(model,".")==0)){
+     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
-             if (h==(int)(calagedate+12*cpt)){
+     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
-               fprintf(ficresf," %.3f", kk1);
+   }
-               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
-             }
-           }
-         }
-         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/
-       }
-       }
-     }
-   }
-   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if (popforecast==1) {
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
-     free_vector(popcount,0,AGESUP);
-   }
-   free_imatrix(s,1,maxwav+1,1,n);
-   free_vector(weight,1,n);*/
-   fclose(ficresf);
-   }/* End forecasting */
    else{
      erreur=108;
-     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);
+     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
    }
    /*---------- Health expectancies and variances ------------*/
- Line 3017  fclose(fichtm);
+ Line 3905  fclose(fichtm);
    strcat(filerest,fileres);
    if((ficrest=fopen(filerest,"w"))==NULL) {
      printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
    }
    printf("Computing Total LEs with variances: file '%s' \n", filerest);
+   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
    strcpy(filerese,"e");
    strcat(filerese,fileres);
    if((ficreseij=fopen(filerese,"w"))==NULL) {
      printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
    }
    printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-  strcpy(fileresv,"v");
+   strcpy(fileresv,"v");
    strcat(fileresv,fileres);
    if((ficresvij=fopen(fileresv,"w"))==NULL) {
      printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
    }
    printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   fprintf(ficlog,"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++){
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        k=k+1;
        fprintf(ficrest,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- Line 3046  fclose(fichtm);
+ Line 3942  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(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);
+       if(popbased==1){
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);
+        }
        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 3974  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 4013  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 4044  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)
+   fprintf(fichtm,"\n</body>");
-     printf("End of Imach with error %d\n",erreur);
+   fclose(fichtm);
-   else   printf("End of Imach\n");
+   fclose(ficgp);
+   if(erreur >0){
+     printf("End of Imach with error or warning %d\n",erreur);
+     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+   }else{
+    printf("End of Imach\n");
+    fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   fclose(ficlog);
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
    /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
- Line 3173  strcpy(fileresvpl,"vpl");
+ Line 4083  strcpy(fileresvpl,"vpl");
  #ifdef windows
    while (z[0] != 'q') {
-     chdir(path);
+     /* chdir(path); */
-     printf("\nType e to edit output files, c to start again, and q for exiting: ");
+     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
      scanf("%s",z);
      if (z[0] == 'c') system("./imach");
-     else if (z[0] == 'e') {
+     else if (z[0] == 'e') system(optionfilehtm);
-       chdir(path);
+     else if (z[0] == 'g') system(plotcmd);
-       system(optionfilehtm);
-     }
      else if (z[0] == 'q') exit(0);
    }
  #endif

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>

Removed from v.1.24
changed lines
	Added in v.1.51