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version 1.35, 2002/03/26 17:08:39 version 1.43, 2002/05/24 13:00:54
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 136  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;
Line 1327  void prevalence(int agemin, float agemax Line 1330  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 1349  void prevalence(int agemin, float agemax Line 1352  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 1500  void tricode(int *Tvar, int **nbcode, in Line 1508  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 1528  void tricode(int *Tvar, int **nbcode, in Line 1536  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)  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, k;    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");
   
   k=1;             /* For example stepm=6 months */    if(estepm < stepm){
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */    }
     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.    /* 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       nhstepm is the number of hstepm from age to agelim
      nstepm is the number of stepm from age to agelin.       nstepm is the number of stepm from age to agelin.
      Look at hpijx to understand the reason of that which relies in memory size       Look at hpijx to understand the reason of that which relies in memory size
      and note for a fixed period like k years */       and note for a fixed period like estepm months */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      survival function given by stepm (the optimization length). Unfortunately it       survival function given by stepm (the optimization length). Unfortunately it
      means that if the survival funtion is printed only each two years of age and if       means that if the survival funtion is printed 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       you sum them up and add 1 year (area under the trapezoids) you won't get the same
      results. So we changed our mind and took the option of the best precision.       results. So we changed our mind and took the option of the best precision.
   */    */
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */    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 */
Line 1566  void evsij(char fileres[], double ***eij Line 1598  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);
   }    }
     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, nstepm, kk;    int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;    int k, cptcode;
   double *xp;    double *xp;
   double **gp, **gm;    double **gp, **gm;
Line 1602  void varevsij(char fileres[], double *** Line 1724  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 1613  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);
     
   kk=1;             /* For example stepm=6 months */    if(estepm < stepm){
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */    }
     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.    /* 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       nhstepm is the number of hstepm from age to agelim
      nstepm is the number of stepm from age to agelin.       nstepm is the number of stepm from age to agelin.
Line 1627  void varevsij(char fileres[], double *** Line 1751  void varevsij(char fileres[], double ***
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       you sum them up and add 1 year (area under the trapezoids) you won't get the same
      results. So we changed our mind and took the option of the best precision.       results. So we changed our mind and took the option of the best precision.
   */    */
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */    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 */
     nstepm=(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 */
Line 1735  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 1804  void varprevlim(char fileres[], double * Line 1928  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 fileres[], 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, j1, z1;
   int k=0, cptcode;    int k=0, cptcode;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double *xp;    double *xp;
Line 1821  void varprob(char fileres[], double **ma Line 1945  void varprob(char fileres[], double **ma
   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);    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);
   
   
     fprintf(ficresprob,"\n");
   
   
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
     
   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 ");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresprob, "**********\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);           
      
       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 (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
       for(i=1; i<=npar; i++)            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);         
           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++){
       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+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++)            for(i=1; i<= (nlstate+ndeath)*(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+ndeath)*(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,1,9,1,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);       /*printf("\n%d ",(int)age);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       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]));         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);
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
     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+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(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_vector(gm,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(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);    free_vector(xp,1,npar);
 fclose(ficresprob);    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 optionfile[], \
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\                    char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
  char version[], int popforecast ){                    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;    FILE *fichtm;
   /*char optionfilehtm[FILENAMELENGTH];*/    /*char optionfilehtm[FILENAMELENGTH];*/
Line 1924  void printinghtml(char fileres[], char t Line 2077  void printinghtml(char fileres[], char t
     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,"<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  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
 \n  \n
 Total number of observations=%d <br>\n  Total number of observations=%d <br>\n
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
 <hr  size=\"2\" color=\"#EC5E5E\">  <hr  size=\"2\" color=\"#EC5E5E\">
  <ul><li>Outputs files<br>\n   <ul><li>Parameter files<br>\n
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><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>\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);
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n     fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><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
  - Life expectancies by age and initial health status: <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);   - 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
  fprintf(fichtm,"\n   - Life expectancies by age and initial health status (estepm=%2d months):
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n     <a href=\"e%s\">e%s</a> <br>\n</li>", \
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
  - 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,fileres,fileres,fileres,fileres,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   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 1965  fprintf(fichtm," <li>Graphs</li><p>"); Line 2123  fprintf(fichtm," <li>Graphs</li><p>");
            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\">",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++){         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>");  fprintf(fichtm,"\n</body>");
    }     }
    }     }
Line 1993  fclose(fichtm); Line 2156  fclose(fichtm);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   strcat(optionfilegnuplot,".gp.txt");    strcat(optionfilegnuplot,".gp.txt");
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
Line 2010  m=pow(2,cptcoveff); Line 2173  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 2032  for (i=1; i<= nlstate ; i ++) { Line 2197  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 2065  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2230  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 2098  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2272  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 2114  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2287  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",stepm/YEARM,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 2656  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 2493  int main(int argc, char *argv[]) Line 2674  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 version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
Line 2733  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2914  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 3021  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",&ageminpar,&agemaxpar, &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 = ageminpar;        bage = ageminpar;
       fage = agemaxpar;        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",ageminpar,agemaxpar,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\n",ageminpar,agemaxpar,bage,fage);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 3105  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3285  while((c=getc(ficpar))=='#' && c!= EOF){
   
 /*--------- index.htm --------*/  /*--------- index.htm --------*/
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);    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);
   
     
   /*--------------- Prevalence limit --------------*/    /*--------------- Prevalence limit --------------*/
Line 3189  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3369  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(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
   fclose(ficrespij);    fclose(ficrespij);
   
Line 3211  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3391  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 3243  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3421  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 3265  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3445  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);          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);
         
   
     
Line 3288  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3469  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);
Removed from v.1.35  
changed lines
  Added in v.1.43

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