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version 1.7, 2001/05/02 17:50:24 version 1.44, 2002/05/24 13:01:48
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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    probability to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month or quarter trimester,
     semester or year) is model as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
     hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    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 "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
Line 67 Line 77
 #define AGEBASE 40  #define AGEBASE 40
   
   
   int erreur; /* Error number */
 int nvar;  int nvar;
 static int cptcov;  int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
 int cptcovn, cptcovage=0, cptcoveff=0;  
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 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 */
   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 */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficgp, *fichtm;  FILE *ficgp,*ficresprob,*ficpop;
 FILE *ficreseij;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];    char filerese[FILENAMELENGTH];
  FILE  *ficresvij;   FILE  *ficresvij;
Line 111  FILE *ficreseij; Line 124  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 123  int imx; Line 136  int imx;
 int stepm;  int stepm;
 /* Stepm, step in month: minimum step interpolation*/  /* Stepm, step in month: minimum step interpolation*/
   
   int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 int m,nb;  int 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;  double **pmmij, ***probs, ***mobaverage;
   double dateintmean=0;
   
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
Line 137  double ftol=FTOL; /* Tolerance for compu Line 154  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 167  static int split( char *path, char *dirc Line 188  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 658  double **prevalim(double **prlim, int nl Line 690  double **prevalim(double **prlim, int nl
     
       for (k=1; k<=cptcovn;k++) {        for (k=1; k<=cptcovn;k++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       }        }
       for (k=1; k<=cptcovage;k++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)        for (k=1; k<=cptcovprod;k++)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
     savm=oldm;      savm=oldm;
Line 693  double **prevalim(double **prlim, int nl Line 723  double **prevalim(double **prlim, int nl
   }    }
 }  }
   
 /*************** transition probabilities **********/  /*************** transition probabilities ***************/
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
Line 719  double **pmij(double **ps, double *cov, Line 749  double **pmij(double **ps, double *cov,
       ps[i][j]=s2;        ps[i][j]=s2;
     }      }
   }    }
       /*ps[3][2]=1;*/
   
   for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
      s1=0;       s1=0;
     for(j=1; j<i; j++)      for(j=1; j<i; j++)
Line 740  double **pmij(double **ps, double *cov, Line 772  double **pmij(double **ps, double *cov,
     }      }
   }    }
   
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     for(jj=1; jj<= nlstate+ndeath; jj++){      for(jj=1; jj<= nlstate+ndeath; jj++){
      printf("%lf ",ps[ii][jj]);       printf("%lf ",ps[ii][jj]);
Line 757  double **pmij(double **ps, double *cov, Line 790  double **pmij(double **ps, double *cov,
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 {  {
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /* in, b, out are matrice of pointers which should have been initialized    /* in, b, out are matrice of pointers which should have been initialized
      before: only the contents of out is modified. The function returns       before: only the contents of out is modified. The function returns
Line 804  double ***hpxij(double ***po, int nhstep Line 837  double ***hpxij(double ***po, int nhstep
       cov[1]=1.;        cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 for (k=1; k<=cptcovage;k++)        for (k=1; k<=cptcovage;k++)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    for (k=1; k<=cptcovprod;k++)        for (k=1; k<=cptcovprod;k++)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   
Line 841  double func( double *x) Line 874  double func( double *x)
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /*for(i=1;i<imx;i++)    /*for(i=1;i<imx;i++)
 printf(" %d\n",s[4][i]);      printf(" %d\n",s[4][i]);
   */    */
   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 (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){      for(mi=1; mi<= wav[i]-1; mi++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(d=0; d<dh[mi][i]; d++){        for(d=0; d<dh[mi][i]; d++){
               newm=savm;          newm=savm;
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               for (kk=1; kk<=cptcovage;kk++) {          for (kk=1; kk<=cptcovage;kk++) {
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  /*printf("%d %d",kk,Tage[kk]);*/          }
               }         
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               /*cov[3]=pow(cov[2],2)/1000.;*/                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          oldm=newm;
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));         
           savm=oldm;         
           oldm=newm;  
   
   
       } /* end mult */        } /* 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]]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
       ipmx +=1;        ipmx +=1;
Line 899  void mlikeli(FILE *ficres,double p[], in Line 929  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 916  void hesscov(double **matcov, double p[] Line 946  void hesscov(double **matcov, double p[]
   void lubksb(double **a, int npar, int *indx, double b[]) ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
   
   hess=matrix(1,npar,1,npar);    hess=matrix(1,npar,1,npar);
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
Line 924  void hesscov(double **matcov, double p[] Line 953  void hesscov(double **matcov, double p[]
     printf("%d",i);fflush(stdout);      printf("%d",i);fflush(stdout);
     hess[i][i]=hessii(p,ftolhess,i,delti);      hess[i][i]=hessii(p,ftolhess,i,delti);
     /*printf(" %f ",p[i]);*/      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
   }    }
    
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
     for (j=1;j<=npar;j++)  {      for (j=1;j<=npar;j++)  {
       if (j>i) {        if (j>i) {
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d%d",i,j);fflush(stdout);
         hess[i][j]=hessij(p,delti,i,j);          hess[i][j]=hessij(p,delti,i,j);
         hess[j][i]=hess[i][j];          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
       }        }
     }      }
   }    }
Line 1035  double hessii( double x[], double delta, Line 1066  double hessii( double x[], double delta,
     }      }
   }    }
   delti[theta]=delts;    delti[theta]=delts;
   return res;    return res;
     
 }  }
   
Line 1148  void lubksb(double **a, int n, int *indx Line 1179  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)  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, 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,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 1168  void  freqsummary(char fileres[], int ag Line 1199  void  freqsummary(char fileres[], int ag
   }    }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   j1=0;    j1=0;
    
   j=cptcoveff;    j=cptcoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
   for(k1=1; k1<=j;k1++){    for(k1=1; k1<=j;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){      for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         for (i=-1; i<=nlstate+ndeath; i++)            scanf("%d", i);*/
          for (jk=-1; jk<=nlstate+ndeath; jk++)          for (i=-1; i<=nlstate+ndeath; i++)  
            for(m=agemin; m <= agemax+3; m++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
              freq[i][jk][m]=0;            for(m=agemin; m <= agemax+3; m++)
                      freq[i][jk][m]=0;
        for (i=1; i<=imx; i++) {       
          bool=1;        dateintsum=0;
          if  (cptcovn>0) {        k2cpt=0;
            for (z1=1; z1<=cptcoveff; z1++)        for (i=1; i<=imx; i++) {
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;          bool=1;
          }          if  (cptcovn>0) {
           if (bool==1) {            for (z1=1; z1<=cptcoveff; z1++)
            for(m=firstpass; m<=lastpass-1; m++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
              if(agev[m][i]==0) agev[m][i]=agemax+1;                bool=0;
              if(agev[m][i]==1) agev[m][i]=agemax+2;          }
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          if (bool==1) {
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            for(m=firstpass; m<=lastpass; m++){
            }              k2=anint[m][i]+(mint[m][i]/12.);
          }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
        }                if(agev[m][i]==0) agev[m][i]=agemax+1;
         if  (cptcovn>0) {                if(agev[m][i]==1) agev[m][i]=agemax+2;
          fprintf(ficresp, "\n#********** Variable ");                if (m<lastpass) {
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
        }                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
        fprintf(ficresp, "**********\n#");                }
        for(i=1; i<=nlstate;i++)               
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
        fprintf(ficresp, "\n");                  dateintsum=dateintsum+k2;
                   k2cpt++;
                 }
               }
             }
           }
         }
                 
   for(i=(int)agemin; i <= (int)agemax+3; i++){        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     if(i==(int)agemax+3)  
       printf("Total");        if  (cptcovn>0) {
     else          fprintf(ficresp, "\n#********** Variable ");
       printf("Age %d", i);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for(jk=1; jk <=nlstate ; jk++){          fprintf(ficresp, "**********\n#");
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
         pp[jk] += freq[jk][m][i];        for(i=1; i<=nlstate;i++)
     }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     for(jk=1; jk <=nlstate ; jk++){        fprintf(ficresp, "\n");
       for(m=-1, pos=0; m <=0 ; m++)       
         pos += freq[jk][m][i];        for(i=(int)agemin; i <= (int)agemax+3; i++){
       if(pp[jk]>=1.e-10)          if(i==(int)agemax+3)
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            printf("Total");
       else          else
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            printf("Age %d", i);
     }          for(jk=1; jk <=nlstate ; jk++){
     for(jk=1; jk <=nlstate ; jk++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)              pp[jk] += freq[jk][m][i];
         pp[jk] += freq[jk][m][i];          }
     }          for(jk=1; jk <=nlstate ; jk++){
     for(jk=1,pos=0; jk <=nlstate ; jk++)            for(m=-1, pos=0; m <=0 ; m++)
       pos += pp[jk];              pos += freq[jk][m][i];
     for(jk=1; jk <=nlstate ; jk++){            if(pp[jk]>=1.e-10)
       if(pos>=1.e-5)              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            else
       else              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          }
       if( i <= (int) agemax){  
         if(pos>=1.e-5)          for(jk=1; jk <=nlstate ; jk++){
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       else              pp[jk] += freq[jk][m][i];
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          }
   
           for(jk=1,pos=0; jk <=nlstate ; jk++)
             pos += pp[jk];
           for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5)
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             else
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             if( i <= (int) agemax){
               if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
                 probs[i][jk][j1]= pp[jk]/pos;
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
               else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
             }
           }
          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           if(i <= (int) agemax)
             fprintf(ficresp,"\n");
           printf("\n");
       }        }
     }      }
     for(jk=-1; jk <=nlstate+ndeath; jk++)    }
       for(m=-1; m <=nlstate+ndeath; m++)    dateintmean=dateintsum/k2cpt;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  
     printf("\n");  
     }  
     }  
  }  
     
   fclose(ficresp);    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 */
   }
   
   /************ Prevalence ********************/
   void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
   {  /* Some frequencies */
    
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
     double *pp;
     double pos, k2;
   
     pp=vector(1,nlstate);
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    
     freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     j1=0;
    
     j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
     for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
        
         for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=agemin; m <= agemax+3; m++)
               freq[i][jk][m]=0;
        
         for (i=1; i<=imx; i++) {
           bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++)
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                 bool=0;
           }
           if (bool==1) {
             for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
                 if(agev[m][i]==1) agev[m][i]=agemax+2;
                 if (m<lastpass) {
                   if (calagedate>0)
                     freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
                   else
                     freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
                 }
               }
             }
           }
         }
         for(i=(int)agemin; i <= (int)agemax+3; i++){
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i];
           }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
           }
          
           for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
           }
          
           for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
          
           for(jk=1; jk <=nlstate ; jk++){    
             if( i <= (int) agemax){
               if(pos>=1.e-5){
                 probs[i][jk][j1]= pp[jk]/pos;
               }
             }
           }
          
         }
       }
     }
   
    
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
    
 }  /* End of Freq */  }  /* End of Freq */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
Line 1268  void  concatwav(int wav[], int **dh, int Line 1410  void  concatwav(int wav[], int **dh, int
      */       */
   
   int i, mi, m;    int i, mi, m;
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 float sum=0.;       double sum=0., jmean=0.;*/
   
     int j, k=0,jk, ju, jl;
     double sum=0.;
     jmin=1e+5;
     jmax=-1;
     jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     mi=0;      mi=0;
     m=firstpass;      m=firstpass;
Line 1300  float sum=0.; Line 1447  float sum=0.;
         dh[mi][i]=1;          dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) {          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
           if(j=0) j=1;  /* Survives at least one month after exam */            if(j==0) j=1;  /* Survives at least one month after exam */
             k=k+1;
             if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
             sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i); */
             }
         }          }
         else{          else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           k=k+1;            k=k+1;
           if (j >= jmax) jmax=j;            if (j >= jmax) jmax=j;
           else if (j <= jmin)jmin=j;            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           sum=sum+j;            sum=sum+j;
         }          }
         jk= j/stepm;          jk= j/stepm;
Line 1322  float sum=0.; Line 1477  float sum=0.;
       }        }
     }      }
   }    }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    jmean=sum/k;
 }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    }
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)  void tricode(int *Tvar, int **nbcode, int imx)
 {  {
Line 1338  void tricode(int *Tvar, int **nbcode, in Line 1494  void tricode(int *Tvar, int **nbcode, in
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) {
       ij=(int)(covar[Tvar[j]][i]);        ij=(int)(covar[Tvar[j]][i]);
       Ndum[ij]++;        Ndum[ij]++;
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       if (ij > cptcode) cptcode=ij;        if (ij > cptcode) cptcode=ij;
     }      }
   
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/  
     for (i=0; i<=cptcode; i++) {      for (i=0; i<=cptcode; i++) {
       if(Ndum[i]!=0) ncodemax[j]++;        if(Ndum[i]!=0) ncodemax[j]++;
     }      }
     ij=1;      ij=1;
   
   
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1; i<=ncodemax[j]; i++) {
       for (k=0; k<=19; k++) {        for (k=0; k<=19; k++) {
         if (Ndum[k] != 0) {          if (Ndum[k] != 0) {
           nbcode[Tvar[j]][ij]=k;            nbcode[Tvar[j]][ij]=k;
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/           
           ij++;            ij++;
         }          }
         if (ij > ncodemax[j]) break;          if (ij > ncodemax[j]) break;
       }          }  
     }      }
   }      }  
  for (i=1; i<=10; i++) {  
    for (k=0; k<19; k++) Ndum[k]=0;
   
    for (i=1; i<=ncovmodel-2; i++) {
       ij=Tvar[i];        ij=Tvar[i];
       Ndum[ij]++;        Ndum[ij]++;
     }      }
   
  ij=1;   ij=1;
  for (i=1; i<=cptcovn; i++) {   for (i=1; i<=10; i++) {
    if((Ndum[i]!=0) && (i<=ncov)){     if((Ndum[i]!=0) && (i<=ncovcol)){
      Tvaraff[i]=ij;       Tvaraff[ij]=i;
    ij++;       ij++;
    }     }
  }   }
     
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      cptcoveff=ij-1;
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];  
    /*printf("j=%d %d\n",j,Tvar[j]);*/  
  }  
    
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);  
     scanf("%d",i);*/  
 }  }
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
   
 {  {
   /* Health expectancies */    /* Health expectancies */
   int i, j, nhstepm, hstepm, h;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   double age, agelim,hf;    double age, agelim, hf;
   double ***p3mat;    double ***p3mat,***varhe;
     double **dnewm,**doldm;
     double *xp;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate*2,1,npar);
     doldm=matrix(1,nlstate*2,1,nlstate*2);
     
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficreseij,"# Health expectancies\n");
   fprintf(ficreseij,"# Age");    fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       fprintf(ficreseij," %1d-%1d",i,j);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   fprintf(ficreseij,"\n");    fprintf(ficreseij,"\n");
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */    if(estepm < stepm){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;  
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear
      * progression inbetween and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
        nhstepm is the number of hstepm from age to agelim
        nstepm is the number of stepm from age to agelin.
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
   
   agelim=AGESUP;    agelim=AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */      /* nhstepm age range expressed in number of stepm */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      nstepm=(int) rint((agelim-age)*YEARM/stepm);
     /* Typically if 20 years = 20*12/6=40 stepm */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
     if (stepm >= YEARM) hstepm=1;      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
       gp=matrix(0,nhstepm,1,nlstate*2);
       gm=matrix(0,nhstepm,1,nlstate*2);
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing Variances of health expectancies */
   
        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    
         cptj=0;
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
           }
         }
        
        
         for(i=1; i<=npar; i++)
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        
         cptj=0;
         for(j=1; j<= nlstate; j++){
           for(i=1;i<=nlstate;i++){
             cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
           }
         }
        
      
   
         for(j=1; j<= nlstate*2; j++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
        }
      
   /* End theta */
   
        trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   
        for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*2;j++)
           for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];
   
   
        for(i=1;i<=nlstate*2;i++)
         for(j=1;j<=nlstate*2;j++)
           varhe[i][j][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
           for(i=1;i<=nlstate*2;i++)
             for(j=1;j<=nlstate*2;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
   
        
       /* Computing expectancies */
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           eij[i][j][(int)age] +=p3mat[i][j][h];            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
            
   /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
         }          }
      
     hf=1;      fprintf(ficreseij,"%3.0f",age );
     if (stepm >= YEARM) hf=stepm/YEARM;      cptj=0;
     fprintf(ficreseij,"%.0f",age );  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          cptj++;
           fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       }        }
     fprintf(ficreseij,"\n");      fprintf(ficreseij,"\n");
      
       free_matrix(gm,0,nhstepm,1,nlstate*2);
       free_matrix(gp,0,nhstepm,1,nlstate*2);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
       free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    }
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*2,1,npar);
     free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
 }  }
   
 /************ Variance ******************/  /************ Variance ******************/
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
 {  {
   /* Variance of health expectancies */    /* Variance of health expectancies */
   /*  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, h;    int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;    int k, cptcode;
    double *xp;    double *xp;
   double **gp, **gm;    double **gp, **gm;
   double ***gradg, ***trgradg;    double ***gradg, ***trgradg;
   double ***p3mat;    double ***p3mat;
   double age,agelim;    double age,agelim, hf;
   int theta;    int theta;
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   fprintf(ficresvij,"# Age");    fprintf(ficresvij,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
Line 1456  void varevsij(char fileres[], double *** Line 1735  void varevsij(char fileres[], double ***
   dnewm=matrix(1,nlstate,1,npar);    dnewm=matrix(1,nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    doldm=matrix(1,nlstate,1,nlstate);
     
   hstepm=1*YEARM; /* Every year of age */    if(estepm < stepm){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;  
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
        nhstepm is the number of hstepm from age to agelim
        nstepm is the number of stepm from age to agelin.
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
   agelim = AGESUP;    agelim = AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
     if (stepm >= YEARM) hstepm=1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     gp=matrix(0,nhstepm,1,nlstate);      gp=matrix(0,nhstepm,1,nlstate);
Line 1474  void varevsij(char fileres[], double *** Line 1767  void varevsij(char fileres[], double ***
       }        }
       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) {
           for(i=1; i<=nlstate;i++)
             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 1485  void varevsij(char fileres[], double *** Line 1784  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) {
           for(i=1; i<=nlstate;i++)
             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, gm[h][j]=0.;i<=nlstate;i++)            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
   
       for(j=1; j<= nlstate; j++)        for(j=1; j<= nlstate; j++)
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
Line 1504  void varevsij(char fileres[], double *** Line 1810  void varevsij(char fileres[], double ***
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate;j++)        for(j=1;j<=nlstate;j++)
         vareij[i][j][(int)age] =0.;          vareij[i][j][(int)age] =0.;
   
     for(h=0;h<=nhstepm;h++){      for(h=0;h<=nhstepm;h++){
       for(k=0;k<=nhstepm;k++){        for(k=0;k<=nhstepm;k++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         for(i=1;i<=nlstate;i++)          for(i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate;j++)            for(j=1;j<=nlstate;j++)
             vareij[i][j][(int)age] += doldm[i][j];              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;  
     fprintf(ficresvij,"%.0f ",age );      fprintf(ficresvij,"%.0f ",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       }        }
     fprintf(ficresvij,"\n");      fprintf(ficresvij,"\n");
     free_matrix(gp,0,nhstepm,1,nlstate);      free_matrix(gp,0,nhstepm,1,nlstate);
Line 1530  void varevsij(char fileres[], double *** Line 1837  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 1552  void varprevlim(char fileres[], double * Line 1859  void varprevlim(char fileres[], double *
   double age,agelim;    double age,agelim;
   int theta;    int theta;
         
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
   fprintf(ficresvpl,"# Age");    fprintf(ficresvpl,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficresvpl," %1d-%1d",i,i);
Line 1620  void varprevlim(char fileres[], double * Line 1927  void varprevlim(char fileres[], double *
   
 }  }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   {
     int i, j, i1, k1, j1, z1;
     int k=0, cptcode;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim, cov[NCOVMAX];
     int theta;
     char fileresprob[FILENAMELENGTH];
   
     strcpy(fileresprob,"prob");
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    
   fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");
     fprintf(ficresprob,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++)
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   
 /***********************************************/  
 /**************** Main Program *****************/  
 /***********************************************/  
   
 /*int main(int argc, char *argv[])*/  
 int main()  
 {  
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;    fprintf(ficresprob,"\n");
   double agedeb, agefin,hf;  
   double agemin=1.e20, agemax=-1.e20;  
   
   double fret;  
   double **xi,tmp,delta;  
   
   double dum; /* Dummy variable */    xp=vector(1,npar);
   double ***p3mat;    dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   int *indx;    doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];  
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
     
   int hstepm, nhstepm;    cov[1]=1;
   double bage, fage, age, agelim, agebase;    j=cptcoveff;
   double ftolpl=FTOL;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double **prlim;    j1=0;
   double *severity;    for(k1=1; k1<=1;k1++){
   double ***param; /* Matrix of parameters */      for(i1=1; i1<=ncodemax[k1];i1++){
   double  *p;      j1++;
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */      if  (cptcovn>0) {
   double *delti; /* Scale */        fprintf(ficresprob, "\n#********** Variable ");
   double ***eij, ***vareij;        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double **varpl; /* Variances of prevalence limits by age */        fprintf(ficresprob, "**********\n#");
   double *epj, vepp;      }
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";     
         for (age=bage; age<=fage; age ++){
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
            
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          
           gradg=matrix(1,npar,1,9);
           trgradg=matrix(1,9,1,npar);
           gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
           gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
      
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:0);
            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
            
             k=0;
             for(i=1; i<= (nlstate+ndeath); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
            
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:0);
      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate+ndeath); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
               gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
          
           matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
          
           pmij(pmmij,cov,ncovmodel,x,nlstate);
          
           k=0;
           for(i=1; i<=(nlstate+ndeath); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               gm[k]=pmmij[i][j];
             }
           }
        
        /*printf("\n%d ",(int)age);
        for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)
             fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));
    
         }
       }
       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);
     }
     free_vector(xp,1,npar);
     fclose(ficresprob);
    
   }
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
                     char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
                     char version[], int popforecast, int estepm ,/* \ */
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     FILE *fichtm;
     /*char optionfilehtm[FILENAMELENGTH];*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li>Parameter files<br>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
   
      fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months):
      <a href=\"e%s\">e%s</a> <br>\n</li>", \
     jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
    fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
    - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
    if(popforecast==1) fprintf(fichtm,"\n
    - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
    - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
           <br>",fileres,fileres,fileres,fileres);
    else
      fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <li>Graphs</li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
          jj1++;
          if (cptcovn > 0) {
            fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
            for (cpt=1; cpt<=cptcoveff;cpt++)
              fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
            fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
          }
          /* Pij */
          fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
   <img src=\"pe%s%d1.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);    
          /* Quasi-incidences */
          fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   <img src=\"pe%s%d2.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);    
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
       for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   fprintf(fichtm,"\n</body>");
      }
      }
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp.txt");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
   
   #ifdef windows
       fprintf(ficgp,"cd \"%s\" \n",pathc);
   #endif
   m=pow(2,cptcoveff);
    
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   
   #ifdef windows
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   #endif
   #ifdef unix
   fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
   #endif
   
   for (i=1; i<= nlstate ; i ++) {
     if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     else fprintf(ficgp," \%%*lf (\%%*lf)");
   }
       fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
     if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     else fprintf(ficgp," \%%*lf (\%%*lf)");
   }
     fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
     if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     else fprintf(ficgp," \%%*lf (\%%*lf)");
   }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   #ifdef unix
   fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
   #endif
      }
     }
     /*2 eme*/
   
     for (k1=1; k1<= m ; k1 ++) {
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
      
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
     if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     else fprintf(ficgp," \%%*lf (\%%*lf)");
   }  
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   }  
         fprintf(ficgp,"\" t\"\" w l 0,");
        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
     if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     else fprintf(ficgp," \%%*lf (\%%*lf)");
   }  
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
    
     /*3eme*/
   
     for (k1=1; k1<= m ; k1 ++) {
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
    for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
    for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   
   */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
   
         }
       }
     }
    
     /* CV preval stat */
       for (k1=1; k1<= m ; k1 ++) {
       for (cpt=1; cpt<nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
        
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);  
       }
     }  
    
     /* proba elementaires */
      for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
          
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++;
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){  
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            }
          }
        }
      }
      fclose(ficgp);
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
   
     int i, cpt, cptcod;
       for (agedeb=ageminpar; agedeb<=fage; agedeb++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
             mobaverage[(int)agedeb][i][cptcod]=0.;
      
       for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
         for (i=1; i<=nlstate;i++){
           for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
             for (cpt=0;cpt<=4;cpt++){
               mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
             }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
           }
         }
       }
      
   }
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     char fileresf[FILENAMELENGTH];
   
    agelim=AGESUP;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    
    
     strcpy(fileresf,"f");
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav==1) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       movingaverage(agedeb, fage, ageminpar, mobaverage);
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
    
     agelim=AGESUP;
    
     hstepm=1;
     hstepm=hstepm/stepm;
     yp1=modf(dateintmean,&yp);
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
    
     fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
    
     for(cptcov=1;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# StartingAge FinalAge");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
        
        
         for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);  
   
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
             nhstepm = nhstepm/hstepm;
            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
          
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
               }
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1)
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                  
                 }
                 if (h==(int)(calagedate+12*cpt)){
                   fprintf(ficresf," %.3f", kk1);
                          
                 }
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
       }
     }
          
     if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   /************** Forecasting ******************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
    
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    
    
     strcpy(filerespop,"pop");
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav==1) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       movingaverage(agedeb, fage, ageminpar, mobaverage);
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
    
     agelim=AGESUP;
    
     hstepm=1;
     hstepm=hstepm/stepm;
    
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
       }
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
      
       i=1;  
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
        
         for (cpt=0; cpt<=0;cpt++) {
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);  
          
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
             nhstepm = nhstepm/hstepm;
            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
          
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               }
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1)
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedate+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);  
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
             nhstepm = nhstepm/hstepm;
            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               }
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      }
     }
    
     if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   
     int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char title[MAXLINE];
     char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    
     char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
     char filerest[FILENAMELENGTH];
     char fileregp[FILENAMELENGTH];
     char popfile[FILENAMELENGTH];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
    
   
     char version[80]="Imach version 0.8e, May 2002, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
   char z[1]="c", occ;    char z[1]="c", occ;
 #include <sys/time.h>  #include <sys/time.h>
 #include <time.h>  #include <time.h>
   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 */
   
   
   printf("\nIMACH, Version 0.64a");  
   printf("\nEnter the parameter file name: ");  
   
 #ifdef windows  
   scanf("%s",pathtot);  
   getcwd(pathcd, size);    getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);    /*cygwin_split_path(pathtot,path,optionfile);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   /* cutv(path,optionfile,pathtot,'\\');*/    /* cutv(path,optionfile,pathtot,'\\');*/
   
 split(pathtot, path,optionfile);    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);    chdir(path);
   replace(pathc,path);    replace(pathc,path);
 #endif  
 #ifdef unix  
   scanf("%s",optionfile);  
 #endif  
   
 /*-------- arguments in the command line --------*/  /*-------- arguments in the command line --------*/
   
   strcpy(fileres,"r");    strcpy(fileres,"r");
   strcat(fileres, optionfile);    strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
   /*---------arguments file --------*/    /*---------arguments file --------*/
   
Line 1725  split(pathtot, path,optionfile); Line 2735  split(pathtot, path,optionfile);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   while((c=getc(ficpar))=='#' && c!= EOF){
   covar=matrix(0,NCOVMAX,1,n);          ungetc(c,ficpar);
   if (strlen(model)<=1) cptcovn=0;      fgets(line, MAXLINE, ficpar);
   else {      puts(line);
     j=0;      fputs(line,ficparo);
     j=nbocc(model,'+');  
     cptcovn=j+1;  
   }    }
     ungetc(c,ficpar);
    
      
     covar=matrix(0,NCOVMAX,1,n);
     cptcovn=0;
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
   ncovmodel=2+cptcovn;    ncovmodel=2+cptcovn;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
Line 1766  split(pathtot, path,optionfile); Line 2780  split(pathtot, path,optionfile);
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
     
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
   
   p=param[1][1];    p=param[1][1];
     
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
Line 1827  split(pathtot, path,optionfile); Line 2842  split(pathtot, path,optionfile);
   printf("\n");    printf("\n");
   
   
     /*-------- data file ----------*/      /*-------- Rewriting paramater file ----------*/
     if((ficres =fopen(fileres,"w"))==NULL) {       strcpy(rfileres,"r");    /* "Rparameterfile */
       printf("Problem with resultfile: %s\n", fileres);goto end;       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
        strcat(rfileres,".");    /* */
        strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
     }      }
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
         
       /*-------- 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;
     }      }
Line 1856  split(pathtot, path,optionfile); Line 2876  split(pathtot, path,optionfile);
     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)) {
                 
Line 1874  split(pathtot, path,optionfile); Line 2894  split(pathtot, path,optionfile);
         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=ncov;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);
          
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/          /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
             printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;          i=i+1;
       }        }
     }      }
       /* 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++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1;
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
    
    
   /* Calculation of the number of parameter from char model*/    /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15);    Tvar=ivector(1,15);
   Tprod=ivector(1,15);    Tprod=ivector(1,15);
Line 1903  split(pathtot, path,optionfile); Line 2934  split(pathtot, path,optionfile);
     cptcovprod=j1;      cptcovprod=j1;
         
     strcpy(modelsav,model);      strcpy(modelsav,model);
    if (j==0) {      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
       if (j1==0){        printf("Error. Non available option model=%s ",model);
         cutv(stra,strb,modelsav,'V');        goto end;
         Tvar[1]=atoi(strb);      }
       }     
       else if (j1==1) {      for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'*');        cutv(stra,strb,modelsav,'+');
         Tage[1]=1; cptcovage++;        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
         if (strcmp(stra,"age")==0) {        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {
           cutv(strd,strc,strb,'*');
           if (strcmp(strc,"age")==0) {
           cptcovprod--;            cptcovprod--;
           cutv(strd,strc,strb,'V');            cutv(strb,stre,strd,'V');
           Tvar[1]=atoi(strc);            Tvar[i]=atoi(stre);
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
         }          }
         else if (strcmp(strb,"age")==0) {          else if (strcmp(strd,"age")==0) {
           cptcovprod--;            cptcovprod--;
           cutv(strd,strc,stra,'V');            cutv(strb,stre,strc,'V');
           Tvar[1]=atoi(strc);            Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
         }          }
         else {          else {
           cutv(strd,strc,strb,'V');            cutv(strb,stre,strc,'V');
           cutv(stre,strd,stra,'V');            Tvar[i]=ncovcol+k1;
           Tvar[1]=ncov+1;            cutv(strb,strc,strd,'V');
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc);
             Tvard[k1][2]=atoi(stre);
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2];
           for (k=1; k<=lastobs;k++)            for (k=1; k<=lastobs;k++)
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
         }            k1++;
         /*printf("%s %s %s\n", stra,strb,modelsav);            k2=k2+2;
 printf("%d ",Tvar[1]);  
 scanf("%d",i);*/  
       }  
     }  
    else {  
       for(i=j; i>=1;i--){  
         cutv(stra,strb,modelsav,'+');  
         /*printf("%s %s %s\n", stra,strb,modelsav);  
           scanf("%d",i);*/  
         if (strchr(strb,'*')) {  
           cutv(strd,strc,strb,'*');  
           if (strcmp(strc,"age")==0) {  
             cptcovprod--;  
             cutv(strb,stre,strd,'V');  
             Tvar[i+1]=atoi(stre);  
             cptcovage++;  
             Tage[cptcovage]=i+1;  
             printf("stre=%s ", stre);  
           }  
           else if (strcmp(strd,"age")==0) {  
             cptcovprod--;  
             cutv(strb,stre,strc,'V');  
             Tvar[i+1]=atoi(stre);  
             cptcovage++;  
             Tage[cptcovage]=i+1;  
           }  
           else {  
             cutv(strb,stre,strc,'V');  
             Tvar[i+1]=ncov+k1;  
             cutv(strb,strc,strd,'V');  
             Tprod[k1]=i+1;  
             Tvard[k1][1]=atoi(strc);  
             Tvard[k1][2]=atoi(stre);  
             Tvar[cptcovn+k2]=Tvard[k1][1];  
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  
             for (k=1; k<=lastobs;k++)  
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
             k1++;  
             k2=k2+2;  
           }  
         }  
         else {  
           cutv(strd,strc,strb,'V');  
           /* printf("%s %s %s", strd,strc,strb);*/  
           Tvar[i+1]=atoi(strc);  
         }          }
         strcpy(modelsav,stra);    
       }        }
       cutv(strd,strc,stra,'V');        else {
       Tvar[1]=atoi(strc);          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
     }      }
   }  }
   /* for (i=1; i<=5; i++)   
      printf("i=%d %d ",i,Tvar[i]);*/    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/    printf("cptcovprod=%d ", cptcovprod);
  /*printf("cptcovprod=%d ", cptcovprod);*/    scanf("%d ",i);*/
   /*  scanf("%d ",i);*/  
     fclose(fic);      fclose(fic);
   
     /*  if(mle==1){*/      /*  if(mle==1){*/
Line 1994  scanf("%d",i);*/ Line 2999  scanf("%d",i);*/
     }      }
     /*-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(m=2; (m<= maxwav); m++) {
          if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
            anint[m][i]=9999;
            s[m][i]=-1;
          }
        if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
         }
       }
   
     for (i=1; i<=imx; i++)  {      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];
             else{              /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
              else {
                 if (andc[i]!=9999){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                printf("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 */
Line 2048  printf("Total number of individuals= %d, Line 3066  printf("Total number of individuals= %d,
     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);
   
Line 2063  printf("Total number of individuals= %d, Line 3081  printf("Total number of individuals= %d,
   
   
       Tcode=ivector(1,100);        Tcode=ivector(1,100);
       nbcode=imatrix(1,nvar,1,8);        nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
       ncodemax[1]=1;        ncodemax[1]=1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        if (cptcovn > 0) tricode(Tvar,nbcode,imx);
             
Line 2076  printf("Total number of individuals= %d, Line 3094  printf("Total number of individuals= %d,
        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;             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
              /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
          }           }
        }         }
      }       }
    }     }
      /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
         codtab[1][2]=1;codtab[2][2]=2; */
    /*for(i=1; i <=m ;i++){     /* for(i=1; i <=m ;i++){
      for(k=1; k <=cptcovn; k++){        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
      }        }
      printf("\n");        printf("\n");
    }        }
    scanf("%d",i);*/        scanf("%d",i);*/
         
    /* Calculates basic frequencies. Computes observed prevalence at single age     /* 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);  
   
      
      
     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]      /* 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] */         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) */      p=param[1][1]; /* *(*(*(param +1)+1)+0) */
Line 2110  printf("Total number of individuals= %d, Line 3130  printf("Total number of individuals= %d,
     }      }
         
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
   
    jk=1;     jk=1;
    fprintf(ficres,"# Parameters\n");     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    printf("# Parameters\n");     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    for(i=1,jk=1; i <=nlstate; i++){     for(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)
Line 2136  printf("Total number of individuals= %d, Line 3157  printf("Total number of individuals= %d,
     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\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales\n");      printf("# 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) {
Line 2152  printf("Total number of individuals= %d, Line 3173  printf("Total number of individuals= %d,
           fprintf(ficres,"\n");            fprintf(ficres,"\n");
         }          }
       }        }
       }       }
         
     k=1;      k=1;
     fprintf(ficres,"# Covariance\n");      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     printf("# Covariance\n");      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1;i<=npar;i++){      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;
Line 2180  printf("Total number of individuals= %d, Line 3201  printf("Total number of individuals= %d,
       fputs(line,ficparo);        fputs(line,ficparo);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
        estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
          if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {      if (fage <= 2) {
       bage = agemin;        bage = ageminpar;
       fage = agemax;        fage = agemaxpar;
     }      }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
 /*------------ 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);  
   }  
    
   /*3eme*/  
   
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(cpt-1);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  
   }    }
     ungetc(c,ficpar);
     
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
        
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);  
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  
   }  
   
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){  
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/  
           /*fprintf(ficgp,"%s",alph[1]);*/  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;  
           fprintf(ficgp,"\n");  
         }  
       }  
     }  
     }  
   
   for(jk=1; jk <=m; jk++) {     dateprev1=anprev1+mprev1/12.+jprev1/365.;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);     dateprev2=anprev2+mprev2/12.+jprev2/365.;
    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);  
      
 chdir(path);  
     free_matrix(agev,1,maxwav,1,imx);  
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  
      
     free_imatrix(s,1,maxwav+1,1,n);  
      
      
     free_ivector(num,1,n);  
     free_vector(agedc,1,n);  
     free_vector(weight,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);  
     fclose(ficres);  
     /*  }*/  
      
    /*________fin mle=1_________*/  
      
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);  
     fprintf(ficres,"pop_based=%d\n",popbased);  
     
     /* No more information from the sample is required now */  
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
Line 2386  chdir(path); Line 3248  chdir(path);
     fputs(line,ficparo);      fputs(line,ficparo);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
    
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/  
   
   if((fichtm=fopen("index.htm","w"))==NULL)    {    fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
     printf("Problem with index.htm \n");goto end;  fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
   fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
   
   
   while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
   }    }
     ungetc(c,ficpar);
   
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n    fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
   
  fprintf(fichtm," <li>Graphs</li>\n<p>");   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
  m=cptcoveff;  /*------------ gnuplot -------------*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}   printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
    
   /*------------ free_vector  -------------*/
    chdir(path);
    
    free_ivector(wav,1,imx);
    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  
    free_ivector(num,1,n);
    free_vector(agedc,1,n);
    /*free_matrix(covar,1,NCOVMAX,1,n);*/
    fclose(ficparo);
    fclose(ficres);
   
  j1=0;  /*--------- index.htm --------*/
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
        j1++;  
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr>************ 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>");  
        }  
        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 2465  fclose(fichtm); Line 3308  fclose(fichtm);
   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 */
   k=0;    k=0;
   agebase=agemin;    agebase=ageminpar;
   agelim=agemax;    agelim=agemaxpar;
   ftolpl=1.e-10;    ftolpl=1.e-10;
   i1=cptcoveff;    i1=cptcoveff;
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
Line 2490  fclose(fichtm); Line 3333  fclose(fichtm);
       }        }
     }      }
   fclose(ficrespl);    fclose(ficrespl);
   
   /*------------- h Pij x at various ages ------------*/    /*------------- h Pij x at various ages ------------*/
     
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
Line 2499  fclose(fichtm); Line 3343  fclose(fichtm);
   printf("Computing pij: result on file '%s' \n", filerespij);    printf("Computing pij: result on file '%s' \n", filerespij);
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=24) stepsize=2;    /*if (stepm<=24) stepsize=2;*/
   
   agelim=AGESUP;    agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */    hstepm=stepsize*YEARM; /* Every year of age */
Line 2525  fclose(fichtm); Line 3369  fclose(fichtm);
             for(j=1; j<=nlstate+ndeath;j++)              for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);                fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");            fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){             for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );              fprintf(ficrespij,"%d %.0f %.0f",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," %.5f", p3mat[i][j][h]);                  fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");              fprintf(ficrespij,"\n");
           }               }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");            fprintf(ficrespij,"\n");
         }          }
     }      }
   }    }
   
     varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
   fclose(ficrespij);    fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     }
     else{
       erreur=108;
       printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
     }
    
   
   /*---------- Health expectancies and variances ------------*/    /*---------- Health expectancies and variances ------------*/
   
   strcpy(filerest,"t");    strcpy(filerest,"t");
Line 2563  fclose(fichtm); Line 3421  fclose(fichtm);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
   }    }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     calagedate=-1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
   k=0;    k=0;
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1;cptcov<=i1;cptcov++){
Line 2575  fclose(fichtm); Line 3435  fclose(fichtm);
   
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
   
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        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, estepm);
           
   
    
       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;  
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);        epj=vector(1,nlstate+1);
       for(age=bage; age <=fage ;age++){        for(age=bage; age <=fage ;age++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
         fprintf(ficrest," %.0f",age);          if (popbased==1) {
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][k];
           }
          
           fprintf(ficrest," %4.0f",age);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(i=1, epj[j]=0.;i <=nlstate;i++) {
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];              epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
           }            }
           epj[nlstate+1] +=epj[j];            epj[nlstate+1] +=epj[j];
         }          }
   
         for(i=1, vepp=0.;i <=nlstate;i++)          for(i=1, vepp=0.;i <=nlstate;i++)
           for(j=1;j <=nlstate;j++)            for(j=1;j <=nlstate;j++)
             vepp += vareij[i][j][(int)age];              vepp += vareij[i][j][(int)age];
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
         for(j=1;j <=nlstate;j++){          for(j=1;j <=nlstate;j++){
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));            fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
         }          }
         fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
       }        }
     }      }
   }    }
          free_matrix(mint,1,maxwav,1,n);
  fclose(ficreseij);      free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
  fclose(ficresvij);      free_vector(weight,1,n);
     fclose(ficreseij);
     fclose(ficresvij);
   fclose(ficrest);    fclose(ficrest);
   fclose(ficpar);    fclose(ficpar);
   free_vector(epj,1,nlstate+1);    free_vector(epj,1,nlstate+1);
   /*  scanf("%d ",i); */   
   
   /*------- Variance limit prevalence------*/      /*------- Variance limit prevalence------*/  
   
 strcpy(fileresvpl,"vpl");    strcpy(fileresvpl,"vpl");
   strcat(fileresvpl,fileres);    strcat(fileresvpl,fileres);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
Line 2635  strcpy(fileresvpl,"vpl"); Line 3504  strcpy(fileresvpl,"vpl");
   }    }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
   
  k=0;    k=0;
  for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1;cptcov<=i1;cptcov++){
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
      k=k+1;        k=k+1;
      fprintf(ficresvpl,"\n#****** ");        fprintf(ficresvpl,"\n#****** ");
      for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
      fprintf(ficresvpl,"******\n");        fprintf(ficresvpl,"******\n");
             
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        varpl=matrix(1,nlstate,(int) bage, (int) fage);
      oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
    }      }
  }   }
   
   fclose(ficresvpl);    fclose(ficresvpl);
Line 2663  strcpy(fileresvpl,"vpl"); Line 3532  strcpy(fileresvpl,"vpl");
   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(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 or warning %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);*/
   /*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
  system("wgnuplot graph.plt");   /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
    strcpy(plotcmd,GNUPLOTPROGRAM);
    strcat(plotcmd," ");
    strcat(plotcmd,optionfilegnuplot);
    system(plotcmd);
   
 #ifdef windows  #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, g to graph again, 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");
     else if (z[0] == 'e') {      else if (z[0] == 'e') system(optionfilehtm);
       chdir(path);      else if (z[0] == 'g') system(plotcmd);
       system("index.htm");  
     }  
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
 #endif  #endif
Removed from v.1.7  
changed lines
  Added in v.1.44

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