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version 1.17, 2002/02/20 17:15:02 version 1.26, 2002/02/27 15:42:00
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      /* $Id$
 /*********************** Imach **************************************             Interpolated Markov Chain
   This program computes Healthy Life Expectancies from cross-longitudinal  
   data. Cross-longitudinal consist in a first survey ("cross") where    Short summary of the programme:
   individuals from different ages are interviewed on their health status   
   or degree of  disability. At least a second wave of interviews    This program computes Healthy Life Expectancies from
   ("longitudinal") should  measure each new individual health status.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Health expectancies are computed from the transistions observed between    first survey ("cross") where individuals from different ages are
   waves and are computed for each degree of severity of disability (number    interviewed on their health status or degree of disability (in the
   of life states). More degrees you consider, more time is necessary to    case of a health survey which is our main interest) -2- at least a
   reach the Maximum Likelihood of the parameters involved in the model.    second wave of interviews ("longitudinal") which measure each change
   The simplest model is the multinomial logistic model where pij is    (if any) in individual health status.  Health expectancies are
   the probabibility to be observed in state j at the second wave conditional    computed from the time spent in each health state according to a
   to be observed in state i at the first wave. Therefore the model is:    model. More health states you consider, more time is necessary to reach the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Maximum Likelihood of the parameters involved in the model.  The
   is a covariate. If you want to have a more complex model than "constant and    simplest model is the multinomial logistic model where pij is the
   age", you should modify the program where the markup    probabibility to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month or quarter trimester,
     semester or year) is model as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
     hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the prevalence limits.
Line 48 Line 56
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
   #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
Line 67 Line 76
 #define AGEBASE 40  #define AGEBASE 40
   
   
   int erreur; /* Error number */
 int nvar;  int nvar;
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;  int npar=NPARMAX;
Line 85  double jmean; /* Mean space between 2 wa Line 95  double jmean; /* Mean space between 2 wa
 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 */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  FILE *ficgp,*ficresprob,*ficpop;
 FILE *ficreseij;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];    char filerese[FILENAMELENGTH];
  FILE  *ficresvij;   FILE  *ficresvij;
Line 113  FILE *ficreseij; Line 123  FILE *ficreseij;
 static double maxarg1,maxarg2;  static double maxarg1,maxarg2;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)  #define rint(a) floor(a+0.5)
   
Line 129  int m,nb; Line 139  int m,nb;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs, ***mobaverage;  double **pmmij, ***probs, ***mobaverage;
   double dateintmean=0;
   
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
Line 139  double ftol=FTOL; /* Tolerance for compu Line 150  double ftol=FTOL; /* Tolerance for compu
 double ftolhess; /* Tolerance for computing hessian */  double ftolhess; /* Tolerance for computing hessian */
   
 /**************** split *************************/  /**************** split *************************/
 static  int split( char *path, char *dirc, char *name )  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
    char *s;                             /* pointer */     char *s;                             /* 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 );
   #ifdef windows
    s = strrchr( path, '\\' );           /* find last / */     s = strrchr( path, '\\' );           /* find last / */
   #else
      s = strrchr( path, '/' );            /* find last / */
   #endif
    if ( s == NULL ) {                   /* no directory, so use current */     if ( s == NULL ) {                   /* no directory, so use current */
 #if     defined(__bsd__)                /* get current working directory */  #if     defined(__bsd__)                /* get current working directory */
       extern char       *getwd( );        extern char       *getwd( );
Line 169  static int split( char *path, char *dirc Line 184  static int split( char *path, char *dirc
       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
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   #else
      if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
      s = strrchr( name, '.' );            /* find last / */
      s++;
      strcpy(ext,s);                       /* save extension */
      l1= strlen( name);
      l2= strlen( s)+1;
      strncpy( finame, name, l1-l2);
      finame[l1-l2]= 0;
    return( 0 );                         /* we're done */     return( 0 );                         /* we're done */
 }  }
   
Line 717  double **pmij(double **ps, double *cov, Line 743  double **pmij(double **ps, double *cov,
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       }        }
       ps[i][j]=(s2);        ps[i][j]=s2;
     }      }
   }    }
     /*ps[3][2]=1;*/      /*ps[3][2]=1;*/
Line 900  void mlikeli(FILE *ficres,double p[], in Line 926  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(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
 }  }
   
Line 1150  void lubksb(double **a, int n, int *indx Line 1176  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, int fprev1,int lprev1,double **mint,double **anint)  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
 {  /* Some frequencies */  {  /* Some frequencies */
     
   int i, m, jk, k1, k2,i1, j1, bool, z1,z2,j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp;    double *pp;
   double pos;    double pos, k2, dateintsum=0,k2cpt=0;
   FILE *ficresp;    FILE *ficresp;
   char fileresp[FILENAMELENGTH];    char fileresp[FILENAMELENGTH];
   
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   probs= ma3x(1,130 ,1,8, 1,8);    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresp,"p");    strcpy(fileresp,"p");
   strcat(fileresp,fileres);    strcat(fileresp,fileres);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
Line 1183  void  freqsummary(char fileres[], int ag Line 1209  void  freqsummary(char fileres[], int ag
          for (jk=-1; jk<=nlstate+ndeath; jk++)             for (jk=-1; jk<=nlstate+ndeath; jk++)  
            for(m=agemin; m <= agemax+3; m++)             for(m=agemin; m <= agemax+3; m++)
              freq[i][jk][m]=0;               freq[i][jk][m]=0;
          
           dateintsum=0;
           k2cpt=0;
        for (i=1; i<=imx; i++) {         for (i=1; i<=imx; i++) {
          bool=1;           bool=1;
          if  (cptcovn>0) {           if  (cptcovn>0) {
Line 1191  void  freqsummary(char fileres[], int ag Line 1219  void  freqsummary(char fileres[], int ag
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                bool=0;                 bool=0;
          }           }
           if (bool==1) {           if (bool==1) {
             for(m=fprev1; m<=lprev1; m++){             for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);               k2=anint[m][i]+(mint[m][i]/12.);
              if ((k2>=1984) && (k2<=1988.5)) {               if ((k2>=dateprev1) && (k2<=dateprev2)) {
              if(agev[m][i]==0) agev[m][i]=agemax+1;                 if(agev[m][i]==0) agev[m][i]=agemax+1;
              if(agev[m][i]==1) agev[m][i]=agemax+2;                 if(agev[m][i]==1) agev[m][i]=agemax+2;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
                  if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
                    dateintsum=dateintsum+k2;
                    k2cpt++;
                  }
   
              }               }
             }             }
           }           }
        }         }
          
          fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
         if  (cptcovn>0) {          if  (cptcovn>0) {
          fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 1261  void  freqsummary(char fileres[], int ag Line 1297  void  freqsummary(char fileres[], int ag
     }      }
     }      }
  }   }
     dateintmean=dateintsum/k2cpt;
     
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   
 }  /* End of Freq */    /* End of Freq */
   }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)  void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
 {  /* 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;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp;    double *pp;
   double pos;    double pos, k2;
   
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   probs= ma3x(1,130 ,1,8, 1,8);    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   j1=0;    j1=0;
Line 1293  void prevalence(int agemin, int agemax, Line 1331  void prevalence(int agemin, int agemax,
       for (i=-1; i<=nlstate+ndeath; i++)          for (i=-1; i<=nlstate+ndeath; i++)  
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for (jk=-1; jk<=nlstate+ndeath; jk++)  
           for(m=agemin; m <= agemax+3; m++)            for(m=agemin; m <= agemax+3; m++)
           freq[i][jk][m]=0;              freq[i][jk][m]=0;
             
       for (i=1; i<=imx; i++) {        for (i=1; i<=imx; i++) {
         bool=1;          bool=1;
Line 1301  void prevalence(int agemin, int agemax, Line 1339  void prevalence(int agemin, int agemax,
           for (z1=1; z1<=cptcoveff; z1++)            for (z1=1; z1<=cptcoveff; z1++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
               bool=0;                bool=0;
               }          }
         if (bool==1) {          if (bool==1) {
           for(m=fprev1; m<=lprev1; m++){            for(m=firstpass; m<=lastpass; m++){
             if(agev[m][i]==0) agev[m][i]=agemax+1;              k2=anint[m][i]+(mint[m][i]/12.);
             if(agev[m][i]==1) agev[m][i]=agemax+2;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                if(agev[m][i]==0) agev[m][i]=agemax+1;
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                if(agev[m][i]==1) agev[m][i]=agemax+2;
                 freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  
               }
           }            }
         }          }
       }        }
        for(i=(int)agemin; i <= (int)agemax+3; i++){       
         for(jk=1; jk <=nlstate ; jk++){          for(i=(int)agemin; i <= (int)agemax+3; i++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            for(jk=1; jk <=nlstate ; jk++){
             pp[jk] += freq[jk][m][i];              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         }                pp[jk] += freq[jk][m][i];
         for(jk=1; jk <=nlstate ; jk++){            }
           for(m=-1, pos=0; m <=0 ; m++)            for(jk=1; jk <=nlstate ; jk++){
               for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][i];              pos += freq[jk][m][i];
         }          }
                 
Line 1336  void prevalence(int agemin, int agemax, Line 1378  void prevalence(int agemin, int agemax,
            }             }
          }           }
                     
          }          }
     }      }
   }    }
     
Line 1345  void prevalence(int agemin, int agemax, Line 1387  void prevalence(int agemin, int agemax,
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
     
 }  /* End of Freq */  }  /* End of Freq */
   
 /************* 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 **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
Line 1580  void varevsij(char fileres[], double *** Line 1623  void varevsij(char fileres[], double ***
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           prlim[i][i]=probs[(int)age][i][ij];            prlim[i][i]=probs[(int)age][i][ij];
       }        }
         
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
Line 1592  void varevsij(char fileres[], double *** Line 1635  void varevsij(char fileres[], double ***
         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);
    
       if (popbased==1) {        if (popbased==1) {
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           prlim[i][i]=probs[(int)age][i][ij];            prlim[i][i]=probs[(int)age][i][ij];
Line 1644  void varevsij(char fileres[], double *** Line 1687  void varevsij(char fileres[], double ***
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   } /* End age */    } /* End age */
     
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(doldm,1,nlstate,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_matrix(dnewm,1,nlstate,1,nlstate);
Line 1836  if (i== 4) fprintf(ficresprob,"%.3e %.3e Line 1879  if (i== 4) fprintf(ficresprob,"%.3e %.3e
 }  }
  free_vector(xp,1,npar);   free_vector(xp,1,npar);
 fclose(ficresprob);  fclose(ficresprob);
  exit(0);  
 }  
   
 /***********************************************/  
 /**************** Main Program *****************/  
 /***********************************************/  
   
 /*int main(int argc, char *argv[])*/  }
 int main()  
 {  
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  /******************* Printing html file ***********/
   double agedeb, agefin,hf;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){
   double agemin=1.e20, agemax=-1.e20;    int jj1, k1, i1, cpt;
     FILE *fichtm;
     /*char optionfilehtm[FILENAMELENGTH];*/
   
   double fret;    strcpy(optionfilehtm,optionfile);
   double **xi,tmp,delta;    strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
   double dum; /* Dummy variable */   fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
   double ***p3mat;  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];  
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;  
   int hstepm, nhstepm;  
   int *popage;  
   
   double bage, fage, age, agelim, agebase;  Total number of observations=%d <br>
   double ftolpl=FTOL;  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
   double **prlim;  <hr  size=\"2\" color=\"#EC5E5E\">
   double *severity;  <li>Outputs files<br><br>\n
   double ***param; /* Matrix of parameters */          - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
   double  *p;  - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
   double **matcov; /* Matrix of covariance */          - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
   double ***delti3; /* Scale */          - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
   double *delti; /* Scale */          - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
   double ***eij, ***vareij;          - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
   double **varpl; /* Variances of prevalence limits by age */          - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
   double *epj, vepp;          - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
   double kk1, kk2;          - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
   double *popeffectif,*popcount;          - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
           <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
    
   fprintf(fichtm," <li>Graphs</li><p>");
   
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";   m=cptcoveff;
   char *alph[]={"a","a","b","c","d","e"}, str[4];   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
          jj1++;
          if (cptcovn > 0) {
            fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
            for (cpt=1; cpt<=cptcoveff;cpt++)
              fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
            fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
          }
          fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
   <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
   <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
       for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.gif <br>
   <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
   <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.gif<br>
   <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   fprintf(fichtm,"\n</body>");
      }
      }
   fclose(fichtm);
   }
   
   char z[1]="c", occ;  /******************* Gnuplot file **************/
 #include <sys/time.h>  void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
   /* long total_usecs;  
   struct timeval start_time, end_time;  
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   
   printf("\nIMACH, Version 0.7");    strcpy(optionfilegnuplot,optionfilefiname);
   printf("\nEnter the parameter file name: ");    strcat(optionfilegnuplot,".plt");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
   
 #ifdef windows  #ifdef windows
   scanf("%s",pathtot);      fprintf(ficgp,"cd \"%s\" \n",pathc);
   getcwd(pathcd, size);  #endif
   /*cygwin_split_path(pathtot,path,optionfile);  m=pow(2,cptcoveff);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/   
   /* cutv(path,optionfile,pathtot,'\\');*/   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   
 split(pathtot, path,optionfile);  #ifdef windows
   chdir(path);      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);
   replace(pathc,path);  
 #endif  #endif
 #ifdef unix  #ifdef unix
   scanf("%s",optionfile);  fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
 #endif  #endif
   
 /*-------- arguments in the command line --------*/  for (i=1; i<= nlstate ; i ++) {
     if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   strcpy(fileres,"r");    else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcat(fileres, optionfile);  }
       fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
   /*---------arguments file --------*/      for (i=1; i<= nlstate ; i ++) {
     if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("Problem with optionfile %s\n",optionfile);  }
     goto end;    fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
   }       for (i=1; i<= nlstate ; i ++) {
     if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   strcpy(filereso,"o");    else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcat(filereso,fileres);  }  
   if((ficparo=fopen(filereso,"w"))==NULL) {       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  #ifdef unix
   }  fprintf(ficgp,"\nset ter gif small size 400,300");
   #endif
   /* Reads comments: lines beginning with '#' */  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
   while((c=getc(ficpar))=='#' && c!= EOF){     }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  
   }    }
   ungetc(c,ficpar);    /*2 eme*/
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    for (k1=1; k1<= m ; k1 ++) {
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);      fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);     
 while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1; i<= nlstate+1 ; i ++) {
     ungetc(c,ficpar);        k=2*i;
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     puts(line);        for (j=1; j<= nlstate+1 ; j ++) {
     fputs(line,ficparo);    if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }    else fprintf(ficgp," \%%*lf (\%%*lf)");
   ungetc(c,ficpar);  }  
          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
  while((c=getc(ficpar))=='#' && c!= EOF){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     ungetc(c,ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fgets(line, MAXLINE, ficpar);  }  
     puts(line);        fprintf(ficgp,"\" t\"\" w l 0,");
     fputs(line,ficparo);       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   }        for (j=1; j<= nlstate+1 ; j ++) {
   ungetc(c,ficpar);    if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      else fprintf(ficgp," \%%*lf (\%%*lf)");
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);  }  
   fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
              else fprintf(ficgp,"\" t\"\" w l 0,");
        }
 while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  
   }    }
   ungetc(c,ficpar);  
    
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);  
     
   covar=matrix(0,NCOVMAX,1,n);    /*3eme*/
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   
   ncovmodel=2+cptcovn;    for (k1=1; k1<= m ; k1 ++) {
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(cpt-1);
         fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);
         }
         fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
       }
       }
    
     /* CV preval stat */
       for (k1=1; k1<= m ; k1 ++) {
       for (cpt=1; cpt<nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
   
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
        
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);  
         fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
       }
     }  
    
     /* proba elementaires */
      for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
          
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++;
             fprintf(ficgp,"\n");
           }
         }
       }
       }
   
       for(jk=1; jk <=m; jk++) {
     fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
      i=1;
      for(k2=1; k2<=nlstate; k2++) {
        k3=i;
        for(k=1; k<=(nlstate+ndeath); k++) {
          if (k != k2){
           fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   ij=1;
           for(j=3; j <=ncovmodel; j++) {
             if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
               fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
               ij++;
             }
             else
             fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           }
             fprintf(ficgp,")/(1");
          
           for(k1=1; k1 <=nlstate; k1++){  
             fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   ij=1;
             for(j=3; j <=ncovmodel; j++){
             if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
               fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
               ij++;
             }
             else
               fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             }
             fprintf(ficgp,")");
           }
           fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           i=i+ncovmodel;
          }
        }
      }
      fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
      }
      
     fclose(ficgp);
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){
   
     int i, cpt, cptcod;
       for (agedeb=agemin; agedeb<=fage; agedeb++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
             mobaverage[(int)agedeb][i][cptcod]=0.;
      
       for (agedeb=agemin+4; agedeb<=fage; agedeb++){
         for (i=1; i<=nlstate;i++){
           for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
             for (cpt=0;cpt<=4;cpt++){
               mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
             }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
           }
         }
       }
      
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   
     int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     double agedeb, agefin,hf;
     double agemin=1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char title[MAXLINE];
     char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    
     char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
   
     char filerest[FILENAMELENGTH];
     char fileregp[FILENAMELENGTH];
     char popfile[FILENAMELENGTH];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int *popage;/*boolprev=0 if date and zero if wave*/
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double *popeffectif,*popcount;
     double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
     double yp,yp1,yp2;
   
     char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
     struct timeval start_time, end_time;
    
     gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
      printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
   /*-------- arguments in the command line --------*/
   
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);
   while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
      
     covar=matrix(0,NCOVMAX,1,n);
     cptcovn=0;
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
   /* Read guess parameters */    /* Read guess parameters */
Line 2147  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2437  while((c=getc(ficpar))=='#' && c!= EOF){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
     }      }
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  
       for (i=1; i<=imx; i++)
       if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/
   
   /* Calculation of the number of parameter from char model*/    /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15);    Tvar=ivector(1,15);
Line 2326  printf("Total number of individuals= %d, Line 2618  printf("Total number of individuals= %d,
        }         }
      }       }
    }     }
   
   
      /*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'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint);  
       
   free_matrix(mint,1,maxwav,1,n);     
   free_matrix(anint,1,maxwav,1,n);      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 */
Line 2350  printf("Total number of individuals= %d, Line 2649  printf("Total number of individuals= %d,
         
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);
    fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);   
    fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);  
   
    jk=1;     jk=1;
    fprintf(ficres,"# Parameters\n");     fprintf(ficres,"# Parameters\n");
Line 2393  printf("Total number of individuals= %d, Line 2691  printf("Total number of individuals= %d,
           fprintf(ficres,"\n");            fprintf(ficres,"\n");
         }          }
       }        }
       }       }
         
     k=1;      k=1;
     fprintf(ficres,"# Covariance\n");      fprintf(ficres,"# Covariance\n");
Line 2428  printf("Total number of individuals= %d, Line 2726  printf("Total number of individuals= %d,
       bage = agemin;        bage = agemin;
       fage = agemax;        fage = agemax;
     }      }
      
     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\n",agemin,agemax,bage,fage);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
       
 /*------------ gnuplot -------------*/      while((c=getc(ficpar))=='#' && c!= EOF){
 chdir(pathcd);      ungetc(c,ficpar);
   if((ficgp=fopen("graph.plt","w"))==NULL) {      fgets(line, MAXLINE, ficpar);
     printf("Problem with file graph.gp");goto end;      puts(line);
       fputs(line,ficparo);
   }    }
 #ifdef windows    ungetc(c,ficpar);
   fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif  
 m=pow(2,cptcoveff);  
     
  /* 1eme*/    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
    for (k1=1; k1<= m ; k1 ++) {   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
        
 #ifdef windows    while((c=getc(ficpar))=='#' && c!= EOF){
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      ungetc(c,ficpar);
 #endif      fgets(line, MAXLINE, ficpar);
 #ifdef unix      puts(line);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      fputs(line,ficparo);
 #endif  
   
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");  
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }  
   }  
   /*2 eme*/  
   
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
      
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }    }
     ungetc(c,ficpar);
     
   /*3eme*/  
   
   for (k1=1; k1<= m ; k1 ++) {     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     for (cpt=1; cpt<= nlstate ; cpt ++) {     dateprev2=anprev2+mprev2/12.+jprev2/365.;
       k=2+nlstate*(cpt-1);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  
   }  
    
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
        
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);  
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  
   }    
   
   /* proba elementaires */    fscanf(ficpar,"pop_based=%d\n",&popbased);
    for(i=1,jk=1; i <=nlstate; i++){     fprintf(ficparo,"pop_based=%d\n",popbased);  
     for(k=1; k <=(nlstate+ndeath); k++){     fprintf(ficres,"pop_based=%d\n",popbased);  
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){  
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/  
           /*fprintf(ficgp,"%s",alph[1]);*/  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;  
           fprintf(ficgp,"\n");  
         }  
       }  
     }  
     }  
   
   for(jk=1; jk <=m; jk++) {    while((c=getc(ficpar))=='#' && c!= EOF){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      ungetc(c,ficpar);
    i=1;      fgets(line, MAXLINE, ficpar);
    for(k2=1; k2<=nlstate; k2++) {      puts(line);
      k3=i;      fputs(line,ficparo);
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;  
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  
           }  
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         }  
           fprintf(ficgp,")/(1");  
          
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
 ij=1;  
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  
           }  
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
           }  
           fprintf(ficgp,")");  
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;  
        }  
      }  
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
   }    }
        ungetc(c,ficpar);
   fclose(ficgp);    fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
      fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
 chdir(path);  fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
      
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
     free_ivector(num,1,n);  
     free_vector(agedc,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);  
     fclose(ficres);  
     /*  }*/  
      
    /*________fin mle=1_________*/  
      
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     /* No more information from the sample is required now */  
   /*------------ gnuplot -------------*/
    printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);
    
   /*------------ free_vector  -------------*/
    chdir(path);
    
    free_ivector(wav,1,imx);
    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  
    free_ivector(num,1,n);
    free_vector(agedc,1,n);
    /*free_matrix(covar,1,NCOVMAX,1,n);*/
    fclose(ficparo);
    fclose(ficres);
    
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 2628  chdir(path); Line 2801  chdir(path);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
 /*--------- index.htm --------*/  /*--------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfile);    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm);goto end;  
   }  
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  
 <hr  size=\"2\" color=\"#EC5E5E\">  
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>  
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
   
  fprintf(fichtm," <li>Graphs</li><p>");  
   
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   
  j1=0;  
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;  
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  
 fprintf(fichtm,"\n</body>");  
    }  
  }  
 fclose(fichtm);  
   
    
   /*--------------- Prevalence limit --------------*/    /*--------------- Prevalence limit --------------*/
     
   strcpy(filerespl,"pl");    strcpy(filerespl,"pl");
Line 2788  fclose(fichtm); Line 2902  fclose(fichtm);
   
   fclose(ficrespij);    fclose(ficrespij);
   
     if(stepm == 1) {
   /*---------- Forecasting ------------------*/    /*---------- Forecasting ------------------*/
     calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
    
    
     prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
    
   strcpy(fileresf,"f");    strcpy(fileresf,"f");
   strcat(fileresf,fileres);    strcat(fileresf,fileres);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
   }    }
   printf("Computing forecasting: result on file '%s' \n", fileresf);    printf("Computing forecasting: result on file '%s' \n", fileresf);
    
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);    free_matrix(mint,1,maxwav,1,n);
     free_matrix(anint,1,maxwav,1,n);
  free_matrix(agev,1,maxwav,1,imx);  
   /* Mobile average */  
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   if (mobilav==1) {    if (mobilav==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      movingaverage(agedeb, fage, agemin, mobaverage);
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;  
      
     for (agedeb=bage+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }  
       }  
     }    
   }    }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
    
   agelim=AGESUP;    agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */   
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    hstepm=1;
     hstepm=hstepm/stepm;
     yp1=modf(dateintmean,&yp);
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
    
     fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
     
   if (popforecast==1) {    if (popforecast==1) {
     if((ficpop=fopen(popfile,"r"))==NULL)    {      if((ficpop=fopen(popfile,"r"))==NULL)    {
Line 2837  fclose(fichtm); Line 2953  fclose(fichtm);
     popage=ivector(0,AGESUP);      popage=ivector(0,AGESUP);
     popeffectif=vector(0,AGESUP);      popeffectif=vector(0,AGESUP);
     popcount=vector(0,AGESUP);      popcount=vector(0,AGESUP);
      
     i=1;        i=1;  
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
       {        {
         i=i+1;          i=i+1;
       }        }
     imx=i;      imx=i;
       
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   }    }
    
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#****** ");        fprintf(ficresf,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }        }
       fprintf(ficresf,"******\n");        fprintf(ficresf,"******\n");
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");        fprintf(ficresf,"# StartingAge FinalAge");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
       if (popforecast==1)  fprintf(ficresf," [Population]");        if (popforecast==1)  fprintf(ficresf," [Population]");
   
       for (agedeb=fage; agedeb>=bage; agedeb--){  
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);  
        if (mobilav==1) {  
         for(j=1; j<=nlstate;j++)  
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);  
         }  
         else {  
           for(j=1; j<=nlstate;j++)  
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);  
         }    
   
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");  
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);  
       }  
             
       for (cpt=1; cpt<=nforecast;cpt++) {        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);  
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
         nhstepm = nhstepm/hstepm;  
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/  
   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         oldm=oldms;savm=savms;  
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
                  
         for (h=0; h<=nhstepm; h++){  
                 
          if (h*hstepm/YEARM*stepm==cpt)          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
                      nhstepm = nhstepm/hstepm;
                     
          for(j=1; j<=nlstate+ndeath;j++) {            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            kk1=0.;kk2=0;            oldm=oldms;savm=savms;
            for(i=1; i<=nlstate;i++) {                    hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
              if (mobilav==1)         
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];            for (h=0; h<=nhstepm; h++){
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];              if (h==(int) (calagedate+YEARM*cpt)) {
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];                fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
               }
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1)
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                   if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
                 }
                 if (h==(int)(calagedate+12*cpt)){
                   fprintf(ficresf," %.3f", kk1);
                
                   if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
                 }
             }              }
            if (h*hstepm/YEARM*stepm==cpt) {  
              fprintf(ficresf," %.3f", kk1);  
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);  
            }  
           }            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }          }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
          
       }  
       }        }
     }      }
   }    }
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   if (popforecast==1) {    if (popforecast==1) {
     free_ivector(popage,0,AGESUP);      free_ivector(popage,0,AGESUP);
     free_vector(popeffectif,0,AGESUP);      free_vector(popeffectif,0,AGESUP);
     free_vector(popcount,0,AGESUP);      free_vector(popcount,0,AGESUP);
   }    }
    
   free_imatrix(s,1,maxwav+1,1,n);    free_imatrix(s,1,maxwav+1,1,n);
   free_vector(weight,1,n);    free_vector(weight,1,n);
   fclose(ficresf);    fclose(ficresf);
     }
   
     /* End forecasting */
     else{
       erreur=108;
       printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);
     }
    
    
   /*---------- Health expectancies and variances ------------*/    /*---------- Health expectancies and variances ------------*/
   
   strcpy(filerest,"t");    strcpy(filerest,"t");
Line 2969  fclose(fichtm); Line 3083  fclose(fichtm);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);  
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
           
   
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
       fprintf(ficrest,"\n");        fprintf(ficrest,"\n");
          
       hf=1;        hf=1;
       if (stepm >= YEARM) hf=stepm/YEARM;        if (stepm >= YEARM) hf=stepm/YEARM;
       epj=vector(1,nlstate+1);        epj=vector(1,nlstate+1);
Line 3013  fclose(fichtm); Line 3129  fclose(fichtm);
   fclose(ficpar);    fclose(ficpar);
   free_vector(epj,1,nlstate+1);    free_vector(epj,1,nlstate+1);
   /*  scanf("%d ",i); */    /*  scanf("%d ",i); */
    
   /*------- Variance limit prevalence------*/      /*------- Variance limit prevalence------*/  
   
 strcpy(fileresvpl,"vpl");  strcpy(fileresvpl,"vpl");
Line 3055  strcpy(fileresvpl,"vpl"); Line 3171  strcpy(fileresvpl,"vpl");
     
   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_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
   printf("End of Imach\n");    if(erreur >0)
       printf("End of Imach with error %d\n",erreur);
     else   printf("End of Imach\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
Line 3068  strcpy(fileresvpl,"vpl"); Line 3186  strcpy(fileresvpl,"vpl");
   
  end:   end:
 #ifdef windows  #ifdef windows
  chdir(pathcd);    /* chdir(pathcd);*/
 #endif  #endif
     /*system("wgnuplot graph.plt");*/
  system("..\\gp37mgw\\wgnuplot graph.plt");   /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
    strcpy(plotcmd,GNUPLOTPROGRAM);
    strcat(plotcmd," ");
    strcat(plotcmd,optionfilegnuplot);
    system(plotcmd);
   
 #ifdef windows  #ifdef windows
   while (z[0] != 'q') {    while (z[0] != 'q') {
     chdir(pathcd);      chdir(path);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      printf("\nType e to edit output files, c to start again, and q for exiting: ");
     scanf("%s",z);      scanf("%s",z);
     if (z[0] == 'c') system("./imach");      if (z[0] == 'c') system("./imach");
Removed from v.1.17  
changed lines
  Added in v.1.26

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