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version 1.36, 2002/03/29 15:27:27 version 1.48, 2002/06/10 13:12:49
Line 14 Line 14
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    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    'age' is age and 'sex' is a covariate. If you want to have a more
Line 56 Line 56
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
Line 75 Line 75
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
   #else
   #define DIRSEPARATOR '/'
   #endif
   
   char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";
 int erreur; /* Error number */  int erreur; /* Error number */
 int nvar;  int nvar;
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
Line 96  double jmean; /* Mean space between 2 wa Line 101  double jmean; /* Mean space between 2 wa
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficgp,*ficresprob,*ficpop;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *fichtm; /* Html File */
 FILE *ficreseij;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
  FILE  *ficresvij;  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
   char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
   
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
Line 161  static int split( char *path, char *dirc Line 178  static int split( char *path, char *dirc
   
    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,  DIRSEPARATOR );          /* 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 1330  void prevalence(int agemin, float agemax Line 1343  void prevalence(int agemin, float agemax
   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++;
         
       for (i=-1; i<=nlstate+ndeath; i++)          for (i=-1; i<=nlstate+ndeath; i++)  
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for (jk=-1; jk<=nlstate+ndeath; jk++)  
           for(m=agemin; m <= agemax+3; m++)            for(m=agemin; m <= agemax+3; m++)
Line 1352  void prevalence(int agemin, float agemax Line 1365  void prevalence(int agemin, float agemax
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
               if(agev[m][i]==1) agev[m][i]=agemax+2;                if(agev[m][i]==1) agev[m][i]=agemax+2;
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                if (m<lastpass) {
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */                  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(i=(int)agemin; i <= (int)agemax+3; 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; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)            for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][i];              pos += freq[jk][m][i];
         }          }
                 
          for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
              pp[jk] += freq[jk][m][i];              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;  
              }  
            }  
          }  
            
         }          }
          
           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_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
Line 1503  void tricode(int *Tvar, int **nbcode, in Line 1521  void tricode(int *Tvar, int **nbcode, in
       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("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/           
           ij++;            ij++;
         }          }
         if (ij > ncodemax[j]) break;          if (ij > ncodemax[j]) break;
Line 1531  void tricode(int *Tvar, int **nbcode, in Line 1549  void tricode(int *Tvar, int **nbcode, in
   
 /*********** 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, int estepm)  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, nstepm;    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");
   
   if(estepm < stepm){    if(estepm < stepm){
Line 1582  void evsij(char fileres[], double ***eij Line 1611  void evsij(char fileres[], double ***eij
     /* if (stepm >= YEARM) hstepm=1;*/      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=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. */      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-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            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]);*/           
   /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
         }          }
   
     fprintf(ficreseij,"%3.0f",age );      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
     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," %9.4f", 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);
   }    }
     printf("\n");
   
     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 ******************/
Line 1618  void varevsij(char fileres[], double *** Line 1733  void varevsij(char fileres[], double ***
   double age,agelim, hf;    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 1753  void varprevlim(char fileres[], double * Line 1868  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 1822  void varprevlim(char fileres[], double * Line 1937  void varprevlim(char fileres[], double *
 }  }
   
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 {  {
   int i, j;    int i, j,  i1, k1, l1;
   int k=0, cptcode;    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
     double **mu;
   double age,agelim, cov[NCOVMAX];    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;    int theta;
   char fileresprob[FILENAMELENGTH];    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
   strcpy(fileresprob,"prob");    strcpy(fileresprob,"prob");
   strcat(fileresprob,fileres);    strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);      printf("Problem with resultfile: %s\n", fileresprob);
   }    }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    strcpy(fileresprobcov,"probcov");
      strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor");
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
     fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
     }
     else{
       fprintf(ficgp,"\n# Routine varprob");
     }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
       exit(0);
     }
     else{
       fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");
       fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   
     }
   cov[1]=1;    cov[1]=1;
   for (age=bage; age<=fage; age ++){    j=cptcoveff;
     cov[2]=age;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     gradg=matrix(1,npar,1,9);    j1=0;
     trgradg=matrix(1,9,1,npar);    for(k1=1; k1<=1;k1++){
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for(i1=1; i1<=ncodemax[k1];i1++){
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      j1++;
   
       if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");
         fprintf(ficresprobcov, "\n#********** Variable ");
         fprintf(ficgp, "\n#********** Variable ");
         fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");
         fprintf(ficresprobcor, "\n#********** Variable ");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresprob, "**********\n#");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresprobcov, "**********\n#");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp, "**********\n#");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp, "**********\n#");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(fichtm, "**********\n#");
       }
         
     for(theta=1; theta <=npar; theta++){        for (age=bage; age<=fage; age ++){
       for(i=1; i<=npar; i++)          cov[2]=age;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (k=1; k<=cptcovn;k++) {
                  cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          }
              for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       k=0;          for (k=1; k<=cptcovprod;k++)
       for(i=1; i<= (nlstate+ndeath); i++){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         for(j=1; j<=(nlstate+ndeath);j++){         
            k=k+1;          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           gp[k]=pmmij[i][j];          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         }          gp=vector(1,(nlstate)*(nlstate+ndeath));
       }          gm=vector(1,(nlstate)*(nlstate+ndeath));
   
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
         
           for(theta=1; theta <=npar; theta++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            for(i=1; i<=npar; i++)
       k=0;              xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(i=1; i<=(nlstate+ndeath); i++){           
         for(j=1; j<=(nlstate+ndeath);j++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           k=k+1;           
           gm[k]=pmmij[i][j];            k=0;
         }            for(i=1; i<= (nlstate); 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); 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++)            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                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(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
      for(i=1; i<=(nlstate+ndeath); i++){            for(theta=1; theta <=npar; theta++)
        for(j=1; j<=(nlstate+ndeath);j++){              trgradg[j][theta]=gradg[theta][j];
          k=k+1;         
          gm[k]=pmmij[i][j];          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
          
           pmij(pmmij,cov,ncovmodel,x,nlstate);
          
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
         }          }
      }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                  for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
      /*printf("\n%d ",(int)age);              varpij[i][j][(int)age] = doldm[i][j];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
          
   
           /*printf("\n%d ",(int)age);
        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      }*/       }*/
   
   fprintf(ficresprob,"\n%d ",(int)age);          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          fprintf(ficresprobcor,"\n%d ",(int)age);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
           /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         for (k1=1; k1<=(nlstate);k1++){
           for (l1=1; l1<=(nlstate+ndeath);l1++){
             if(l1==k1) continue;
             i=(k1-1)*(nlstate+ndeath)+l1;
             for (k2=1; k2<=(nlstate);k2++){
               for (l2=1; l2<=(nlstate+ndeath);l2++){
                 if(l2==k2) continue;
                 j=(k2-1)*(nlstate+ndeath)+l2;
                 if(j<=i) continue;
                 for (age=bage; age<=fage; age ++){
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     /* Computing eigen value of matrix of covariance */
                     lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
                     lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     v21=sqrt(1.-v11*v11);
                     v12=-v21;
                     v22=v11;
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;set nolabel");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);
                       fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
                               mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
                     }else{
                       first=0;
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
                               mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
       free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     }
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     fclose(fichtm);
 }  }
  free_vector(xp,1,npar);  
 fclose(ficresprob);  
   
 }  
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
  int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\                    int popforecast, int estepm ,\
  char version[], int popforecast, int estepm ){                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   FILE *fichtm;  
   /*char optionfilehtm[FILENAMELENGTH];*/    /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);      printf("Problem with %s \n",optionfilehtm), exit(0);
   }    }
   
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n     fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<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
 \n   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
 Total number of observations=%d <br>\n   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n   - Life expectancies by age and initial health status (estepm=%2d months):
 <hr  size=\"2\" color=\"#EC5E5E\">     <a href=\"e%s\">e%s</a> <br>\n</li>", \
  <ul><li>Outputs files<br>\n    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n   fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%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
  fprintf(fichtm,"\n   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n  
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  
   
  if(popforecast==1) fprintf(fichtm,"\n   if(popforecast==1) fprintf(fichtm,"\n
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
Line 1976  fprintf(fichtm," <li>Graphs</li><p>"); Line 2254  fprintf(fichtm," <li>Graphs</li><p>");
  jj1=0;   jj1=0;
  for(k1=1; k1<=m;k1++){   for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;       jj1++;
        if (cptcovn > 0) {       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++)         for (cpt=1; cpt<=cptcoveff;cpt++)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }       }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>       /* Pij */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           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\">",stepm,strtok(optionfile, "."),jj1,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\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
          /* Stable prevalence in each health state */
        for(cpt=1; cpt<nlstate;cpt++){         for(cpt=1; cpt<nlstate;cpt++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }         }
     for(cpt=1; cpt<=nlstate;cpt++) {      for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
 interval) in state (%d): v%s%d%d.gif <br>  interval) in state (%d): v%s%d%d.png <br>
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       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>          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.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  <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       fprintf(fichtm,"\n<br>- Total life expectancy by age and
 health expectancies in states (1) and (2): e%s%d.gif<br>  health expectancies in states (1) and (2): e%s%d.png<br>
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
 fprintf(fichtm,"\n</body>");  
    }  
    }     }
    }
 fclose(fichtm);  fclose(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   strcpy(optionfilegnuplot,optionfilefiname);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   strcat(optionfilegnuplot,".gp.txt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
   }    }
   
Line 2028  m=pow(2,cptcoveff); Line 2308  m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) {
   
 #ifdef windows  #ifdef windows
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);       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  #endif
 #ifdef unix  #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);  fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
 #endif  #endif
   
Line 2050  for (i=1; i<= nlstate ; i ++) { Line 2332  for (i=1; i<= nlstate ; i ++) {
 }    }  
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
 #ifdef unix  #ifdef unix
 fprintf(ficgp,"\nset ter gif small size 400,300");  fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
 #endif  #endif
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }     }
   }    }
   /*2 eme*/    /*2 eme*/
   
   for (k1=1; k1<= m ; k1 ++) {    for (k1=1; k1<= m ; k1 ++) {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);      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 ++) {      for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;        k=2*i;
Line 2083  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2365  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       else 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*/    /*3eme*/
   
   for (k1=1; k1<= m ; k1 ++) {    for (k1=1; k1<= m ; k1 ++) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(cpt-1);        k=2+nlstate*(2*cpt-2);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        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 ++) {        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," ,\"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);
   
       }        }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  
     }      }
     }
     
   /* CV preval stat */    /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) {      for (k1=1; k1<= m ; k1 ++) {
     for (cpt=1; cpt<nlstate ; cpt ++) {      for (cpt=1; cpt<nlstate ; cpt ++) {
       k=3;        k=3;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        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 ++)        for (i=1; i< nlstate ; i ++)
         fprintf(ficgp,"+$%d",k+i+1);          fprintf(ficgp,"+$%d",k+i+1);
Line 2116  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2407  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
         fprintf(ficgp,"+$%d",l+i+1);          fprintf(ficgp,"+$%d",l+i+1);
       }        }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+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);  
     }      }
   }      }  
     
Line 2132  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2422  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
         }          }
       }        }
     }      }
     }     }
   
     for(jk=1; jk <=m; jk++) {     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);       for(jk=1; jk <=m; jk++) {
    i=1;         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
    for(k2=1; k2<=nlstate; k2++) {         if (ng==2)
      k3=i;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
      for(k=1; k<=(nlstate+ndeath); k++) {         else
        if (k != k2){           fprintf(ficgp,"\nset title \"Probability\"\n");
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 ij=1;         i=1;
         for(j=3; j <=ncovmodel; j++) {         for(k2=1; k2<=nlstate; k2++) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {           k3=i;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);           for(k=1; k<=(nlstate+ndeath); k++) {
             ij++;             if (k != k2){
           }               if(ng==2)
           else                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);               else
         }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
           fprintf(ficgp,")/(1");               ij=1;
                       for(j=3; j <=ncovmodel; j++) {
         for(k1=1; k1 <=nlstate; k1++){                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 ij=1;                   ij++;
           for(j=3; j <=ncovmodel; j++){                 }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                 else
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             ij++;               }
           }               fprintf(ficgp,")/(1");
           else               
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);               for(k1=1; k1 <=nlstate; k1++){  
           }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           fprintf(ficgp,")");                 ij=1;
         }                 for(j=3; j <=ncovmodel; j++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         i=i+ncovmodel;                     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);
    }  
      
   fclose(ficgp);  
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
Line 2475  int main(int argc, char *argv[]) Line 2773  int main(int argc, char *argv[])
   double ***p3mat;    double ***p3mat;
   int *indx;    int *indx;
   char line[MAXLINE], linepar[MAXLINE];    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];    char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */    int sdeb, sfin; /* Status at beginning and end */
Line 2493  int main(int argc, char *argv[]) Line 2782  int main(int argc, char *argv[])
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm, nhstepm;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   
   double bage, fage, age, agelim, agebase;    double bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;    double ftolpl=FTOL;
Line 2511  int main(int argc, char *argv[]) Line 2800  int main(int argc, char *argv[])
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
     
   
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
Line 2751  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3039  while((c=getc(ficpar))=='#' && c!= EOF){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
     }*/      }*/
       /*  for (i=1; i<=imx; i++){
   /* for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;       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]));}       printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
   */   
     
   /* Calculation of the number of parameter from char model*/    /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15);    Tvar=ivector(1,15);
Line 3107  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3394  while((c=getc(ficpar))=='#' && c!= EOF){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
 /*------------ gnuplot -------------*/  /*------------ gnuplot -------------*/
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     fclose(ficgp);
    printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
   /*--------- index.htm --------*/
   
     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);
     fclose(fichtm);
   
    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
     
 /*------------ free_vector  -------------*/  /*------------ free_vector  -------------*/
  chdir(path);   chdir(path);
Line 3121  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3434  while((c=getc(ficpar))=='#' && c!= EOF){
  fclose(ficparo);   fclose(ficparo);
  fclose(ficres);   fclose(ficres);
   
 /*--------- index.htm --------*/  
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);  
   
    
   /*--------------- Prevalence limit --------------*/    /*--------------- Prevalence limit --------------*/
     
   strcpy(filerespl,"pl");    strcpy(filerespl,"pl");
Line 3207  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3516  while((c=getc(ficpar))=='#' && c!= EOF){
             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);*/    varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
   fclose(ficrespij);    fclose(ficrespij);
   
Line 3229  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3538  while((c=getc(ficpar))=='#' && c!= EOF){
   if((stepm == 1) && (strcmp(model,".")==0)){    if((stepm == 1) && (strcmp(model,".")==0)){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      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);      if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     free_matrix(mint,1,maxwav,1,n);    }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);}  
   else{    else{
     erreur=108;      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);      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);
Line 3261  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3568  while((c=getc(ficpar))=='#' && c!= EOF){
     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 3283  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3592  while((c=getc(ficpar))=='#' && c!= EOF){
   
       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, estepm);          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, estepm);         varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
Line 3306  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3616  while((c=getc(ficpar))=='#' && c!= EOF){
         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]*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," %7.2f (%7.2f)", epj[nlstate+1],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," %7.2f (%7.2f)", epj[j],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);
       free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
       free_vector(weight,1,n);
   fclose(ficreseij);    fclose(ficreseij);
   fclose(ficresvij);    fclose(ficresvij);
   fclose(ficrest);    fclose(ficrest);
Line 3371  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3685  while((c=getc(ficpar))=='#' && c!= EOF){
   free_matrix(agev,1,maxwav,1,imx);    free_matrix(agev,1,maxwav,1,imx);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
    
   
   if(erreur >0)    if(erreur >0)
     printf("End of Imach with error or warning %d\n",erreur);      printf("End of Imach with error or warning %d\n",erreur);
   else   printf("End of Imach\n");    else   printf("End of Imach\n");
Removed from v.1.36  
changed lines
  Added in v.1.48

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