Diff for /imach/src/imach.c between versions 1.56 and 1.70

version 1.56, 2002/07/24 17:28:25 version 1.70, 2003/02/05 12:40:38
Line 32 Line 32
   hPijx is the probability to be observed in state i at age x+h    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    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
Line 83 Line 83
 #define ODIRSEPARATOR '\\'  #define ODIRSEPARATOR '\\'
 #endif  #endif
   
 char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";  char version[80]="Imach version 0.92, February 2003, INED-EUROREVES ";
 int erreur; /* Error number */  int erreur; /* Error number */
 int nvar;  int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
Line 99  int jmin, jmax; /* min, max spacing betw Line 99  int jmin, jmax; /* min, max spacing betw
 int mle, weightopt;  int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  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 */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double jmean; /* Mean space between 2 waves */  double jmean; /* Mean space between 2 waves */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
Line 177  double ftolhess; /* Tolerance for comput Line 179  double ftolhess; /* Tolerance for comput
 /**************** split *************************/  /**************** split *************************/
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
    char *s;                             /* pointer */    char  *ss;                            /* pointer */
    int  l1, l2;                         /* length counters */    int   l1, l2;                         /* length counters */
   
    l1 = strlen( path );                 /* length of path */    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
    if ( s == NULL ) {                   /* no directory, so use current */    if ( ss == NULL ) {                   /* no directory, so use current */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #if     defined(__bsd__)                /* get current working directory */  #if     defined(__bsd__)                /* get current working directory */
       extern char       *getwd( );      extern char *getwd( );
   
       if ( getwd( dirc ) == NULL ) {      if ( getwd( dirc ) == NULL ) {
 #else  #else
       extern char       *getcwd( );      extern char *getcwd( );
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 #endif  #endif
          return( GLOCK_ERROR_GETCWD );        return( GLOCK_ERROR_GETCWD );
       }      }
       strcpy( name, path );             /* we've got it */      strcpy( name, path );               /* we've got it */
    } else {                             /* strip direcotry from path */    } else {                              /* strip direcotry from path */
       s++;                              /* after this, the filename */      ss++;                               /* after this, the filename */
       l2 = strlen( s );                 /* length of filename */      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, s );                /* save file name */      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                  /* add zero */      dirc[l1-l2] = 0;                    /* add zero */
    }    }
    l1 = strlen( dirc );                 /* length of directory */    l1 = strlen( dirc );                  /* length of directory */
 #ifdef windows  #ifdef windows
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 #else  #else
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 #endif  #endif
    s = strrchr( name, '.' );            /* find last / */    ss = strrchr( name, '.' );            /* find last / */
    s++;    ss++;
    strcpy(ext,s);                       /* save extension */    strcpy(ext,ss);                       /* save extension */
    l1= strlen( name);    l1= strlen( name);
    l2= strlen( s)+1;    l2= strlen(ss)+1;
    strncpy( finame, name, l1-l2);    strncpy( finame, name, l1-l2);
    finame[l1-l2]= 0;    finame[l1-l2]= 0;
    return( 0 );                         /* we're done */    return( 0 );                          /* we're done */
 }  }
   
   
Line 277  void nrerror(char error_text[]) Line 279  void nrerror(char error_text[])
 {  {
   fprintf(stderr,"ERREUR ...\n");    fprintf(stderr,"ERREUR ...\n");
   fprintf(stderr,"%s\n",error_text);    fprintf(stderr,"%s\n",error_text);
   exit(1);    exit(EXIT_FAILURE);
 }  }
 /*********************** vector *******************/  /*********************** vector *******************/
 double *vector(int nl, int nh)  double *vector(int nl, int nh)
Line 854  double **matprod2(double **out, double * Line 856  double **matprod2(double **out, double *
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month     /* Computes the transition matrix starting at age 'age' over 
      duration (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
      (typically every 2 years instead of every month which is too big).       (typically every 2 years instead of every month which is too big 
        for the memory).
      Model is determined by parameters x and covariates have to be        Model is determined by parameters x and covariates have to be 
      included manually here.        included manually here. 
   
Line 914  double func( double *x) Line 918  double func( double *x)
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
     int s1, s2;
     double bbh, survp;
   long ipmx;    long ipmx;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
Line 924  double func( double *x) Line 930  double func( double *x)
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    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];    if(mle==1){
     for(mi=1; mi<= wav[i]-1; mi++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for(mi=1; mi<= wav[i]-1; mi++){
       for(d=0; d<dh[mi][i]; d++){          for (ii=1;ii<=nlstate+ndeath;ii++)
         newm=savm;            for (j=1;j<=nlstate+ndeath;j++){
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (kk=1; kk<=cptcovage;kk++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];            }
         }          for(d=0; d<dh[mi][i]; d++){
                     newm=savm;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));            for (kk=1; kk<=cptcovage;kk++) {
         savm=oldm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         oldm=newm;            }
                     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,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]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
            */
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
            */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));  /* linear interpolation */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }  else if(mle==2){
       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 (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,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]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
            */
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
            */
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
       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 (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,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]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
            */
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
            */
           /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }else{  /* ml=4 no inter-extrapolation */
       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 (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
                   
       } /* end mult */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,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]]);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          ipmx +=1;
       ipmx +=1;          sw += weight[i];
       sw += weight[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        } /* end of wave */
     } /* end of wave */      } /* end of individual */
   } /* end of individual */    } /* End of if */
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
Line 974  void mlikeli(FILE *ficres,double p[], in Line 1133  void mlikeli(FILE *ficres,double p[], in
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
 }  }
Line 1237  void lubksb(double **a, int n, int *indx Line 1396  void lubksb(double **a, int n, int *indx
 }   } 
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, 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 */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
Line 1284  void  freqsummary(char fileres[], int ag Line 1443  void  freqsummary(char fileres[], int ag
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
               bool=0;                bool=0;
         }          }
         if (bool==1) {          if (bool==1){
           for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){
             k2=anint[m][i]+(mint[m][i]/12.);              k2=anint[m][i]+(mint[m][i]/12.);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
Line 1397  void  freqsummary(char fileres[], int ag Line 1556  void  freqsummary(char fileres[], int ag
 }  }
   
 /************ Prevalence ********************/  /************ 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)  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, int firstpass, int lastpass)
 {  /* Some frequencies */  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
     
   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 ***freq; /* Frequencies */
   double *pp;    double *pp;
   double pos, k2;    double pos; 
     double  y2; /* in fractional years */
   
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
       
Line 1422  void prevalence(int agemin, float agemax Line 1586  void prevalence(int agemin, float agemax
           for(m=agemin; m <= agemax+3; m++)            for(m=agemin; m <= agemax+3; m++)
             freq[i][jk][m]=0;              freq[i][jk][m]=0;
             
       for (i=1; i<=imx; i++) {        for (i=1; i<=imx; i++) { /* Each individual */
         bool=1;          bool=1;
         if  (cptcovn>0) {          if  (cptcovn>0) {
           for (z1=1; z1<=cptcoveff; z1++)             for (z1=1; z1<=cptcoveff; z1++) 
Line 1430  void prevalence(int agemin, float agemax Line 1594  void prevalence(int agemin, float agemax
               bool=0;                bool=0;
         }           } 
         if (bool==1) {           if (bool==1) { 
           for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
             k2=anint[m][i]+(mint[m][i]/12.);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               if(agev[m][i]==0) agev[m][i]=agemax+1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
               if(agev[m][i]==1) agev[m][i]=agemax+2;                if(agev[m][i]==1) agev[m][i]=agemax+2;
               if (m<lastpass) {                if (m<lastpass) {
                 if (calagedate>0)                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  
                 else  
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];                   freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
               }                }
             }              }
           }            } /* end selection of waves */
         }          }
       }        }
       for(i=(int)agemin; i <= (int)agemax+3; i++){         for(i=(int)agemin; i <= (int)agemax+3; i++){ 
Line 1482  void prevalence(int agemin, float agemax Line 1643  void prevalence(int agemin, float agemax
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 {  {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      Death is a valid wave (if date is known).       Death is a valid wave (if date is known).
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      and mw[mi+1][i]. dh depends on stepm.       and mw[mi+1][i]. dh depends on stepm.
      */       */
   
Line 1545  void  concatwav(int wav[], int **dh, int Line 1706  void  concatwav(int wav[], int **dh, int
           if (j <= jmin) jmin=j;            if (j <= jmin) jmin=j;
           sum=sum+j;            sum=sum+j;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            /*if (j<0) printf("j=%d num=%d \n",j,i); */
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           }            }
         }          }
         else{          else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           k=k+1;            k=k+1;
           if (j >= jmax) jmax=j;            if (j >= jmax) jmax=j;
           else if (j <= jmin)jmin=j;            else if (j <= jmin)jmin=j;
Line 1558  void  concatwav(int wav[], int **dh, int Line 1721  void  concatwav(int wav[], int **dh, int
         jk= j/stepm;          jk= j/stepm;
         jl= j -jk*stepm;          jl= j -jk*stepm;
         ju= j -(jk+1)*stepm;          ju= j -(jk+1)*stepm;
         if(jl <= -ju)          if(mle <=1){ 
           dh[mi][i]=jk;            if(jl==0){
         else              dh[mi][i]=jk;
           dh[mi][i]=jk+1;              bh[mi][i]=0;
         if(dh[mi][i]==0)            }else{ /* We want a negative bias in order to only have interpolation ie
           dh[mi][i]=1; /* At least one step */                    * at the price of an extra matrix product in likelihood */
       }              dh[mi][i]=jk+1;
     }              bh[mi][i]=ju;
             }
           }else{
             if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
             else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
               printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
             }
           }
         } /* end if mle */
       } /* end wave */
   }    }
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
Line 1575  void  concatwav(int wav[], int **dh, int Line 1758  void  concatwav(int wav[], int **dh, int
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)  void tricode(int *Tvar, int **nbcode, int imx)
 {  {
   int Ndum[20],ij=1, k, j, i;    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   int cptcode=0;    int cptcode=0;
   cptcoveff=0;     cptcoveff=0; 
     
   for (k=0; k<19; k++) Ndum[k]=0;    for (k=0; k<maxncov; k++) Ndum[k]=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (k=1; k<=7; k++) ncodemax[k]=0;
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       ij=(int)(covar[Tvar[j]][i]);                                 modality*/ 
       Ndum[ij]++;         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       if (ij > cptcode) cptcode=ij;         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
     }      }
   
     for (i=0; i<=cptcode; i++) {      for (i=0; i<=cptcode; i++) {
       if(Ndum[i]!=0) ncodemax[j]++;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
     }      }
     ij=1;   
   
   
       ij=1; 
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1; i<=ncodemax[j]; i++) {
       for (k=0; k<=19; k++) {        for (k=0; k<= maxncov; k++) {
         if (Ndum[k] != 0) {          if (Ndum[k] != 0) {
           nbcode[Tvar[j]][ij]=k;             nbcode[Tvar[j]][ij]=k; 
             /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                       
           ij++;            ij++;
         }          }
Line 1608  void tricode(int *Tvar, int **nbcode, in Line 1795  void tricode(int *Tvar, int **nbcode, in
     }       } 
   }      }  
   
  for (k=0; k<19; k++) Ndum[k]=0;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
  for (i=1; i<=ncovmodel-2; i++) {   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    ij=Tvar[i];     ij=Tvar[i];
    Ndum[ij]++;      Ndum[ij]++;
  }   }
   
  ij=1;   ij=1;
  for (i=1; i<=10; i++) {   for (i=1; i<= maxncov; i++) {
    if((Ndum[i]!=0) && (i<=ncovcol)){     if((Ndum[i]!=0) && (i<=ncovcol)){
      Tvaraff[ij]=i;        Tvaraff[ij]=i; /*For printing */
      ij++;       ij++;
    }     }
  }   }
     
  cptcoveff=ij-1;   cptcoveff=ij-1; /*Number of simple covariates*/
 }  }
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
Line 1661  void evsij(char fileres[], double ***eij Line 1849  void evsij(char fileres[], double ***eij
    * This is mainly to measure the difference between two models: for example     * 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     * 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      * we are calculating an estimate of the Life Expectancy assuming a linear 
    * progression inbetween and thus overestimating or underestimating according     * progression in between and thus overestimating or underestimating according
    * to the curvature of the survival function. If, for the same date, we      * 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     * 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      * to compare the new estimate of Life expectancy with the same linear 
Line 1824  void varevsij(char optionfilefiname[], d Line 2012  void varevsij(char optionfilefiname[], d
   char fileresprobmorprev[FILENAMELENGTH];    char fileresprobmorprev[FILENAMELENGTH];
   
   if(popbased==1){    if(popbased==1){
     if(mobilav==1)      if(mobilav!=0)
       strcpy(digitp,"-populbased-mobilav-");        strcpy(digitp,"-populbased-mobilav-");
     else strcpy(digitp,"-populbased-nomobil-");      else strcpy(digitp,"-populbased-nomobil-");
   }    }
Line 1851  void varevsij(char optionfilefiname[], d Line 2039  void varevsij(char optionfilefiname[], d
   }    }
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficresprobmorprev," p.%-d SE",j);      fprintf(ficresprobmorprev," p.%-d SE",j);
Line 1873  void varevsij(char optionfilefiname[], d Line 2061  void varevsij(char optionfilefiname[], d
     exit(0);      exit(0);
   }    }
   else{    else{
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   }    }
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
Line 1908  void varevsij(char optionfilefiname[], d Line 2096  void varevsij(char optionfilefiname[], d
      and note for a fixed period like k years */       and note for a fixed period like k years */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* 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       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       means that if the survival funtion is printed every two years of age and if
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        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.       results. So we changed our mind and took the option of the best precision.
   */    */
Line 1924  void varevsij(char optionfilefiname[], d Line 2112  void varevsij(char optionfilefiname[], d
   
   
     for(theta=1; theta <=npar; theta++){      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
Line 1946  void varevsij(char optionfilefiname[], d Line 2134  void varevsij(char optionfilefiname[], d
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
       /* This for computing forces of mortality (h=1)as a weighted average */        /* This for computing probability of death (h=1 means
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){           computed over hstepm matrices product = hstepm*stepm months) 
         for(i=1; i<= nlstate; i++)           as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
           gpp[j] += prlim[i][i]*p3mat[i][j][1];            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       }            }    
       /* end force of mortality */        /* end probability of death */
   
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
Line 1974  void varevsij(char optionfilefiname[], d Line 2165  void varevsij(char optionfilefiname[], d
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
       /* This for computing force of mortality (h=1)as a weighted average */        /* This for computing probability of death (h=1 means
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){           computed over hstepm matrices product = hstepm*stepm months) 
         for(i=1; i<= nlstate; i++)           as a weighted average of prlim.
           gmp[j] += prlim[i][i]*p3mat[i][j][1];        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
       }            }    
       /* end force of mortality */        /* end probability of death */
   
       for(j=1; j<= nlstate; j++) /* vareij */        for(j=1; j<= nlstate; j++) /* vareij */
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         }          }
   
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       }        }
Line 2001  void varevsij(char optionfilefiname[], d Line 2196  void varevsij(char optionfilefiname[], d
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       for(theta=1; theta <=npar; theta++)        for(theta=1; theta <=npar; theta++)
         trgradgp[j][theta]=gradgp[theta][j];          trgradgp[j][theta]=gradgp[theta][j];
     
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
Line 2016  void varevsij(char optionfilefiname[], d Line 2212  void varevsij(char optionfilefiname[], d
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
     
     /* pptj */      /* pptj */
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
Line 2024  void varevsij(char optionfilefiname[], d Line 2220  void varevsij(char optionfilefiname[], d
       for(i=nlstate+1;i<=nlstate+ndeath;i++)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         varppt[j][i]=doldmp[j][i];          varppt[j][i]=doldmp[j][i];
     /* end ppptj */      /* end ppptj */
       /*  x centered again */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     
Line 2036  void varevsij(char optionfilefiname[], d Line 2233  void varevsij(char optionfilefiname[], d
           prlim[i][i]=mobaverage[(int)age][i][ij];            prlim[i][i]=mobaverage[(int)age][i][ij];
       }        }
     }      }
                    
     /* This for computing force of mortality (h=1)as a weighted average */      /* This for computing probability of death (h=1 means
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       for(i=1; i<= nlstate; i++)         as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     }          }    
     /* end force of mortality */      /* end probability of death */
   
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2072  void varevsij(char optionfilefiname[], d Line 2272  void varevsij(char optionfilefiname[], d
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
 */  */
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
Line 2091  void varevsij(char optionfilefiname[], d Line 2294  void varevsij(char optionfilefiname[], d
   fclose(ficresprobmorprev);    fclose(ficresprobmorprev);
   fclose(ficgp);    fclose(ficgp);
   fclose(fichtm);    fclose(fichtm);
 }  }  
   
 /************ Variance of prevlim ******************/  /************ Variance of prevlim ******************/
 void varprevlim(char fileres[], double **varpl, 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 varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double **newm;    double **newm;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
Line 2237  void varprob(char optionfilefiname[], do Line 2440  void varprob(char optionfilefiname[], do
       fprintf(ficresprobcov," p%1d-%1d ",i,j);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     }        }  
   fprintf(ficresprob,"\n");   /* fprintf(ficresprob,"\n");
   fprintf(ficresprobcov,"\n");    fprintf(ficresprobcov,"\n");
   fprintf(ficresprobcor,"\n");    fprintf(ficresprobcor,"\n");
   xp=vector(1,npar);   */
    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
Line 2269  void varprob(char optionfilefiname[], do Line 2473  void varprob(char optionfilefiname[], do
   
   }    }
   
    
   cov[1]=1;    cov[1]=1;
   tj=cptcoveff;    tj=cptcoveff;
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
Line 2277  void varprob(char optionfilefiname[], do Line 2480  void varprob(char optionfilefiname[], do
   for(t=1; t<=tj;t++){    for(t=1; t<=tj;t++){
     for(i1=1; i1<=ncodemax[t];i1++){       for(i1=1; i1<=ncodemax[t];i1++){ 
       j1++;        j1++;
         
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");           fprintf(ficresprob, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresprob, "**********\n#");          fprintf(ficresprob, "**********\n#\n");
         fprintf(ficresprobcov, "\n#********** Variable ");           fprintf(ficresprobcov, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresprobcov, "**********\n#");          fprintf(ficresprobcov, "**********\n#\n");
                   
         fprintf(ficgp, "\n#********** Variable ");           fprintf(ficgp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp, "**********\n#");          fprintf(ficgp, "**********\n#\n");
                   
                   
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
Line 2297  void varprob(char optionfilefiname[], do Line 2499  void varprob(char optionfilefiname[], do
                   
         fprintf(ficresprobcor, "\n#********** Variable ");              fprintf(ficresprobcor, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp, "**********\n#");              fprintf(ficresprobcor, "**********\n#");    
       }        }
               
       for (age=bage; age<=fage; age ++){         for (age=bage; age<=fage; age ++){ 
Line 2350  void varprob(char optionfilefiname[], do Line 2552  void varprob(char optionfilefiname[], do
                   
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                   free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
         pmij(pmmij,cov,ncovmodel,x,nlstate);          pmij(pmmij,cov,ncovmodel,x,nlstate);
                   
         k=0;          k=0;
Line 2365  void varprob(char optionfilefiname[], do Line 2571  void varprob(char optionfilefiname[], do
             varpij[i][j][(int)age] = doldm[i][j];              varpij[i][j][(int)age] = doldm[i][j];
   
         /*printf("\n%d ",(int)age);          /*printf("\n%d ",(int)age);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      }*/            }*/
   
         fprintf(ficresprob,"\n%d ",(int)age);          fprintf(ficresprob,"\n%d ",(int)age);
         fprintf(ficresprobcov,"\n%d ",(int)age);          fprintf(ficresprobcov,"\n%d ",(int)age);
Line 2396  void varprob(char optionfilefiname[], do Line 2602  void varprob(char optionfilefiname[], do
   
       /* Confidence intervalle of pij  */        /* Confidence intervalle of pij  */
       /*        /*
       fprintf(ficgp,"\nset noparametric;unset label");          fprintf(ficgp,"\nset noparametric;unset label");
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       */        */
   
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
Line 2474  void varprob(char optionfilefiname[], do Line 2680  void varprob(char optionfilefiname[], do
         } /*l1 */          } /*l1 */
       }/* k1 */        }/* k1 */
     } /* loop covariates */      } /* loop covariates */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   fclose(ficresprob);    fclose(ficresprob);
   fclose(ficresprobcov);    fclose(ficresprobcov);
Line 2616  m=pow(2,cptcoveff); Line 2818  m=pow(2,cptcoveff);
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else 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);        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
Line 2773  m=pow(2,cptcoveff); Line 2975  m=pow(2,cptcoveff);
 int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
   int i, cpt, cptcod;    int i, cpt, cptcod;
     int modcovmax =1;
   int mobilavrange, mob;    int mobilavrange, mob;
   double age;    double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     if(mobilav==1) mobilavrange=5; /* default */      if(mobilav==1) mobilavrange=5; /* default */
     else mobilavrange=mobilav;      else mobilavrange=mobilav;
     for (age=bage; age<=fage; age++)      for (age=bage; age<=fage; age++)
       for (i=1; i<=nlstate;i++)        for (i=1; i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for (cptcod=1;cptcod<=modcovmax;cptcod++)
           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     /* We keep the original values on the extreme ages bage, fage and for       /* We keep the original values on the extreme ages bage, fage and for 
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
Line 2789  int movingaverage(double ***probs, doubl Line 2997  int movingaverage(double ***probs, doubl
     for (mob=3;mob <=mobilavrange;mob=mob+2){      for (mob=3;mob <=mobilavrange;mob=mob+2){
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
         for (i=1; i<=nlstate;i++){          for (i=1; i<=nlstate;i++){
           for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for (cptcod=1;cptcod<=modcovmax;cptcod++){
             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
               for (cpt=1;cpt<=(mob-1)/2;cpt++){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
Line 2806  int movingaverage(double ***probs, doubl Line 3014  int movingaverage(double ***probs, doubl
   
   
 /************** Forecasting ******************/  /************** 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){  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
       /* proj1, year, month, day of starting projection 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h;
   int *popage;    int *popage;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    double ***mobaverage;
   char fileresf[FILENAMELENGTH];    char fileresf[FILENAMELENGTH];
   
  agelim=AGESUP;    agelim=AGESUP;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
    
     
   strcpy(fileresf,"f");     strcpy(fileresf,"f"); 
   strcat(fileresf,fileres);    strcat(fileresf,fileres);
Line 2844  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 3054  calagedate=(anproj1+mproj1/12.+jproj1/36
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
       
   agelim=AGESUP;  
     
   hstepm=1;    hstepm=1;
   hstepm=hstepm/stepm;     hstepm=hstepm/stepm; 
   yp1=modf(dateintmean,&yp);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
   anprojmean=yp;    anprojmean=yp;
   yp2=modf((yp1*12),&yp);    yp2=modf((yp1*12),&yp);
   mprojmean=yp;    mprojmean=yp;
Line 2857  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 3066  calagedate=(anproj1+mproj1/12.+jproj1/36
   if(jprojmean==0) jprojmean=1;    if(jprojmean==0) jprojmean=1;
   if(mprojmean==0) jprojmean=1;    if(mprojmean==0) jprojmean=1;
       
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficresf,"#****** Routine prevforecast **\n");
     for(cptcov=1, k=0;cptcov<=cptcoveff;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#******");        fprintf(ficresf,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }        }
       fprintf(ficresf,"******\n");        fprintf(ficresf,"******\n");
       fprintf(ficresf,"# StartingAge FinalAge");        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for(j=1; j<=nlstate+ndeath;j++){ 
                 for(i=1; i<=nlstate;i++)              
                   fprintf(ficresf," p%d%d",i,j);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp++) { 
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);             fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){           for (agec=fage; agec>=ageminpar; agec--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;             nhstepm = nhstepm/hstepm; 
             
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;            oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {              if (h==(int) (YEARM*yearp)) {
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);                fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
               kk1=0.;kk2=0;                ppij=0.;
               for(i=1; i<=nlstate;i++) {                              for(i=1; i<=nlstate;i++) {              
                 if (mobilav==1)                   if (mobilav==1) 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec+1][i][cptcod];
                 else {                  else {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec+1)][i][cptcod];
                 }                  }
                                   if (h==(int)(YEARM*yearp))
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
               }                }
               if (h==(int)(calagedate+12*cpt)){                if (h==(int)(YEARM*yearp)){
                 fprintf(ficresf," %.3f", kk1);                  fprintf(ficresf," %.3f", ppij);
                           
               }                }
             }              }
           }            }
Line 2913  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 3127  calagedate=(anproj1+mproj1/12.+jproj1/36
   
   fclose(ficresf);    fclose(ficresf);
 }  }
 /************** Forecasting ******************/  
   /************** Forecasting *****not tested NB*************/
 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){  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 cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double calagedatem, agelim, kk1, kk2;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat,***tabpop,***tabpopprev;    double ***p3mat,***tabpop,***tabpopprev;
   double ***mobaverage;    double ***mobaverage;
Line 2927  populforecast(char fileres[], double anp Line 3142  populforecast(char fileres[], double anp
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   agelim=AGESUP;    agelim=AGESUP;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
       
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       
       
   strcpy(filerespop,"pop");     strcpy(filerespop,"pop"); 
Line 2975  populforecast(char fileres[], double anp Line 3190  populforecast(char fileres[], double anp
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   }    }
   
   for(cptcov=1;cptcov<=i2;cptcov++){    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficrespop,"\n#******");        fprintf(ficrespop,"\n#******");
Line 2990  populforecast(char fileres[], double anp Line 3205  populforecast(char fileres[], double anp
       for (cpt=0; cpt<=0;cpt++) {         for (cpt=0; cpt<=0;cpt++) { 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,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--){           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;             nhstepm = nhstepm/hstepm; 
                       
Line 2999  populforecast(char fileres[], double anp Line 3214  populforecast(char fileres[], double anp
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {              if (h==(int) (calagedatem+YEARM*cpt)) {
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
Line 3011  populforecast(char fileres[], double anp Line 3226  populforecast(char fileres[], double anp
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                 }                  }
               }                }
               if (h==(int)(calagedate+12*cpt)){                if (h==(int)(calagedatem+12*cpt)){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   /*fprintf(ficrespop," %.3f", kk1);                    /*fprintf(ficrespop," %.3f", kk1);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
Line 3022  populforecast(char fileres[], double anp Line 3237  populforecast(char fileres[], double anp
                 for(j=1; j<=nlstate;j++){                  for(j=1; j<=nlstate;j++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                     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)];                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
             }              }
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3036  populforecast(char fileres[], double anp Line 3251  populforecast(char fileres[], double anp
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,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--){           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;             nhstepm = nhstepm/hstepm; 
                       
Line 3044  populforecast(char fileres[], double anp Line 3259  populforecast(char fileres[], double anp
           oldm=oldms;savm=savms;            oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {              if (h==(int) (calagedatem+YEARM*cpt)) {
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
Line 3052  populforecast(char fileres[], double anp Line 3267  populforecast(char fileres[], double anp
               for(i=1; i<=nlstate;i++) {                              for(i=1; i<=nlstate;i++) {              
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                      kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
               }                }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
             }              }
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3079  populforecast(char fileres[], double anp Line 3294  populforecast(char fileres[], double anp
   
 int main(int argc, char *argv[])  int main(int argc, char *argv[])
 {  {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   double agedeb, agefin,hf;    double agedeb, agefin,hf;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
Line 3098  int main(int argc, char *argv[]) Line 3313  int main(int argc, char *argv[])
   int c,  h , cpt,l;    int c,  h , cpt,l;
   int ju,jl, mi;    int ju,jl, mi;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm, nhstepm;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
   
   double bage, fage, age, agelim, agebase;    double bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;    double ftolpl=FTOL;
Line 3117  int main(int argc, char *argv[]) Line 3333  int main(int argc, char *argv[])
   double *epj, vepp;    double *epj, vepp;
   double kk1, kk2;    double kk1, kk2;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
     
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
Line 3128  int main(int argc, char *argv[]) Line 3343  int main(int argc, char *argv[])
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     
   /* long total_usecs;    /* long total_usecs;
   struct timeval start_time, end_time;       struct timeval start_time, end_time;
       
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   getcwd(pathcd, size);    getcwd(pathcd, size);
   
   printf("\n%s",version);    printf("\n%s",version);
Line 3147  int main(int argc, char *argv[]) Line 3362  int main(int argc, char *argv[])
   /* cutv(path,optionfile,pathtot,'\\');*/    /* cutv(path,optionfile,pathtot,'\\');*/
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);    chdir(path);
   replace(pathc,path);    replace(pathc,path);
   
 /*-------- arguments in the command line --------*/    /*-------- arguments in the command line --------*/
   
   /* Log file */    /* Log file */
   strcat(filelog, optionfilefiname);    strcat(filelog, optionfilefiname);
Line 3199  int main(int argc, char *argv[]) Line 3414  int main(int argc, char *argv[])
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d 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 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 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 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){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     puts(line);      puts(line);
Line 3209  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3424  while((c=getc(ficpar))=='#' && c!= EOF){
       
         
   covar=matrix(0,NCOVMAX,1,n);     covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0;     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
   ncovmodel=2+cptcovn;    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
       
   /* Read guess parameters */    /* Read guess parameters */
Line 3226  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3441  while((c=getc(ficpar))=='#' && c!= EOF){
   ungetc(c,ficpar);    ungetc(c,ficpar);
       
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)    for(i=1; i <=nlstate; i++)
     for(j=1; j <=nlstate+ndeath-1; j++){      for(j=1; j <=nlstate+ndeath-1; j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        fscanf(ficpar,"%1d%1d",&i1,&j1);
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficparo,"%1d%1d",i1,j1);
Line 3250  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3465  while((c=getc(ficpar))=='#' && c!= EOF){
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
       
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
   p=param[1][1];    p=param[1][1];
       
Line 3323  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3538  while((c=getc(ficpar))=='#' && c!= EOF){
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/    /*-------- Rewriting paramater file ----------*/
      strcpy(rfileres,"r");    /* "Rparameterfile */    strcpy(rfileres,"r");    /* "Rparameterfile */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
      strcat(rfileres,".");    /* */    strcat(rfileres,".");    /* */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {    if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }    }
     fprintf(ficres,"#%s\n",version);    fprintf(ficres,"#%s\n",version);
           
     /*-------- data file ----------*/    /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;      printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }    }
   
     n= lastobs;    n= lastobs;
     severity = vector(1,maxwav);    severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);    outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);    num=ivector(1,n);
     moisnais=vector(1,n);    moisnais=vector(1,n);
     annais=vector(1,n);    annais=vector(1,n);
     moisdc=vector(1,n);    moisdc=vector(1,n);
     andc=vector(1,n);    andc=vector(1,n);
     agedc=vector(1,n);    agedc=vector(1,n);
     cod=ivector(1,n);    cod=ivector(1,n);
     weight=vector(1,n);    weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);    s=imatrix(1,maxwav+1,1,n);
     adl=imatrix(1,maxwav+1,1,n);        tab=ivector(1,NCOVMAX);
     tab=ivector(1,NCOVMAX);    ncodemax=ivector(1,8);
     ncodemax=ivector(1,8);  
     i=1;
     i=1;    while (fgets(line, MAXLINE, fic) != NULL)    {
     while (fgets(line, MAXLINE, fic) != NULL)    {      if ((i >= firstobs) && (i <=lastobs)) {
       if ((i >= firstobs) && (i <=lastobs)) {  
                   
         for (j=maxwav;j>=1;j--){        for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);          strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }        }
                   
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){        for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }         } 
         num[i]=atol(stra);        num[i]=atol(stra);
                   
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        /*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;}*/          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;        i=i+1;
       }      }
     }     }
     /* printf("ii=%d", ij);    /* printf("ii=%d", ij);
        scanf("%d",i);*/       scanf("%d",i);*/
   imx=i-1; /* Number of individuals */    imx=i-1; /* Number of individuals */
   
   /* for (i=1; i<=imx; i++){    /* for (i=1; i<=imx; i++){
Line 3409  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3623  while((c=getc(ficpar))=='#' && c!= EOF){
   Tvard=imatrix(1,15,1,2);    Tvard=imatrix(1,15,1,2);
   Tage=ivector(1,15);          Tage=ivector(1,15);      
         
   if (strlen(model) >1){    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=1, k2=1;      j=0, j1=0, k1=1, k2=1;
     j=nbocc(model,'+');      j=nbocc(model,'+'); /* j=Number of '+' */
     j1=nbocc(model,'*');      j1=nbocc(model,'*'); /* j1=Number of '*' */
     cptcovn=j+1;      cptcovn=j+1; 
     cptcovprod=j1;      cptcovprod=j1; /*Number of products */
           
     strcpy(modelsav,model);       strcpy(modelsav,model); 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
Line 3423  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3637  while((c=getc(ficpar))=='#' && c!= EOF){
       goto end;        goto end;
     }      }
           
       /* This loop fills the array Tvar from the string 'model'.*/
   
     for(i=(j+1); i>=1;i--){      for(i=(j+1); i>=1;i--){
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
       /*scanf("%d",i);*/        /*scanf("%d",i);*/
       if (strchr(strb,'*')) {  /* Model includes a product */        if (strchr(strb,'*')) {  /* Model includes a product */
Line 3472  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3688  while((c=getc(ficpar))=='#' && c!= EOF){
     } /* end of loop + */      } /* end of loop + */
   } /* end model */    } /* end model */
       
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   printf("cptcovprod=%d ", cptcovprod);    printf("cptcovprod=%d ", cptcovprod);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   scanf("%d ",i);*/  
     fclose(fic);    scanf("%d ",i);
     fclose(fic);*/
   
     /*  if(mle==1){*/      /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/    if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;      for(i=1;i<=n;i++) weight[i]=1.0;
     }    }
     /*-calculation of age at interview from date of interview and age at death -*/      /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);    agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {    for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {      for(m=2; (m<= maxwav); m++) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;          anint[m][i]=9999;
          s[m][i]=-1;          s[m][i]=-1;
        }        }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) 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++)  {    for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){      for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){        if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)            if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)              if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
            else {              else {
               if (andc[i]!=9999){                if (andc[i]!=9999){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                  printf("Warning negative age at death: %d line:%d\n",num[i],i);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
               agev[m][i]=-1;                  agev[m][i]=-1;
               }                }
             }              }
           }          }
           else if(s[m][i] !=9){ /* Should no more exist */          else if(s[m][i] !=9){ /* Standard case, age in fractional
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                                   years but with the precision of a
             if(mint[m][i]==99 || anint[m][i]==9999)                                   month */
               agev[m][i]=1;            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             else if(agev[m][i] <agemin){             if(mint[m][i]==99 || anint[m][i]==9999)
               agemin=agev[m][i];  
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
             }  
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/  
           }  
           else { /* =9 */  
             agev[m][i]=1;              agev[m][i]=1;
             s[m][i]=-1;            else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
           }            }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
         }          }
         else /*= 0 Unknown */          else { /* =9 */
           agev[m][i]=1;            agev[m][i]=1;
             s[m][i]=-1;
           }
       }        }
             else /*= 0 Unknown */
           agev[m][i]=1;
     }      }
     for (i=1; i<=imx; i++)  {      
       for(m=1; (m<= maxwav); m++){    }
         if (s[m][i] > (nlstate+ndeath)) {    for (i=1; i<=imx; i++)  {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);         for(m=1; (m<= maxwav); m++){
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);           if (s[m][i] > (nlstate+ndeath)) {
           goto end;          printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         }          fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
       }        }
     }      }
     }
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);    free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);    free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);    free_vector(moisnais,1,n);
     free_vector(annais,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(moisdc,1,n);
     free_vector(andc,1,n);    free_vector(andc,1,n);
   
         
     wav=ivector(1,imx);    wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    dh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
         
     /* Concatenates waves */    /* Concatenates waves */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
       Tcode=ivector(1,100);    Tcode=ivector(1,100);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     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);    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
    h=0;                                   the estimations*/
    m=pow(2,cptcoveff);    h=0;
     m=pow(2,cptcoveff);
     
    for(k=1;k<=cptcoveff; k++){    for(k=1;k<=cptcoveff; k++){
      for(i=1; i <=(m/pow(2,k));i++){      for(i=1; i <=(m/pow(2,k));i++){
        for(j=1; j <= ncodemax[k]; j++){        for(j=1; j <= ncodemax[k]; j++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
            h++;            h++;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[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("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
          }           } 
        }  
      }  
    }   
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);   
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){   
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  
       }  
       printf("\n");  
       }        }
       scanf("%d",i);*/      }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
           
    /* Calculates basic frequencies. Computes observed prevalence at single age    /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */       and prints on file fileres'p'. */
   
       
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= 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 */      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= 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 */      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] */    /* For Powell, parameters are in a vector p[] starting at p[1]
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle==1){    if(mle>=1){ /* Could be 1 or 2 */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }    }
           
     /*--------- results files --------------*/    /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);    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;    jk=1;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
      for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i)         if (k != i) 
          {          {
            printf("%d%d ",i,k);            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficres,"%1d%1d ",i,k);
            for(j=1; j <=ncovmodel; j++){            for(j=1; j <=ncovmodel; j++){
              printf("%f ",p[jk]);              printf("%f ",p[jk]);
              fprintf(ficlog,"%f ",p[jk]);              fprintf(ficlog,"%f ",p[jk]);
              fprintf(ficres,"%f ",p[jk]);              fprintf(ficres,"%f ",p[jk]);
              jk++;               jk++; 
            }            }
            printf("\n");            printf("\n");
            fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");            fprintf(ficres,"\n");
          }          }
      }      }
    }    }
    if(mle==1){    if(mle==1){
      /* Computing hessian and covariance matrix */      /* Computing hessian and covariance matrix */
      ftolhess=ftol; /* Usually correct */      ftolhess=ftol; /* Usually correct */
      hesscov(matcov, p, npar, delti, ftolhess, func);      hesscov(matcov, p, npar, delti, ftolhess, func);
    }    }
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
    printf("# Scales (for hessian or gradient estimation)\n");    printf("# Scales (for hessian or gradient estimation)\n");
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
    for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
      for(j=1; j <=nlstate+ndeath; j++){      for(j=1; j <=nlstate+ndeath; j++){
        if (j!=i) {        if (j!=i) {
          fprintf(ficres,"%1d%1d",i,j);          fprintf(ficres,"%1d%1d",i,j);
          printf("%1d%1d",i,j);          printf("%1d%1d",i,j);
          fprintf(ficlog,"%1d%1d",i,j);          fprintf(ficlog,"%1d%1d",i,j);
          for(k=1; k<=ncovmodel;k++){          for(k=1; k<=ncovmodel;k++){
            printf(" %.5e",delti[jk]);            printf(" %.5e",delti[jk]);
            fprintf(ficlog," %.5e",delti[jk]);            fprintf(ficlog," %.5e",delti[jk]);
            fprintf(ficres," %.5e",delti[jk]);            fprintf(ficres," %.5e",delti[jk]);
            jk++;            jk++;
          }          }
          printf("\n");          printf("\n");
          fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
          fprintf(ficres,"\n");          fprintf(ficres,"\n");
        }        }
      }      }
    }    }
         
    k=1;    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    if(mle==1)
    if(mle==1)      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
    fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    for(i=1,k=1;i<=npar;i++){
    for(i=1;i<=npar;i++){      /*  if (k>nlstate) k=1;
      /*  if (k>nlstate) k=1;          i1=(i-1)/(ncovmodel*nlstate)+1; 
          i1=(i-1)/(ncovmodel*nlstate)+1;           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          printf("%s%d%d",alph[k],i1,tab[i]);
          printf("%s%d%d",alph[k],i1,tab[i]);*/      */
      fprintf(ficres,"%3d",i);      fprintf(ficres,"%3d",i);
      if(mle==1)      if(mle==1)
        printf("%3d",i);        printf("%3d",i);
      fprintf(ficlog,"%3d",i);      fprintf(ficlog,"%3d",i);
      for(j=1; j<=i;j++){      for(j=1; j<=i;j++){
        fprintf(ficres," %.5e",matcov[i][j]);        fprintf(ficres," %.5e",matcov[i][j]);
        if(mle==1)        if(mle==1)
          printf(" %.5e",matcov[i][j]);          printf(" %.5e",matcov[i][j]);
        fprintf(ficlog," %.5e",matcov[i][j]);        fprintf(ficlog," %.5e",matcov[i][j]);
      }      }
      fprintf(ficres,"\n");      fprintf(ficres,"\n");
      if(mle==1)      if(mle==1)
        printf("\n");        printf("\n");
      fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
      k++;      k++;
    }    }
         
    while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
      puts(line);      puts(line);
      fputs(line,ficparo);      fputs(line,ficparo);
    }    }
    ungetc(c,ficpar);    ungetc(c,ficpar);
    estepm=0;  
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    estepm=0;
    if (estepm==0 || estepm < stepm) estepm=stepm;    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
    if (fage <= 2) {    if (estepm==0 || estepm < stepm) estepm=stepm;
      bage = ageminpar;    if (fage <= 2) {
      fage = agemaxpar;      bage = ageminpar;
    }      fage = agemaxpar;
     }
         
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
         
    while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
      puts(line);      puts(line);
      fputs(line,ficparo);      fputs(line,ficparo);
    }    }
    ungetc(c,ficpar);    ungetc(c,ficpar);
       
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav);    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav);    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
         
    while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
      puts(line);      puts(line);
      fputs(line,ficparo);      fputs(line,ficparo);
    }    }
    ungetc(c,ficpar);    ungetc(c,ficpar);
     
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    fscanf(ficpar,"pop_based=%d\n",&popbased);
   fprintf(ficparo,"pop_based=%d\n",popbased);       fprintf(ficparo,"pop_based=%d\n",popbased);   
Line 3753  printf("Total number of individuals= %d, Line 3980  printf("Total number of individuals= %d,
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",&prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
 while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     puts(line);      puts(line);
Line 3770  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3999  while((c=getc(ficpar))=='#' && c!= EOF){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 /*------------ gnuplot -------------*/  
  strcpy(optionfilegnuplot,optionfilefiname);    /*------------ gnuplot -------------*/
  strcat(optionfilegnuplot,".gp");    strcpy(optionfilegnuplot,optionfilefiname);
  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    strcat(optionfilegnuplot,".gp");
    printf("Problem with file %s",optionfilegnuplot);    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
  }      printf("Problem with file %s",optionfilegnuplot);
  else{    }
    fprintf(ficgp,"\n# %s\n", version);     else{
    fprintf(ficgp,"# %s\n", optionfilegnuplot);       fprintf(ficgp,"\n# %s\n", version); 
    fprintf(ficgp,"set missing 'NaNq'\n");      fprintf(ficgp,"# %s\n", optionfilegnuplot); 
 }      fprintf(ficgp,"set missing 'NaNq'\n");
  fclose(ficgp);    }
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    fclose(ficgp);
 /*--------- index.htm --------*/    printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfile);    strcpy(optionfilehtm,optionfile);
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
Line 3804  Interval (in months) between two waves: Line 4034  Interval (in months) between two waves:
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);   - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
   fclose(fichtm);    fclose(fichtm);
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
     
 /*------------ free_vector  -------------*/    /*------------ free_vector  -------------*/
  chdir(path);    chdir(path);
     
  free_ivector(wav,1,imx);    free_ivector(wav,1,imx);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
  free_ivector(num,1,n);    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
  free_vector(agedc,1,n);    free_ivector(num,1,n);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    free_vector(agedc,1,n);
  fclose(ficparo);    /*free_matrix(covar,0,NCOVMAX,1,n);*/
  fclose(ficres);    /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
   /*--------------- Prevalence limit  (stable prevalence) --------------*/    /*--------------- Prevalence limit  (stable prevalence) --------------*/
Line 3835  Interval (in months) between two waves: Line 4067  Interval (in months) between two waves:
   fprintf(ficrespl,"\n");    fprintf(ficrespl,"\n");
       
   prlim=matrix(1,nlstate,1,nlstate);    prlim=matrix(1,nlstate,1,nlstate);
   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 */  
   k=0;  
   agebase=ageminpar;    agebase=ageminpar;
   agelim=agemaxpar;    agelim=agemaxpar;
   ftolpl=1.e-10;    ftolpl=1.e-10;
   i1=cptcoveff;    i1=cptcoveff;
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;        k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");        fprintf(ficrespl,"\n#******");
         printf("\n#******");        printf("\n#******");
         fprintf(ficlog,"\n#******");        fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }        }
         fprintf(ficrespl,"******\n");        fprintf(ficrespl,"******\n");
         printf("******\n");        printf("******\n");
         fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
                   
         for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f",age );          fprintf(ficrespl,"%.0f ",age );
           for(i=1; i<=nlstate;i++)          for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
           fprintf(ficrespl," %.5f", prlim[i][i]);            fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");          fprintf(ficrespl,"\n");
         }  
       }        }
     }      }
     }
   fclose(ficrespl);    fclose(ficrespl);
   
   /*------------- h Pij x at various ages ------------*/    /*------------- h Pij x at various ages ------------*/
Line 3893  Interval (in months) between two waves: Line 4122  Interval (in months) between two waves:
   
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   
   k=0;    fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;        k=k+1;
         fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
                   
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");          fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
           for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)              for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);                fprintf(ficrespij," %.5f", p3mat[i][j][h]);
           fprintf(ficrespij,"\n");  
            for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");  
              }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");            fprintf(ficrespij,"\n");
         }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
     }      }
   }    }
   
Line 3935  Interval (in months) between two waves: Line 4164  Interval (in months) between two waves:
   
   
   /*---------- Forecasting ------------------*/    /*---------- Forecasting ------------------*/
   if((stepm == 1) && (strcmp(model,".")==0)){    /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    if(prevfcast==1){
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      if(stepm ==1){
   }         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
   else{        if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     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);      else{
     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);        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);
         fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       }
   }    }
       
   
Line 3975  Interval (in months) between two waves: Line 4207  Interval (in months) between two waves:
   }    }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   calagedate=-1;  
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   
   if (mobilav!=0) {    if (mobilav!=0) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
Line 3985  Interval (in months) between two waves: Line 4218  Interval (in months) between two waves:
     }      }
   }    }
   
   k=0;    for(cptcov=1,k=0;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(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
Line 4013  Interval (in months) between two waves: Line 4245  Interval (in months) between two waves:
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);        varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
       if(popbased==1){        if(popbased==1){
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
        }        }
   
     
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
Line 4051  Interval (in months) between two waves: Line 4283  Interval (in months) between two waves:
         }          }
         fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
       }        }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
     }      }
   }    }
 free_matrix(mint,1,maxwav,1,n);    free_vector(weight,1,n);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    free_imatrix(Tvard,1,15,1,2);
     free_vector(weight,1,n);    free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
   fclose(ficreseij);    fclose(ficreseij);
   fclose(ficresvij);    fclose(ficresvij);
   fclose(ficrest);    fclose(ficrest);
   fclose(ficpar);    fclose(ficpar);
   free_vector(epj,1,nlstate+1);  
       
   /*------- Variance of stable prevalence------*/       /*------- Variance of stable prevalence------*/   
   
Line 4072  free_matrix(mint,1,maxwav,1,n); Line 4310  free_matrix(mint,1,maxwav,1,n);
   }    }
   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);    printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
   k=0;    for(cptcov=1,k=0;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#****** ");
Line 4083  free_matrix(mint,1,maxwav,1,n); Line 4320  free_matrix(mint,1,maxwav,1,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);        varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     }      }
  }    }
   
   fclose(ficresvpl);    fclose(ficresvpl);
   
   /*---------- End : free ----------------*/    /*---------- End : free ----------------*/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
     
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
     
     
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(newms, 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(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
      
     free_matrix(covar,0,NCOVMAX,1,n);
   free_matrix(matcov,1,npar,1,npar);    free_matrix(matcov,1,npar,1,npar);
   free_vector(delti,1,npar);    free_vector(delti,1,npar);
   free_matrix(agev,1,maxwav,1,imx);    free_matrix(agev,1,maxwav,1,imx);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
   fprintf(fichtm,"\n</body>");    fprintf(fichtm,"\n</body>");
   fclose(fichtm);    fclose(fichtm);
Line 4127  free_matrix(mint,1,maxwav,1,n); Line 4366  free_matrix(mint,1,maxwav,1,n);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    /*printf("Total time was %d uSec.\n", total_usecs);*/
   /*------ End -----------*/    /*------ End -----------*/
   
     end:
  end:  
 #ifdef windows  #ifdef windows
   /* chdir(pathcd);*/    /* chdir(pathcd);*/
 #endif   #endif 
Line 4136  free_matrix(mint,1,maxwav,1,n); Line 4374  free_matrix(mint,1,maxwav,1,n);
  /*system("../gp37mgw/wgnuplot graph.plt");*/   /*system("../gp37mgw/wgnuplot graph.plt");*/
  /*system("cd ../gp37mgw");*/   /*system("cd ../gp37mgw");*/
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/   /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
  strcpy(plotcmd,GNUPLOTPROGRAM);    strcpy(plotcmd,GNUPLOTPROGRAM);
  strcat(plotcmd," ");    strcat(plotcmd," ");
  strcat(plotcmd,optionfilegnuplot);    strcat(plotcmd,optionfilegnuplot);
  printf("Starting: %s\n",plotcmd);fflush(stdout);    printf("Starting: %s\n",plotcmd);fflush(stdout);
  system(plotcmd);    system(plotcmd);
   
  /*#ifdef windows*/   /*#ifdef windows*/
   while (z[0] != 'q') {    while (z[0] != 'q') {

Removed from v.1.56  
changed lines
  Added in v.1.70


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