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Diff for /imach/src/imach.c between versions 1.6 and 1.40

-version 1.6, 2001/05/02 17:47:10
+version 1.40, 2002/04/19 13:46:19
  Line 1
+ /* $Id$
- /*********************** Imach **************************************
+    Interpolated Markov Chain
-   This program computes Healthy Life Expectancies from cross-longitudinal
-   data. Cross-longitudinal consist in a first survey ("cross") where
+   Short summary of the programme:
-   individuals from different ages are interviewed on their health status
-   or degree of  disability. At least a second wave of interviews
+   This program computes Healthy Life Expectancies from
-   ("longitudinal") should  measure each new individual health status.
+   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
-   Health expectancies are computed from the transistions observed between
+   first survey ("cross") where individuals from different ages are
-   waves and are computed for each degree of severity of disability (number
+   interviewed on their health status or degree of disability (in the
-   of life states). More degrees you consider, more time is necessary to
+   case of a health survey which is our main interest) -2- at least a
-   reach the Maximum Likelihood of the parameters involved in the model.
+   second wave of interviews ("longitudinal") which measure each change
-   The simplest model is the multinomial logistic model where pij is
+   (if any) in individual health status.  Health expectancies are
-   the probabibility to be observed in state j at the second wave conditional
+   computed from the time spent in each health state according to a
-   to be observed in state i at the first wave. Therefore the model is:
+   model. More health states you consider, more time is necessary to reach the
-   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'
+   Maximum Likelihood of the parameters involved in the model.  The
-   is a covariate. If you want to have a more complex model than "constant and
+   simplest model is the multinomial logistic model where pij is the
-   age", you should modify the program where the markup
+   probability to be observed in state j at the second wave
-     *Covariates have to be included here again* invites you to do it.
+   conditional to be observed in state i at the first wave. Therefore
-   More covariates you add, less is the speed of the convergence.
+   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
-   The advantage that this computer programme claims, comes from that if the
+   complex model than "constant and age", you should modify the program
-   delay between waves is not identical for each individual, or if some
+   where the markup *Covariates have to be included here again* invites
-   individual missed an interview, the information is not rounded or lost, but
+   you to do it.  More covariates you add, slower the
-   taken into account using an interpolation or extrapolation.
+   convergence.
-   hPijx is the probability to be
-   observed in state i at age x+h conditional to the observed state i at age
+   The advantage of this computer programme, compared to a simple
-   x. The delay 'h' can be split into an exact number (nh*stepm) of
+   multinomial logistic model, is clear when the delay between waves is not
-   unobserved intermediate  states. This elementary transition (by month or
+   identical for each individual. Also, if a individual missed an
-   quarter trimester, semester or year) is model as a multinomial logistic.
+   intermediate interview, the information is lost, but taken into
-   The hPx matrix is simply the matrix product of nh*stepm elementary matrices
+   account using an interpolation or extrapolation.
-   and the contribution of each individual to the likelihood is simply hPijx.
+   hPijx is the probability to be observed in state i at age x+h
+   conditional to the observed state i at age x. The delay 'h' can be
+   split into an exact number (nh*stepm) of unobserved intermediate
+   states. This elementary transition (by month or quarter trimester,
+   semester or year) is model as a multinomial logistic.  The hPx
+   matrix is simply the matrix product of nh*stepm elementary matrices
+   and the contribution of each individual to the likelihood is simply
+   hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the prevalence limits.
- Line 48
+ Line 56
  #include <unistd.h>
  #define MAXLINE 256
+ #define GNUPLOTPROGRAM "wgnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
  #define FILENAMELENGTH 80
  /*#define DEBUG*/
  #define windows
- Line 67
+ Line 77
  #define AGEBASE 40
+ int erreur; /* Error number */
  int nvar;
- static int cptcov;
+ int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
- int cptcovn, cptcovage=0;
  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 */
  int maxwav; /* Maxim number of waves */
+ int jmin, jmax; /* min, max spacing between 2 waves */
  int mle, weightopt;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ 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;
+ FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficgp, *fichtm;
+ FILE *ficgp,*ficresprob,*ficpop;
  FILE *ficreseij;
    char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
- Line 111  FILE *ficreseij;
+ Line 124  FILE *ficreseij;
  static double maxarg1,maxarg2;
  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  #define rint(a) floor(a+0.5)
- Line 123  int imx;
+ Line 136  int imx;
  int stepm;
  /* Stepm, step in month: minimum step interpolation*/
+ int estepm;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  int m,nb;
  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij;
+ double **pmmij, ***probs, ***mobaverage;
+ double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc, **covar, idx;
- int **nbcode, *Tcode, *Tvar, **codtab;
+ int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
  double ftolhess; /* Tolerance for computing hessian */
+ /**************** split *************************/
- static  int split( char *path, char *dirc, char *name )
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
  {
     char *s;                             /* pointer */
     int  l1, l2;                         /* length counters */
     l1 = strlen( path );                 /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #ifdef windows
     s = strrchr( path, '\\' );           /* find last / */
+ #else
+    s = strrchr( path, '/' );            /* find last / */
+ #endif
     if ( s == NULL ) {                   /* no directory, so use current */
  #if     defined(__bsd__)                /* get current working directory */
        extern char       *getwd( );
- Line 167  static int split( char *path, char *dirc
+ Line 188  static int split( char *path, char *dirc
        dirc[l1-l2] = 0;                  /* add zero */
     }
     l1 = strlen( dirc );                 /* length of directory */
+ #ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+ #else
+    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+ #endif
+    s = strrchr( name, '.' );            /* find last / */
+    s++;
+    strcpy(ext,s);                       /* save extension */
+    l1= strlen( name);
+    l2= strlen( s)+1;
+    strncpy( finame, name, l1-l2);
+    finame[l1-l2]= 0;
     return( 0 );                         /* we're done */
  }
- Line 657  double **prevalim(double **prlim, int nl
+ Line 689  double **prevalim(double **prlim, int nl
       cov[2]=agefin;
        for (k=1; k<=cptcovn;k++) {
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[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]]);*/
- /*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/
        }
-       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 688  double **prevalim(double **prlim, int nl
+ Line 723  double **prevalim(double **prlim, int nl
    }
  }
- /*************** transition probabilities **********/
+ /*************** transition probabilities ***************/
  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
- Line 714  double **pmij(double **ps, double *cov,
+ Line 749  double **pmij(double **ps, double *cov,
        ps[i][j]=s2;
      }
    }
+     /*ps[3][2]=1;*/
    for(i=1; i<= nlstate; i++){
       s1=0;
      for(j=1; j<i; j++)
- Line 735  double **pmij(double **ps, double *cov,
+ Line 772  double **pmij(double **ps, double *cov,
      }
    }
    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
      for(jj=1; jj<= nlstate+ndeath; jj++){
       printf("%lf ",ps[ii][jj]);
- Line 752  double **pmij(double **ps, double *cov,
+ Line 790  double **pmij(double **ps, double *cov,
  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
  {
-   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
    /* in, b, out are matrice of pointers which should have been initialized
       before: only the contents of out is modified. The function returns
- Line 798  double ***hpxij(double ***po, int nhstep
+ Line 836  double ***hpxij(double ***po, int nhstep
        /* Covariates have to be included here again */
        cov[1]=1.;
        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       if (cptcovn>0){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][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]]];
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 832  double func( double *x)
+ Line 874  double func( double *x)
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
    /*for(i=1;i<imx;i++)
- printf(" %d\n",s[4][i]);
+     printf(" %d\n",s[4][i]);
    */
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-        for(mi=1; mi<= wav[i]-1; mi++){
+     for(mi=1; mi<= wav[i]-1; mi++){
        for (ii=1;ii<=nlstate+ndeath;ii++)
          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             for(d=0; d<dh[mi][i]; d++){
+       for(d=0; d<dh[mi][i]; d++){
-               newm=savm;
+         newm=savm;
-               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-               for (kk=1; kk<=cptcovage;kk++) {
+         for (kk=1; kk<=cptcovage;kk++) {
-                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-                  /*printf("%d %d",kk,Tage[kk]);*/
+         }
-               }
-               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-               /*cov[3]=pow(cov[2],2)/1000.;*/
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         savm=oldm;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         oldm=newm;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
-           oldm=newm;
        } /* end mult */
        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
        ipmx +=1;
- Line 890  void mlikeli(FILE *ficres,double p[], in
+ Line 929  void mlikeli(FILE *ficres,double p[], in
    powell(p,xi,npar,ftol,&iter,&fret,func);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  }
- Line 907  void hesscov(double **matcov, double p[]
+ Line 946  void hesscov(double **matcov, double p[]
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
    hess=matrix(1,npar,1,npar);
    printf("\nCalculation of the hessian matrix. Wait...\n");
- Line 915  void hesscov(double **matcov, double p[]
+ Line 953  void hesscov(double **matcov, double p[]
      printf("%d",i);fflush(stdout);
      hess[i][i]=hessii(p,ftolhess,i,delti);
      /*printf(" %f ",p[i]);*/
+     /*printf(" %lf ",hess[i][i]);*/
    }
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++)  {
        if (j>i) {
          printf(".%d%d",i,j);fflush(stdout);
          hess[i][j]=hessij(p,delti,i,j);
          hess[j][i]=hess[i][j];
+         /*printf(" %lf ",hess[i][j]);*/
        }
      }
    }
- Line 1026  double hessii( double x[], double delta,
+ Line 1066  double hessii( double x[], double delta,
      }
    }
    delti[theta]=delts;
    return res;
  }
- Line 1139  void lubksb(double **a, int n, int *indx
+ Line 1179  void lubksb(double **a, int n, int *indx
  }
  /************ Frequencies ********************/
- void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)
+ 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 i, m, jk, k1,i1, j1, bool, z1,z2,j;
    double ***freq; /* Frequencies */
    double *pp;
-   double pos;
+   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) {
- Line 1159  void  freqsummary(char fileres[], int ag
+ Line 1199  void  freqsummary(char fileres[], int ag
    }
    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
    j1=0;
-   j=cptcovn;
+   j=cptcoveff;
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    for(k1=1; k1<=j;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+     for(i1=1; i1<=ncodemax[k1];i1++){
-        j1++;
+       j1++;
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-         for (i=-1; i<=nlstate+ndeath; i++)
+         scanf("%d", i);*/
-          for (jk=-1; jk<=nlstate+ndeath; jk++)
+       for (i=-1; i<=nlstate+ndeath; i++)
-            for(m=agemin; m <= agemax+3; m++)
+         for (jk=-1; jk<=nlstate+ndeath; jk++)
-              freq[i][jk][m]=0;
+           for(m=agemin; m <= agemax+3; m++)
+             freq[i][jk][m]=0;
-        for (i=1; i<=imx; i++) {
-          bool=1;
+       dateintsum=0;
-          if  (cptcovn>0) {
+       k2cpt=0;
-            for (z1=1; z1<=cptcovn; z1++)
+       for (i=1; i<=imx; i++) {
-              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;
+         bool=1;
-          }
+         if  (cptcovn>0) {
-           if (bool==1) {
+           for (z1=1; z1<=cptcoveff; z1++)
-            for(m=firstpass; m<=lastpass-1; m++){
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-              if(agev[m][i]==0) agev[m][i]=agemax+1;
+               bool=0;
-              if(agev[m][i]==1) agev[m][i]=agemax+2;
+         }
-              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+         if (bool==1) {
-              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
+           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  (cptcovn>0) {
+               if(agev[m][i]==1) agev[m][i]=agemax+2;
-          fprintf(ficresp, "\n#Variable");
+               if (m<lastpass) {
-          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);
+                 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];
-        fprintf(ficresp, "\n#");
+               }
-        for(i=1; i<=nlstate;i++)
-          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
-        fprintf(ficresp, "\n");
+                 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");
+       if  (cptcovn>0) {
-     else
+         fprintf(ficresp, "\n#********** Variable ");
-       printf("Age %d", 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 ; jk++){
+         fprintf(ficresp, "**********\n#");
-       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+       }
-         pp[jk] += freq[jk][m][i];
+       for(i=1; i<=nlstate;i++)
-     }
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-     for(jk=1; jk <=nlstate ; jk++){
+       fprintf(ficresp, "\n");
-       for(m=-1, pos=0; m <=0 ; m++)
-         pos += freq[jk][m][i];
+       for(i=(int)agemin; i <= (int)agemax+3; i++){
-       if(pp[jk]>=1.e-10)
+         if(i==(int)agemax+3)
-         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           printf("Total");
-       else
+         else
-         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           printf("Age %d", 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,pos=0; jk <=nlstate ; jk++)
+           for(m=-1, pos=0; m <=0 ; m++)
-       pos += pp[jk];
+             pos += freq[jk][m][i];
-     for(jk=1; jk <=nlstate ; jk++){
+           if(pp[jk]>=1.e-10)
-       if(pos>=1.e-5)
+             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           else
-       else
+             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+         }
-       if( i <= (int) agemax){
-         if(pos>=1.e-5)
+         for(jk=1; jk <=nlstate ; jk++){
-           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-       else
+             pp[jk] += freq[jk][m][i];
-           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+         }
+         for(jk=1,pos=0; jk <=nlstate ; jk++)
+           pos += pp[jk];
+         for(jk=1; jk <=nlstate ; jk++){
+           if(pos>=1.e-5)
+             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           else
+             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           if( i <= (int) agemax){
+             if(pos>=1.e-5){
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+               probs[i][jk][j1]= pp[jk]/pos;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+             }
+             else
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+           }
+         }
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
+           for(m=-1; m <=nlstate+ndeath; m++)
+             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+         if(i <= (int) agemax)
+           fprintf(ficresp,"\n");
+         printf("\n");
        }
      }
-     for(jk=-1; jk <=nlstate+ndeath; jk++)
+   }
-       for(m=-1; m <=nlstate+ndeath; m++)
+   dateintmean=dateintsum/k2cpt;
-         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");
-     }
-     }
-  }
    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, 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;
+   double ***freq; /* Frequencies */
+   double *pp;
+   double pos, k2;
+   pp=vector(1,nlstate);
+   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+   j1=0;
+   j=cptcoveff;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+  for(k1=1; k1<=j;k1++){
+     for(i1=1; i1<=ncodemax[k1];i1++){
+       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;
+               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */
+             }
+           }
+         }
+       }
+         for(i=(int)agemin; i <= (int)agemax+3; i++){
+           for(jk=1; jk <=nlstate ; jk++){
+             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+               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];
+         }
+          for(jk=1; jk <=nlstate ; jk++){
+            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+              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;
+              }
+            }
+          }
+         }
+     }
+   }
+   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+   free_vector(pp,1,nlstate);
  }  /* End of Freq */
  /************* Waves Concatenation ***************/
- Line 1259  void  concatwav(int wav[], int **dh, int
+ Line 1405  void  concatwav(int wav[], int **dh, int
       */
    int i, mi, m;
-   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
- float sum=0.;
+      double sum=0., jmean=0.;*/
+   int j, k=0,jk, ju, jl;
+   double sum=0.;
+   jmin=1e+5;
+   jmax=-1;
+   jmean=0.;
    for(i=1; i<=imx; i++){
      mi=0;
      m=firstpass;
- Line 1291  float sum=0.;
+ Line 1442  float sum=0.;
          dh[mi][i]=1;
        else{
          if (s[mw[mi+1][i]][i] > nlstate) {
+           if (agedc[i] < 2*AGESUP) {
            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           if(j=0) j=1;  /* Survives at least one month after exam */
+           if(j==0) j=1;  /* Survives at least one month after exam */
+           k=k+1;
+           if (j >= jmax) jmax=j;
+           if (j <= jmin) jmin=j;
+           sum=sum+j;
+           /*if (j<0) printf("j=%d num=%d \n",j,i); */
+           }
          }
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
            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); */
            sum=sum+j;
          }
          jk= j/stepm;
- Line 1313  float sum=0.;
+ Line 1472  float sum=0.;
        }
      }
    }
-   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);
+   jmean=sum/k;
- }
+   printf("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)
  {
-   int Ndum[80],ij=1, k, j, i, Ntvar[20];
+   int Ndum[20],ij=1, k, j, i;
    int cptcode=0;
-   for (k=0; k<79; k++) Ndum[k]=0;
+   cptcoveff=0;
+   for (k=0; k<19; k++) Ndum[k]=0;
    for (k=1; k<=7; k++) ncodemax[k]=0;
-   for (j=1; j<=cptcovn; j++) {
+   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
      for (i=1; i<=imx; i++) {
        ij=(int)(covar[Tvar[j]][i]);
        Ndum[ij]++;
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
        if (ij > cptcode) cptcode=ij;
      }
-     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/
      for (i=0; i<=cptcode; i++) {
        if(Ndum[i]!=0) ncodemax[j]++;
      }
      ij=1;
      for (i=1; i<=ncodemax[j]; i++) {
-       for (k=0; k<=79; k++) {
+       for (k=0; k<=19; k++) {
          if (Ndum[k] != 0) {
            nbcode[Tvar[j]][ij]=k;
            ij++;
          }
          if (ij > ncodemax[j]) break;
        }
      }
    }
+  for (k=0; k<19; k++) Ndum[k]=0;
+  for (i=1; i<=ncovmodel-2; i++) {
+       ij=Tvar[i];
+       Ndum[ij]++;
+     }
+  ij=1;
+  for (i=1; i<=10; i++) {
+    if((Ndum[i]!=0) && (i<=ncovcol)){
+      Tvaraff[ij]=i;
+      ij++;
+    }
+  }
+     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)
  {
    /* Health expectancies */
-   int i, j, nhstepm, hstepm, h;
+   int i, j, nhstepm, hstepm, h, nstepm;
-   double age, agelim,hf;
+   double age, agelim, hf;
    double ***p3mat;
    fprintf(ficreseij,"# Health expectancies\n");
- Line 1364  void evsij(char fileres[], double ***eij
+ Line 1545  void evsij(char fileres[], double ***eij
        fprintf(ficreseij," %1d-%1d",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);
      /* 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);
+     /*for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++) printf("%f %.5f\n", age*12+h, p3mat[1][1][h]);*/
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      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]);*/
          }
+     fprintf(ficreseij,"%3.0f",age );
-     hf=1;
-     if (stepm >= YEARM) hf=stepm/YEARM;
-     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]);
+         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);
        }
      fprintf(ficreseij,"\n");
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- Line 1399  void evsij(char fileres[], double ***eij
+ Line 1606  void evsij(char fileres[], double ***eij
  }
  /************ Variance ******************/
- void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+ void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
  {
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    double **newm;
    double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm, h;
+   int i, j, nhstepm, hstepm, h, nstepm ;
    int k, cptcode;
-    double *xp;
+   double *xp;
    double **gp, **gm;
    double ***gradg, ***trgradg;
    double ***p3mat;
-   double age,agelim;
+   double age,agelim, hf;
    int theta;
     fprintf(ficresvij,"# Covariances of life expectancies\n");
- Line 1425  void varevsij(char fileres[], double ***
+ Line 1632  void varevsij(char fileres[], double ***
    dnewm=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
-   hstepm=1*YEARM; /* Every year of age */
+   if(estepm < stepm){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like k years */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
    agelim = AGESUP;
    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     if (stepm >= YEARM) hstepm=1;
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
      gp=matrix(0,nhstepm,1,nlstate);
- Line 1443  void varevsij(char fileres[], double ***
+ Line 1664  void varevsij(char fileres[], double ***
        }
        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];
+       }
        for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
- Line 1454  void varevsij(char fileres[], double ***
+ Line 1681  void varevsij(char fileres[], double ***
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if (popbased==1) {
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=probs[(int)age][i][ij];
+       }
        for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){
            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
        for(j=1; j<= nlstate; j++)
          for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
- Line 1473  void varevsij(char fileres[], double ***
+ Line 1707  void varevsij(char fileres[], double ***
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)
          vareij[i][j][(int)age] =0.;
      for(h=0;h<=nhstepm;h++){
        for(k=0;k<=nhstepm;k++){
          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
          for(i=1;i<=nlstate;i++)
            for(j=1;j<=nlstate;j++)
-             vareij[i][j][(int)age] += doldm[i][j];
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        }
      }
-     h=1;
-     if (stepm >= YEARM) h=stepm/YEARM;
      fprintf(ficresvij,"%.0f ",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
-         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
        }
      fprintf(ficresvij,"\n");
      free_matrix(gp,0,nhstepm,1,nlstate);
- Line 1499  void varevsij(char fileres[], double ***
+ Line 1734  void varevsij(char fileres[], double ***
      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    } /* End age */
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,npar);
    free_matrix(dnewm,1,nlstate,1,nlstate);
- Line 1589  void varprevlim(char fileres[], double *
+ Line 1824  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, int *Tvar, int **nbcode, int *ncodemax)
- /***********************************************/
- /**************** Main Program *****************/
- /***********************************************/
- /*int main(int argc, char *argv[])*/
- int main()
  {
+   int i, j, i1, k1, j1, z1;
+   int k=0, cptcode;
+   double **dnewm,**doldm;
+   double *xp;
+   double *gp, *gm;
+   double **gradg, **trgradg;
+   double age,agelim, cov[NCOVMAX];
+   int theta;
+   char fileresprob[FILENAMELENGTH];
-   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;
+   strcpy(fileresprob,"prob");
-   double agedeb, agefin,hf;
+   strcat(fileresprob,fileres);
-   double agemin=1.e20, agemax=-1.e20;
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprob);
-   double fret;
+   }
-   double **xi,tmp,delta;
+   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
-   double dum; /* Dummy variable */
-   double ***p3mat;
-   int *indx;
-   char line[MAXLINE], linepar[MAXLINE];
-   char title[MAXLINE];
-   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
-   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
-   char filerest[FILENAMELENGTH];
-   char fileregp[FILENAMELENGTH];
-   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
-   int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
-   int c,  h , cpt,l;
-   int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
-   int hstepm, nhstepm;
-   double bage, fage, age, agelim, agebase;
-   double ftolpl=FTOL;
-   double **prlim;
-   double *severity;
-   double ***param; /* Matrix of parameters */
-   double  *p;
-   double **matcov; /* Matrix of covariance */
-   double ***delti3; /* Scale */
-   double *delti; /* Scale */
-   double ***eij, ***vareij;
-   double **varpl; /* Variances of prevalence limits by age */
-   double *epj, vepp;
-   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
-   char z[1]="c", occ;
+   xp=vector(1,npar);
- #include <sys/time.h>
+   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
- #include <time.h>
+   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   /* long total_usecs;
-   struct timeval start_time, end_time;
-   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   cov[1]=1;
+   j=cptcoveff;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   j1=0;
+   for(k1=1; k1<=1;k1++){
+     for(i1=1; i1<=ncodemax[k1];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#");
+     }
+       for (age=bage; age<=fage; age ++){
+         cov[2]=age;
+         for (k=1; k<=cptcovn;k++) {
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+         }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+         for (k=1; k<=cptcovprod;k++)
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         gradg=matrix(1,npar,1,9);
+         trgradg=matrix(1,9,1,npar);
+         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
+         for(theta=1; theta <=npar; theta++){
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<= (nlstate+ndeath); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gp[k]=pmmij[i][j];
+             }
+           }
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] - (i==theta ?delti[theta]:0);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+           k=0;
+           for(i=1; i<=(nlstate+ndeath); i++){
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
+               gm[k]=pmmij[i][j];
+             }
+           }
+           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
+             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
+         }
-   printf("\nIMACH, Version 0.64a");
+         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
-   printf("\nEnter the parameter file name: ");
+           for(theta=1; theta <=npar; theta++)
+             trgradg[j][theta]=gradg[theta][j];
+         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
+         k=0;
+         for(i=1; i<=(nlstate+ndeath); i++){
+           for(j=1; j<=(nlstate+ndeath);j++){
+             k=k+1;
+             gm[k]=pmmij[i][j];
+           }
+         }
+      /*printf("\n%d ",(int)age);
+      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
+        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+      }*/
- #ifdef windows
+         fprintf(ficresprob,"\n%d ",(int)age);
-   scanf("%s",pathtot);
-   getcwd(pathcd, size);
-   /*cygwin_split_path(pathtot,path,optionfile);
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-   /* cutv(path,optionfile,pathtot,'\\');*/
- split(pathtot, path,optionfile);
+         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)
-   chdir(path);
+           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],doldm[i][i]);
-   replace(pathc,path);
- #endif
+       }
- #ifdef unix
+     }
-   scanf("%s",optionfile);
+     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
- #endif
+     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   }
+   free_vector(xp,1,npar);
+   fclose(ficresprob);
+ }
- /*-------- arguments in the command line --------*/
+ /******************* Printing html file ***********/
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+  int lastpass, int stepm, int weightopt, char model[],\
+  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
+  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
+  char version[], int popforecast, int estepm ){
+   int jj1, k1, i1, cpt;
+   FILE *fichtm;
+   /*char optionfilehtm[FILENAMELENGTH];*/
+   strcpy(optionfilehtm,optionfile);
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtm), exit(0);
+   }
+  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
+ \n
+ Total number of observations=%d <br>\n
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
+ <hr  size=\"2\" color=\"#EC5E5E\">
+  <ul><li>Outputs files<br>\n
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n
+  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n
+  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n
+  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+  fprintf(fichtm,"\n
+  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
+  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n
+  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+  if(popforecast==1) fprintf(fichtm,"\n
+  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
+  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
+         <br>",fileres,fileres,fileres,fileres);
+  else
+    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
+ fprintf(fichtm," <li>Graphs</li><p>");
-   strcpy(fileres,"r");
+  m=cptcoveff;
-   strcat(fileres, optionfile);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   /*---------arguments file --------*/
+  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\">");
+        }
+        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
+ <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+        for(cpt=1; cpt<nlstate;cpt++){
+          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
+ <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+        }
+     for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+ interval) in state (%d): v%s%d%d.gif <br>
+ <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
+         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
+ <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+      }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and
+ health expectancies in states (1) and (2): e%s%d.gif<br>
+ <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ fprintf(fichtm,"\n</body>");
+    }
+    }
+ fclose(fichtm);
+ }
+ /******************* Gnuplot file **************/
+ void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   strcpy(optionfilegnuplot,optionfilefiname);
+   strcat(optionfilegnuplot,".gp.txt");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
+   }
+ #ifdef windows
+     fprintf(ficgp,"cd \"%s\" \n",pathc);
+ #endif
+ m=pow(2,cptcoveff);
+  /* 1eme*/
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
+    for (k1=1; k1<= m ; k1 ++) {
+ #ifdef windows
+     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+ #endif
+ #ifdef unix
+ 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 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] ",ageminpar,fage);
+     for (i=1; i<= nlstate+1 ; i ++) {
+       k=2*i;
+       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       fprintf(ficgp,"\" t\"\" w l 0,");
+      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
+   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       else fprintf(ficgp,"\" t\"\" w l 0,");
+     }
+     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
+   }
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++) {
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       k=2+nlstate*(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",ageminpar,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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+       for (i=1; i< nlstate ; i ++)
+         fprintf(ficgp,"+$%d",k+i+1);
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+       l=3+(nlstate+ndeath)*cpt;
+       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+       for (i=1; i< nlstate ; i ++) {
+         l=3+(nlstate+ndeath)*cpt;
+         fprintf(ficgp,"+$%d",l+i+1);
+       }
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
+     }
+   }
+   /* proba elementaires */
+    for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         for(j=1; j <=ncovmodel; j++){
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
+           fprintf(ficgp,"\n");
+         }
+       }
+     }
+     }
+     for(jk=1; jk <=m; jk++) {
+   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+    i=1;
+    for(k2=1; k2<=nlstate; k2++) {
+      k3=i;
+      for(k=1; k<=(nlstate+ndeath); k++) {
+        if (k != k2){
+         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+ ij=1;
+         for(j=3; j <=ncovmodel; j++) {
+           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+             ij++;
+           }
+           else
+           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+         }
+           fprintf(ficgp,")/(1");
+         for(k1=1; k1 <=nlstate; k1++){
+           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+ ij=1;
+           for(j=3; j <=ncovmodel; j++){
+           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+             ij++;
+           }
+           else
+             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+           }
+           fprintf(ficgp,")");
+         }
+         fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+         i=i+ncovmodel;
+        }
+      }
+    }
+    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
+    }
+   fclose(ficgp);
+ }  /* end gnuplot */
+ /*************** Moving average **************/
+ void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
+   int i, cpt, cptcod;
+     for (agedeb=ageminpar; agedeb<=fage; agedeb++)
+       for (i=1; i<=nlstate;i++)
+         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
+           mobaverage[(int)agedeb][i][cptcod]=0.;
+     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
+       for (i=1; i<=nlstate;i++){
+         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+           for (cpt=0;cpt<=4;cpt++){
+             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
+           }
+           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
+         }
+       }
+     }
+ }
+ /************** Forecasting ******************/
+ prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   int *popage;
+   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat;
+   char fileresf[FILENAMELENGTH];
+  agelim=AGESUP;
+ calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   strcpy(fileresf,"f");
+   strcat(fileresf,fileres);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
+   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav==1) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     movingaverage(agedeb, fage, ageminpar, mobaverage);
+   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   agelim=AGESUP;
+   hstepm=1;
+   hstepm=hstepm/stepm;
+   yp1=modf(dateintmean,&yp);
+   anprojmean=yp;
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
+   if(mprojmean==0) jprojmean=1;
+   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
+   for(cptcov=1;cptcov<=i2;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficresf,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficresf,"******\n");
+       fprintf(ficresf,"# StartingAge FinalAge");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
+         fprintf(ficresf,"\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
+               if (h==(int)(calagedate+12*cpt)){
+                 fprintf(ficresf," %.3f", kk1);
+               }
+             }
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+     }
+   }
+   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresf);
+ }
+ /************** Forecasting ******************/
+ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   int *popage;
+   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat,***tabpop,***tabpopprev;
+   char filerespop[FILENAMELENGTH];
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   agelim=AGESUP;
+   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+   strcpy(filerespop,"pop");
+   strcat(filerespop,fileres);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", filerespop);
+   }
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav==1) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     movingaverage(agedeb, fage, ageminpar, mobaverage);
+   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   agelim=AGESUP;
+   hstepm=1;
+   hstepm=hstepm/stepm;
+   if (popforecast==1) {
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
+     }
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
+     popcount=vector(0,AGESUP);
+     i=1;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   }
+   for(cptcov=1;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficrespop,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+                 }
+               }
+               if (h==(int)(calagedate+12*cpt)){
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
+             }
+             for(i=1; i<=nlstate;i++){
+               kk1=0.;
+                 for(j=1; j<=nlstate;j++){
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+                 }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+             }
+             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+   /******/
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedate+YEARM*cpt)) {
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+               }
+               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+             }
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
+       }
+    }
+   }
+   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if (popforecast==1) {
+     free_ivector(popage,0,AGESUP);
+     free_vector(popeffectif,0,AGESUP);
+     free_vector(popcount,0,AGESUP);
+   }
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficrespop);
+ }
+ /***********************************************/
+ /**************** Main Program *****************/
+ /***********************************************/
+ int main(int argc, char *argv[])
+ {
+   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+   double agedeb, agefin,hf;
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double fret;
+   double **xi,tmp,delta;
+   double dum; /* Dummy variable */
+   double ***p3mat;
+   int *indx;
+   char line[MAXLINE], linepar[MAXLINE];
+   char title[MAXLINE];
+   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+   char filerest[FILENAMELENGTH];
+   char fileregp[FILENAMELENGTH];
+   char popfile[FILENAMELENGTH];
+   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
+   int firstobs=1, lastobs=10;
+   int sdeb, sfin; /* Status at beginning and end */
+   int c,  h , cpt,l;
+   int ju,jl, mi;
+   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+   int mobilav=0,popforecast=0;
+   int hstepm, nhstepm;
+   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
+   double bage, fage, age, agelim, agebase;
+   double ftolpl=FTOL;
+   double **prlim;
+   double *severity;
+   double ***param; /* Matrix of parameters */
+   double  *p;
+   double **matcov; /* Matrix of covariance */
+   double ***delti3; /* Scale */
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
+   double **varpl; /* Variances of prevalence limits by age */
+   double *epj, vepp;
+   double kk1, kk2;
+   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";
+   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   char z[1]="c", occ;
+ #include <sys/time.h>
+ #include <time.h>
+   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   /* long total_usecs;
+   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){
+     printf("\nEnter the parameter file name: ");
+     scanf("%s",pathtot);
+   }
+   else{
+     strcpy(pathtot,argv[1]);
+   }
+   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
+   /*cygwin_split_path(pathtot,path,optionfile);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+   chdir(path);
+   replace(pathc,path);
+ /*-------- arguments in the command line --------*/
+   strcpy(fileres,"r");
+   strcat(fileres, optionfilefiname);
+   strcat(fileres,".txt");    /* Other files have txt extension */
+   /*---------arguments file --------*/
    if((ficpar=fopen(optionfile,"r"))==NULL)    {
      printf("Problem with optionfile %s\n",optionfile);
- Line 1694  split(pathtot, path,optionfile);
+ Line 2593  split(pathtot, path,optionfile);
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+ while((c=getc(ficpar))=='#' && c!= EOF){
-   covar=matrix(0,NCOVMAX,1,n);
+     ungetc(c,ficpar);
-   if (strlen(model)<=1) cptcovn=0;
+     fgets(line, MAXLINE, ficpar);
-   else {
+     puts(line);
-     j=0;
+     fputs(line,ficparo);
-     j=nbocc(model,'+');
-     cptcovn=j+1;
    }
+   ungetc(c,ficpar);
+   covar=matrix(0,NCOVMAX,1,n);
+   cptcovn=0;
+   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
    ncovmodel=2+cptcovn;
    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
- Line 1735  split(pathtot, path,optionfile);
+ Line 2638  split(pathtot, path,optionfile);
        fprintf(ficparo,"\n");
      }
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
    p=param[1][1];
    /* Reads comments: lines beginning with '#' */
- Line 1796  split(pathtot, path,optionfile);
+ Line 2700  split(pathtot, path,optionfile);
    printf("\n");
-     /*-------- data file ----------*/
+     /*-------- Rewriting paramater file ----------*/
-     if((ficres =fopen(fileres,"w"))==NULL) {
+      strcpy(rfileres,"r");    /* "Rparameterfile */
-       printf("Problem with resultfile: %s\n", fileres);goto end;
+      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+      strcat(rfileres,".");    /* */
+      strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
      }
      fprintf(ficres,"#%s\n",version);
+     /*-------- data file ----------*/
      if((fic=fopen(datafile,"r"))==NULL)    {
        printf("Problem with datafile: %s\n", datafile);goto end;
      }
- Line 1825  split(pathtot, path,optionfile);
+ Line 2734  split(pathtot, path,optionfile);
      tab=ivector(1,NCOVMAX);
      ncodemax=ivector(1,8);
      i=1;
      while (fgets(line, MAXLINE, fic) != NULL)    {
        if ((i >= firstobs) && (i <=lastobs)) {
- Line 1843  split(pathtot, path,optionfile);
+ Line 2752  split(pathtot, path,optionfile);
          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);
-         /*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]));*/
+         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+           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])); ij=ij+1;}*/
          i=i+1;
        }
      }
+     /* printf("ii=%d", ij);
-     /*scanf("%d",i);*/
+        scanf("%d",i);*/
    imx=i-1; /* Number of individuals */
+   /* for (i=1; i<=imx; i++){
+     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++){
+      if (s[4][i]==9)  s[4][i]=-1;
+      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
    /* Calculation of the number of parameter from char model*/
    Tvar=ivector(1,15);
+   Tprod=ivector(1,15);
+   Tvaraff=ivector(1,15);
+   Tvard=imatrix(1,15,1,2);
    Tage=ivector(1,15);
    if (strlen(model) >1){
-     j=0, j1=0;
+     j=0, j1=0, k1=1, k2=1;
      j=nbocc(model,'+');
      j1=nbocc(model,'*');
      cptcovn=j+1;
+     cptcovprod=j1;
      strcpy(modelsav,model);
-     if (j==0) {
+     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
-       if (j1==0){
+       printf("Error. Non available option model=%s ",model);
-        cutv(stra,strb,modelsav,'V');
+       goto end;
-        Tvar[1]=atoi(strb);
-       }
-       else if (j1==1) {
-        cutv(stra,strb,modelsav,'*');
-        /*      printf("stra=%s strb=%s modelsav=%s ",stra,strb,modelsav);*/
-        Tage[1]=1; cptcovage++;
-        if (strcmp(stra,"age")==0) {
-          cutv(strd,strc,strb,'V');
-          Tvar[1]=atoi(strc);
-        }
-        else if (strcmp(strb,"age")==0) {
-          cutv(strd,strc,stra,'V');
-          Tvar[1]=atoi(strc);
-        }
-        else {printf("Error"); exit(0);}
-       }
      }
-     else {
-       for(i=j; i>=1;i--){
+     for(i=(j+1); i>=1;i--){
-         cutv(stra,strb,modelsav,'+');
+       cutv(stra,strb,modelsav,'+');
-         /*printf("%s %s %s\n", stra,strb,modelsav);*/
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
-         if (strchr(strb,'*')) {
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-           cutv(strd,strc,strb,'*');
+       /*scanf("%d",i);*/
-           if (strcmp(strc,"age")==0) {
+       if (strchr(strb,'*')) {
-             cutv(strb,stre,strd,'V');
+         cutv(strd,strc,strb,'*');
-             Tvar[i+1]=atoi(stre);
+         if (strcmp(strc,"age")==0) {
-             cptcovage++;
+           cptcovprod--;
-             Tage[cptcovage]=i+1;
+           cutv(strb,stre,strd,'V');
-             printf("stre=%s ", stre);
+           Tvar[i]=atoi(stre);
-           }
+           cptcovage++;
-           else if (strcmp(strd,"age")==0) {
+             Tage[cptcovage]=i;
-             cutv(strb,stre,strc,'V');
+             /*printf("stre=%s ", stre);*/
-             Tvar[i+1]=atoi(stre);
+         }
-             cptcovage++;
+         else if (strcmp(strd,"age")==0) {
-             Tage[cptcovage]=i+1;
+           cptcovprod--;
-           }
+           cutv(strb,stre,strc,'V');
-           else {
+           Tvar[i]=atoi(stre);
-             cutv(strb,stre,strc,'V');
+           cptcovage++;
-             Tvar[i+1]=ncov+1;
+           Tage[cptcovage]=i;
-             cutv(strb,strc,strd,'V');
-             for (k=1; k<=lastobs;k++)
-               covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
-           }
          }
          else {
-           cutv(strd,strc,strb,'V');
+           cutv(strb,stre,strc,'V');
-           /* printf("%s %s %s", strd,strc,strb);*/
+           Tvar[i]=ncovcol+k1;
+           cutv(strb,strc,strd,'V');
-         Tvar[i+1]=atoi(strc);
+           Tprod[k1]=i;
-         }
+           Tvard[k1][1]=atoi(strc);
-         strcpy(modelsav,stra);
+           Tvard[k1][2]=atoi(stre);
-       }
+           Tvar[cptcovn+k2]=Tvard[k1][1];
-       cutv(strd,strc,stra,'V');
+           Tvar[cptcovn+k2+1]=Tvard[k1][2];
-       Tvar[1]=atoi(strc);
+           for (k=1; k<=lastobs;k++)
+             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+           k1++;
+           k2=k2+2;
+         }
+       }
+       else {
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+        /*  scanf("%d",i);*/
+       cutv(strd,strc,strb,'V');
+       Tvar[i]=atoi(strc);
+       }
+       strcpy(modelsav,stra);
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+         scanf("%d",i);*/
      }
-   }
+ }
-   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-      scanf("%d ",i);*/
+   printf("cptcovprod=%d ", cptcovprod);
+   scanf("%d ",i);*/
      fclose(fic);
-    if(mle==1){
+     /*  if(mle==1){*/
      if (weightopt != 1) { /* Maximisation without weights*/
        for(i=1;i<=n;i++) weight[i]=1.0;
      }
      /*-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(m=2; (m<= maxwav); m++) {
+        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
+          anint[m][i]=9999;
+          s[m][i]=-1;
+        }
+      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
+       }
+     }
      for (i=1; i<=imx; i++)  {
        agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
        for(m=1; (m<= maxwav); m++){
          if(s[m][i] >0){
-           if (s[m][i] == nlstate+1) {
+           if (s[m][i] >= nlstate+1) {
              if(agedc[i]>0)
                if(moisdc[i]!=99 && andc[i]!=9999)
-               agev[m][i]=agedc[i];
+                 agev[m][i]=agedc[i];
-             else{
+             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+            else {
+               if (andc[i]!=9999){
                printf("Warning negative age at death: %d line:%d\n",num[i],i);
                agev[m][i]=-1;
+               }
              }
            }
            else if(s[m][i] !=9){ /* Should no more exist */
- Line 1992  printf("Total number of individuals= %d,
+ Line 2924  printf("Total number of individuals= %d,
      free_imatrix(outcome,1,maxwav+1,1,n);
      free_vector(moisnais,1,n);
      free_vector(annais,1,n);
-     free_matrix(mint,1,maxwav,1,n);
+     /* free_matrix(mint,1,maxwav,1,n);
-     free_matrix(anint,1,maxwav,1,n);
+        free_matrix(anint,1,maxwav,1,n);*/
      free_vector(moisdc,1,n);
      free_vector(andc,1,n);
- Line 2007  printf("Total number of individuals= %d,
+ Line 2939  printf("Total number of individuals= %d,
        Tcode=ivector(1,100);
-    nbcode=imatrix(1,nvar,1,8);
+       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-    ncodemax[1]=1;
+       ncodemax[1]=1;
-    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
     codtab=imatrix(1,100,1,10);
     h=0;
-    m=pow(2,cptcovn);
+    m=pow(2,cptcoveff);
-    for(k=1;k<=cptcovn; k++){
+    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,cptcovn+1-k)); cpt++){
+          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
-            if (h>m) h=1;codtab[h][k]=j;
+            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           }
         }
       }
     }
+    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+       codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){
-      for(k=1; k <=cptcovn; k++){
+       for(k=1; k <=cptcovn; k++){
-        printf("i=%d k=%d %d ",i,k,codtab[i][k]);
+       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-      }
+       }
-      printf("\n");
+       printf("\n");
-    }
+       }
-    scanf("%d",i);*/
+       scanf("%d",i);*/
     /* Calculates basic frequencies. Computes observed prevalence at single age
         and prints on file fileres'p'. */
-    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
      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) */
-     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     if(mle==1){
+     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
      /*--------- results files --------------*/
-     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     jk=1;
-    fprintf(ficres,"# Parameters\n");
+    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-    printf("# Parameters\n");
+    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i)
- Line 2073  printf("Total number of individuals= %d,
+ Line 3010  printf("Total number of individuals= %d,
           }
       }
     }
+  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");
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath; j++){
          if (j!=i) {
- Line 2093  printf("Total number of individuals= %d,
+ Line 3031  printf("Total number of individuals= %d,
            fprintf(ficres,"\n");
          }
        }
-       }
+      }
      k=1;
-     fprintf(ficres,"# Covariance\n");
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     printf("# Covariance\n");
+     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      for(i=1;i<=npar;i++){
        /*  if (k>nlstate) k=1;
        i1=(i-1)/(ncovmodel*nlstate)+1;
- Line 2121  printf("Total number of individuals= %d,
+ Line 3059  printf("Total number of individuals= %d,
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
+     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
      if (fage <= 2) {
-       bage = agemin;
+       bage = ageminpar;
-       fage = agemax;
+       fage = agemaxpar;
      }
      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
- /*------------ gnuplot -------------*/
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
- chdir(pathcd);
-   if((ficgp=fopen("graph.plt","w"))==NULL) {
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     printf("Problem with file graph.gp");goto end;
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
    }
- #ifdef windows
+   ungetc(c,ficpar);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
- #endif
- m=pow(2,cptcovn);
-  /* 1eme*/
+   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
-    for (k1=1; k1<= m ; k1 ++) {
+  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
- #ifdef windows
+   while((c=getc(ficpar))=='#' && c!= EOF){
-     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);
+     ungetc(c,ficpar);
- #endif
+     fgets(line, MAXLINE, ficpar);
- #ifdef unix
+     puts(line);
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
+     fputs(line,ficparo);
- #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);
-     }
    }
+   ungetc(c,ficpar);
-   /* CV preval stat */
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<nlstate ; cpt ++) {
-       k=3;
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
-       for (i=1; i< nlstate ; i ++)
-         fprintf(ficgp,"+$%d",k+i+1);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-       l=3+(nlstate+ndeath)*cpt;
-       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
-       for (i=1; i< nlstate ; i ++) {
-         l=3+(nlstate+ndeath)*cpt;
-         fprintf(ficgp,"+$%d",l+i+1);
-       }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-     }
-   }
-   /* proba elementaires */
-    for(i=1,jk=1; i <=nlstate; i++){
-     for(k=1; k <=(nlstate+ndeath); k++){
-       if (k != i) {
-         for(j=1; j <=ncovmodel; j++){
-           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
-           /*fprintf(ficgp,"%s",alph[1]);*/
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-           jk++;
-           fprintf(ficgp,"\n");
-         }
-       }
-     }
-     }
-   for(jk=1; jk <=m; jk++) {
-   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
-    i=1;
-    for(k2=1; k2<=nlstate; k2++) {
-      k3=i;
-      for(k=1; k<=(nlstate+ndeath); k++) {
-        if (k != k2){
-         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-         for(j=3; j <=ncovmodel; j++)
+    dateprev1=anprev1+mprev1/12.+jprev1/365.;
-           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+    dateprev2=anprev2+mprev2/12.+jprev2/365.;
-         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);
-           for(j=3; j <=ncovmodel; j++)
-             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-           fprintf(ficgp,")");
-         }
-         fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-         i=i+ncovmodel;
-        }
-      }
-    }
-    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
-   }
-   fclose(ficgp);
- chdir(path);
-     free_matrix(agev,1,maxwav,1,imx);
-     free_ivector(wav,1,imx);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-     free_imatrix(s,1,maxwav+1,1,n);
-     free_ivector(num,1,n);
-     free_vector(agedc,1,n);
-     free_vector(weight,1,n);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-     fclose(ficparo);
-     fclose(ficres);
-    }
-    /*________fin mle=1_________*/
+   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 2312  chdir(path);
+ Line 3106  chdir(path);
      fputs(line,ficparo);
    }
    ungetc(c,ficpar);
-   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
-   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
-   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
- /*--------- index.htm --------*/
-   if((fichtm=fopen("index.htm","w"))==NULL)    {
+   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("Problem with index.htm \n");goto end;
+ fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+ fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+ while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
+     puts(line);
+     fputs(line,ficparo);
    }
+   ungetc(c,ficpar);
-  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n
+   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
-         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
- - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
+   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
-         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
-         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
-         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
-         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
-         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
-         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
-         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
-  fprintf(fichtm," <li>Graphs</li>\n<p>");
+  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
-  m=cptcovn;
+ /*------------ gnuplot -------------*/
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
+ /*------------ free_vector  -------------*/
+  chdir(path);
+  free_ivector(wav,1,imx);
+  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+  free_ivector(num,1,n);
+  free_vector(agedc,1,n);
+  /*free_matrix(covar,1,NCOVMAX,1,n);*/
+  fclose(ficparo);
+  fclose(ficres);
-  j1=0;
+ /*--------- index.htm --------*/
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
-        j1++;
-        if (cptcovn > 0) {
-          fprintf(fichtm,"<hr>************ Results for covariates");
-          for (cpt=1; cpt<=cptcovn;cpt++)
-            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);
-          fprintf(fichtm," ************\n<hr>");
-        }
-        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);
+   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);
    /*--------------- Prevalence limit --------------*/
    strcpy(filerespl,"pl");
- Line 2391  fclose(fichtm);
+ Line 3166  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=cptcovn;
+   i1=cptcoveff;
    if (cptcovn < 1){i1=1;}
    for(cptcov=1;cptcov<=i1;cptcov++){
- Line 2402  fclose(fichtm);
+ Line 3177  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<=cptcovn;j++)
+         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespl," V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          fprintf(ficrespl,"******\n");
          for (age=agebase; age<=agelim; age++){
- Line 2416  fclose(fichtm);
+ Line 3191  fclose(fichtm);
        }
      }
    fclose(ficrespl);
    /*------------- h Pij x at various ages ------------*/
    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
- Line 2425  fclose(fichtm);
+ Line 3201  fclose(fichtm);
    printf("Computing pij: result on file '%s' \n", filerespij);
    stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (stepm<=24) stepsize=2;
+   /*if (stepm<=24) stepsize=2;*/
    agelim=AGESUP;
    hstepm=stepsize*YEARM; /* Every year of age */
- Line 2436  fclose(fichtm);
+ Line 3212  fclose(fichtm);
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        k=k+1;
          fprintf(ficrespij,"\n#****** ");
-         for(j=1;j<=cptcovn;j++)
+         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          fprintf(ficrespij,"******\n");
          for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
- Line 2451  fclose(fichtm);
+ Line 3227  fclose(fichtm);
              for(j=1; j<=nlstate+ndeath;j++)
                fprintf(ficrespij," %1d-%1d",i,j);
            fprintf(ficrespij,"\n");
-           for (h=0; h<=nhstepm; h++){
+            for (h=0; h<=nhstepm; h++){
              fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
              for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate+ndeath;j++)
                  fprintf(ficrespij," %.5f", p3mat[i][j][h]);
              fprintf(ficrespij,"\n");
-           }
+              }
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            fprintf(ficrespij,"\n");
          }
      }
    }
+   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
    fclose(ficrespij);
+   /*---------- 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 (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
+     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);}
+   else{
+     erreur=108;
+     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+   }
    /*---------- Health expectancies and variances ------------*/
    strcpy(filerest,"t");
- Line 2495  fclose(fichtm);
+ Line 3287  fclose(fichtm);
      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        k=k+1;
        fprintf(ficrest,"\n#****** ");
-       for(j=1;j<=cptcovn;j++)
+       for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        fprintf(ficrest,"******\n");
        fprintf(ficreseij,"\n#****** ");
-       for(j=1;j<=cptcovn;j++)
+       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<=cptcovn;j++)
+       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);
        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
        fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
        for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
        fprintf(ficrest,"\n");
-       hf=1;
-       if (stepm >= YEARM) hf=stepm/YEARM;
        epj=vector(1,nlstate+1);
        for(age=bage; age <=fage ;age++){
          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-         fprintf(ficrest," %.0f",age);
+         if (popbased==1) {
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][k];
+         }
+         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];
            }
            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");
        }
      }
    }
-  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 2561  strcpy(fileresvpl,"vpl");
+ Line 3357  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<=cptcovn;j++)
+       for(j=1;j<=cptcoveff;j++)
-        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[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 2589  strcpy(fileresvpl,"vpl");
+ Line 3385  strcpy(fileresvpl,"vpl");
    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
    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);
-   printf("End of Imach\n");
+   if(erreur >0)
+     printf("End of Imach with error or warning %d\n",erreur);
+   else   printf("End of Imach\n");
    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
    /* 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);*/
    /*printf("Total time was %d uSec.\n", total_usecs);*/
    /*------ End -----------*/
   end:
  #ifdef windows
-  chdir(pathcd);
+   /* chdir(pathcd);*/
  #endif
-  system("wgnuplot graph.plt");
+  /*system("wgnuplot graph.plt");*/
+  /*system("../gp37mgw/wgnuplot graph.plt");*/
+  /*system("cd ../gp37mgw");*/
+  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
+  strcpy(plotcmd,GNUPLOTPROGRAM);
+  strcat(plotcmd," ");
+  strcat(plotcmd,optionfilegnuplot);
+  system(plotcmd);
  #ifdef windows
    while (z[0] != 'q') {
-     chdir(pathcd);
+     /* 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("index.htm");
-     }
      else if (z[0] == 'q') exit(0);
    }
  #endif

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