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Diff for /imach/src/imach.c between versions 1.58 and 1.67

version 1.58, 2002/07/26 12:29:55 version 1.67, 2003/01/28 17:41:19
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 0.91, November 2002, 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;
   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 1482  void prevalence(int agemin, float agemax Line 1641  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 1558  void  concatwav(int wav[], int **dh, int Line 1717  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);
             }
             if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
           }
         } /* 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 1666  void evsij(char fileres[], double ***eij Line 1846  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 1856  void varevsij(char optionfilefiname[], d Line 2036  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 1878  void varevsij(char optionfilefiname[], d Line 2058  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 1913  void varevsij(char optionfilefiname[], d Line 2093  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 1929  void varevsij(char optionfilefiname[], d Line 2109  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 1951  void varevsij(char optionfilefiname[], d Line 2131  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
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
         for(i=1; i<= nlstate; i++)          for(i=1; 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 1979  void varevsij(char optionfilefiname[], d Line 2162  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
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
         for(i=1; i<= nlstate; i++)          for(i=1; 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 */
   
       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++){
Line 2029  void varevsij(char optionfilefiname[], d Line 2215  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 2042  void varevsij(char optionfilefiname[], d Line 2229  void varevsij(char optionfilefiname[], d
       }        }
     }      }
           
     /* This for computing force of mortality (h=1)as a weighted average */      /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
       for(i=1; i<= nlstate; i++)        for(i=1; 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 2077  void varevsij(char optionfilefiname[], d Line 2267  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 2102  void varevsij(char optionfilefiname[], d Line 2295  void varevsij(char optionfilefiname[], d
 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 2274  void varprob(char optionfilefiname[], do Line 2467  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 2282  void varprob(char optionfilefiname[], do Line 2474  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]]);
Line 2355  void varprob(char optionfilefiname[], do Line 2546  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 2370  void varprob(char optionfilefiname[], do Line 2565  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 2401  void varprob(char optionfilefiname[], do Line 2596  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 2479  void varprob(char optionfilefiname[], do Line 2674  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 2929  populforecast(char fileres[], double anp Line 3120  populforecast(char fileres[], double anp
       
   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 calagedate, agelim, kk1, kk2;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat,***tabpop,***tabpopprev;    double ***p3mat,***tabpop,***tabpopprev;
   double ***mobaverage;    double ***mobaverage;
Line 3090  populforecast(char fileres[], double anp Line 3281  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 3109  int main(int argc, char *argv[]) Line 3300  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 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, calagedate;
Line 3128  int main(int argc, char *argv[]) Line 3319  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 3139  int main(int argc, char *argv[]) Line 3329  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 3158  int main(int argc, char *argv[]) Line 3348  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 3210  int main(int argc, char *argv[]) Line 3400  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 3237  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3427  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 3261  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3451  while((c=getc(ficpar))=='#' && c!= EOF){
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
       
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
   p=param[1][1];    p=param[1][1];
       
Line 3334  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3524  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 3434  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3623  while((c=getc(ficpar))=='#' && c!= EOF){
       goto end;        goto end;
     }      }
           
     /* This loop fill the array Tvar from the string 'model'.*/      /* 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 3496  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3685  while((c=getc(ficpar))=='#' && c!= EOF){
   fclose(fic);*/    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){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)            if(mint[m][i]==99 || anint[m][i]==9999)
               agev[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 { /* =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 */    /* 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); /* Cross tabulation to get the order of     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                      the estimations*/                                   the estimations*/
    h=0;    h=0;
    m=pow(2,cptcoveff);    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);
         
    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+mprev1/12.+jprev1/365.;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
   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 3773  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3963  while((c=getc(ficpar))=='#' && c!= EOF){
   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,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,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 3789  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3979  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 -------------*/    /*------------ gnuplot -------------*/
  strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
  strcat(optionfilegnuplot,".gp");    strcat(optionfilegnuplot,".gp");
  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
    printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
  }    }
  else{    else{
    fprintf(ficgp,"\n# %s\n", version);       fprintf(ficgp,"\n# %s\n", version); 
    fprintf(ficgp,"# %s\n", optionfilegnuplot);       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
    fprintf(ficgp,"set missing 'NaNq'\n");      fprintf(ficgp,"set missing 'NaNq'\n");
 }    }
  fclose(ficgp);    fclose(ficgp);
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
 /*--------- index.htm --------*/    /*--------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfile);    strcpy(optionfilehtm,optionfile);
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
Line 3824  Interval (in months) between two waves: Line 4014  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 3855  Interval (in months) between two waves: Line 4047  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(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 3913  Interval (in months) between two waves: Line 4100  Interval (in months) between two waves:
   
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   
   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(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,"# Age");
           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 %f %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 4008  Interval (in months) between two waves: Line 4194  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 4036  Interval (in months) between two waves: Line 4221  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 4074  Interval (in months) between two waves: Line 4259  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 4095  free_matrix(mint,1,maxwav,1,n); Line 4286  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 4106  free_matrix(mint,1,maxwav,1,n); Line 4296  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 4150  free_matrix(mint,1,maxwav,1,n); Line 4342  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 4159  free_matrix(mint,1,maxwav,1,n); Line 4350  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.1.58  
changed lines
  Added in v.1.67

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