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version 1.10, 2001/05/09 14:25:42 version 1.21, 2002/02/21 18:42:24
Line 8 Line 8
   Health expectancies are computed from the transistions observed between    Health expectancies are computed from the transistions observed between
   waves and are computed for each degree of severity of disability (number    waves and are computed for each degree of severity of disability (number
   of life states). More degrees you consider, more time is necessary to    of life states). More degrees you consider, more time is necessary to
   reach the Maximum Likelihood of the parameters involved in the model.    reach 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 conditional    the probabibility to be observed in state j at the second wave conditional
   to be observed in state i at the first wave. Therefore the model is:    to be observed in state i at the first wave. Therefore the model is:
Line 22 Line 22
   delay between waves is not identical for each individual, or if some    delay between waves is not identical for each individual, or if some
   individual missed an interview, the information is not rounded or lost, but    individual missed an interview, the information is not rounded or lost, but
   taken into account using an interpolation or extrapolation.    taken into account using an interpolation or extrapolation.
   hPijx is the probability to be    hPijx is the probability to be
   observed in state i at age x+h conditional to the observed state i at age    observed in state i at age x+h conditional to the observed state i at age
   x. The delay 'h' can be split into an exact number (nh*stepm) of    x. The delay 'h' can be split into an exact number (nh*stepm) of
   unobserved intermediate  states. This elementary transition (by month or    unobserved intermediate  states. This elementary transition (by month or
Line 67 Line 67
 #define AGEBASE 40  #define AGEBASE 40
   
   
   int erreur; /* Error number */
 int nvar;  int nvar;
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav; /* Maxim number of waves */
Line 83  int **dh; /* dh[mi][i] is number of step Line 85  int **dh; /* dh[mi][i] is number of step
 double jmean; /* Mean space between 2 waves */  double jmean; /* Mean space between 2 waves */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;
 FILE *ficgp, *fichtm;  FILE *ficgp, *fichtm,*ficresprob,*ficpop;
 FILE *ficreseij;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];    char filerese[FILENAMELENGTH];
  FILE  *ficresvij;   FILE  *ficresvij;
Line 127  int stepm; Line 129  int stepm;
 int m,nb;  int m,nb;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij;  double **pmmij, ***probs, ***mobaverage;
   double dateintmean=0;
   
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
Line 693  double **prevalim(double **prlim, int nl Line 696  double **prevalim(double **prlim, int nl
   }    }
 }  }
   
 /*************** transition probabilities **********/  /*************** transition probabilities ***************/
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
Line 716  double **pmij(double **ps, double *cov, Line 719  double **pmij(double **ps, double *cov,
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       }        }
       ps[i][j]=s2;        ps[i][j]=(s2);
     }      }
   }    }
       /*ps[3][2]=1;*/
   
   for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
      s1=0;       s1=0;
     for(j=1; j<i; j++)      for(j=1; j<i; j++)
Line 740  double **pmij(double **ps, double *cov, Line 745  double **pmij(double **ps, double *cov,
     }      }
   }    }
   
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     for(jj=1; jj<= nlstate+ndeath; jj++){      for(jj=1; jj<= nlstate+ndeath; jj++){
      printf("%lf ",ps[ii][jj]);       printf("%lf ",ps[ii][jj]);
Line 757  double **pmij(double **ps, double *cov, Line 763  double **pmij(double **ps, double *cov,
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 {  {
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /* in, b, out are matrice of pointers which should have been initialized    /* in, b, out are matrice of pointers which should have been initialized
      before: only the contents of out is modified. The function returns       before: only the contents of out is modified. The function returns
Line 804  double ***hpxij(double ***po, int nhstep Line 810  double ***hpxij(double ***po, int nhstep
       cov[1]=1.;        cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 for (k=1; k<=cptcovage;k++)        for (k=1; k<=cptcovage;k++)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    for (k=1; k<=cptcovprod;k++)        for (k=1; k<=cptcovprod;k++)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   
Line 896  void mlikeli(FILE *ficres,double p[], in Line 902  void mlikeli(FILE *ficres,double p[], in
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
 }  }
   
Line 913  void hesscov(double **matcov, double p[] Line 919  void hesscov(double **matcov, double p[]
   void lubksb(double **a, int npar, int *indx, double b[]) ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
   
   hess=matrix(1,npar,1,npar);    hess=matrix(1,npar,1,npar);
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
Line 921  void hesscov(double **matcov, double p[] Line 926  void hesscov(double **matcov, double p[]
     printf("%d",i);fflush(stdout);      printf("%d",i);fflush(stdout);
     hess[i][i]=hessii(p,ftolhess,i,delti);      hess[i][i]=hessii(p,ftolhess,i,delti);
     /*printf(" %f ",p[i]);*/      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
   }    }
    
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
     for (j=1;j<=npar;j++)  {      for (j=1;j<=npar;j++)  {
       if (j>i) {        if (j>i) {
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d%d",i,j);fflush(stdout);
         hess[i][j]=hessij(p,delti,i,j);          hess[i][j]=hessij(p,delti,i,j);
         hess[j][i]=hess[i][j];          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
       }        }
     }      }
   }    }
Line 1032  double hessii( double x[], double delta, Line 1039  double hessii( double x[], double delta,
     }      }
   }    }
   delti[theta]=delts;    delti[theta]=delts;
   return res;    return res;
     
 }  }
   
Line 1145  void lubksb(double **a, int n, int *indx Line 1152  void lubksb(double **a, int n, int *indx
 }  }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)
 {  /* Some frequencies */  {  /* Some frequencies */
     
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp;    double *pp;
   double pos;    double pos, k2, dateintsum=0,k2cpt=0;
   FILE *ficresp;    FILE *ficresp;
   char fileresp[FILENAMELENGTH];    char fileresp[FILENAMELENGTH];
   
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresp,"p");    strcpy(fileresp,"p");
   strcat(fileresp,fileres);    strcat(fileresp,fileres);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
Line 1178  void  freqsummary(char fileres[], int ag Line 1185  void  freqsummary(char fileres[], int ag
          for (jk=-1; jk<=nlstate+ndeath; jk++)             for (jk=-1; jk<=nlstate+ndeath; jk++)  
            for(m=agemin; m <= agemax+3; m++)             for(m=agemin; m <= agemax+3; m++)
              freq[i][jk][m]=0;               freq[i][jk][m]=0;
          
           dateintsum=0;
           k2cpt=0;
        for (i=1; i<=imx; i++) {         for (i=1; i<=imx; i++) {
          bool=1;           bool=1;
          if  (cptcovn>0) {           if  (cptcovn>0) {
Line 1186  void  freqsummary(char fileres[], int ag Line 1195  void  freqsummary(char fileres[], int ag
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                bool=0;                 bool=0;
          }           }
           if (bool==1) {           if (bool==1) {
            for(m=firstpass; m<=lastpass-1; m++){             for(m=firstpass; m<=lastpass; m++){
              if(agev[m][i]==0) agev[m][i]=agemax+1;               k2=anint[m][i]+(mint[m][i]/12.);
              if(agev[m][i]==1) agev[m][i]=agemax+2;               if ((k2>=dateprev1) && (k2<=dateprev2)) {
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                 if(agev[m][i]==0) agev[m][i]=agemax+1;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                 if(agev[m][i]==1) agev[m][i]=agemax+2;
                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
                  if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
                    dateintsum=dateintsum+k2;
                    k2cpt++;
                  }
   
                }
            }             }
          }           }
        }         }
Line 1211  void  freqsummary(char fileres[], int ag Line 1228  void  freqsummary(char fileres[], int ag
       printf("Age %d", i);        printf("Age %d", i);
     for(jk=1; jk <=nlstate ; jk++){      for(jk=1; jk <=nlstate ; jk++){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         pp[jk] += freq[jk][m][i];          pp[jk] += freq[jk][m][i];
     }      }
     for(jk=1; jk <=nlstate ; jk++){      for(jk=1; jk <=nlstate ; jk++){
       for(m=-1, pos=0; m <=0 ; m++)        for(m=-1, pos=0; m <=0 ; m++)
Line 1221  void  freqsummary(char fileres[], int ag Line 1238  void  freqsummary(char fileres[], int ag
       else        else
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     }      }
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)       for(jk=1; jk <=nlstate ; jk++){
         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++)      for(jk=1,pos=0; jk <=nlstate ; jk++)
       pos += pp[jk];        pos += pp[jk];
     for(jk=1; jk <=nlstate ; jk++){      for(jk=1; jk <=nlstate ; jk++){
Line 1233  void  freqsummary(char fileres[], int ag Line 1252  void  freqsummary(char fileres[], int ag
       else        else
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       if( i <= (int) agemax){        if( i <= (int) agemax){
         if(pos>=1.e-5)          if(pos>=1.e-5){
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
             probs[i][jk][j1]= pp[jk]/pos;
             /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           }
       else        else
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
       }        }
Line 1248  void  freqsummary(char fileres[], int ag Line 1270  void  freqsummary(char fileres[], int ag
     }      }
     }      }
  }   }
     dateintmean=dateintsum/k2cpt;
     
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   
     /* End of Freq */
   }
   
   /************ Prevalence ********************/
   void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
   {  /* Some frequencies */
    
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
     double *pp;
     double pos, k2;
   
     pp=vector(1,nlstate);
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    
     freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     j1=0;
    
     j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
    
         for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=agemin; m <= agemax+3; m++)
               freq[i][jk][m]=0;
        
         for (i=1; i<=imx; i++) {
           bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++)
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                 bool=0;
           }
           if (bool==1) {
             for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
                 if(agev[m][i]==1) agev[m][i]=agemax+2;
                 freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  
               }
             }
           }
         }
        
           for(i=(int)agemin; i <= (int)agemax+3; i++){
             for(jk=1; jk <=nlstate ; jk++){
               for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                 pp[jk] += freq[jk][m][i];
             }
             for(jk=1; jk <=nlstate ; jk++){
               for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
           }
          
            for(jk=1; jk <=nlstate ; jk++){
              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                pp[jk] += freq[jk][m][i];
            }
            
            for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
   
            for(jk=1; jk <=nlstate ; jk++){          
              if( i <= (int) agemax){
                if(pos>=1.e-5){
                  probs[i][jk][j1]= pp[jk]/pos;
                }
              }
            }
            
           }
       }
     }
    
    
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
    
 }  /* End of Freq */  }  /* End of Freq */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
Line 1270  void  concatwav(int wav[], int **dh, int Line 1376  void  concatwav(int wav[], int **dh, int
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      double sum=0., jmean=0.;*/       double sum=0., jmean=0.;*/
   
 int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
      double sum=0.;    double sum=0.;
 jmin=1e+5;    jmin=1e+5;
  jmax=-1;    jmax=-1;
 jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     mi=0;      mi=0;
     m=firstpass;      m=firstpass;
Line 1309  jmean=0.; Line 1415  jmean=0.;
           if(j==0) j=1;  /* Survives at least one month after exam */            if(j==0) j=1;  /* Survives at least one month after exam */
           k=k+1;            k=k+1;
           if (j >= jmax) jmax=j;            if (j >= jmax) jmax=j;
           else if (j <= jmin)jmin=j;            if (j <= jmin) jmin=j;
           sum=sum+j;            sum=sum+j;
           if (j<0) printf("j=%d num=%d ",j,i);            /* if (j<10) printf("j=%d num=%d ",j,i); */
           }            }
         }          }
         else{          else{
Line 1319  jmean=0.; Line 1425  jmean=0.;
           k=k+1;            k=k+1;
           if (j >= jmax) jmax=j;            if (j >= jmax) jmax=j;
           else if (j <= jmin)jmin=j;            else if (j <= jmin)jmin=j;
             /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           sum=sum+j;            sum=sum+j;
         }          }
         jk= j/stepm;          jk= j/stepm;
Line 1335  jmean=0.; Line 1442  jmean=0.;
   }    }
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 }   }
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)  void tricode(int *Tvar, int **nbcode, int imx)
 {  {
Line 1373  void tricode(int *Tvar, int **nbcode, in Line 1480  void tricode(int *Tvar, int **nbcode, in
   
  for (k=0; k<19; k++) Ndum[k]=0;   for (k=0; k<19; k++) Ndum[k]=0;
   
  for (i=1; i<=ncovmodel; i++) {   for (i=1; i<=ncovmodel-2; i++) {
       ij=Tvar[i];        ij=Tvar[i];
       Ndum[ij]++;        Ndum[ij]++;
     }      }
Line 1448  void varevsij(char fileres[], double *** Line 1555  void varevsij(char fileres[], double ***
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm, h;    int i, j, nhstepm, hstepm, h;
   int k, cptcode;    int k, cptcode;
    double *xp;    double *xp;
   double **gp, **gm;    double **gp, **gm;
   double ***gradg, ***trgradg;    double ***gradg, ***trgradg;
   double ***p3mat;    double ***p3mat;
Line 1484  void varevsij(char fileres[], double *** Line 1591  void varevsij(char fileres[], double ***
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }
        
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
Line 1495  void varevsij(char fileres[], double *** Line 1608  void varevsij(char fileres[], double ***
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }
   
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
   
       for(j=1; j<= nlstate; j++)        for(j=1; j<= nlstate; j++)
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
Line 1630  void varprevlim(char fileres[], double * Line 1750  void varprevlim(char fileres[], double *
   
 }  }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
   {
     int i, j;
     int k=0, cptcode;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim, cov[NCOVMAX];
     int theta;
     char fileresprob[FILENAMELENGTH];
   
     strcpy(fileresprob,"prob");
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
     }
     printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
    
   
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
    
     cov[1]=1;
     for (age=bage; age<=fage; age ++){
       cov[2]=age;
       gradg=matrix(1,npar,1,9);
       trgradg=matrix(1,9,1,npar);
       gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
       gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
      
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++)
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
        
         pmij(pmmij,cov,ncovmodel,xp,nlstate);
      
         k=0;
         for(i=1; i<= (nlstate+ndeath); i++){
           for(j=1; j<=(nlstate+ndeath);j++){
              k=k+1;
             gp[k]=pmmij[i][j];
           }
         }
   
         for(i=1; i<=npar; i++)
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
      
   
         pmij(pmmij,cov,ncovmodel,xp,nlstate);
         k=0;
         for(i=1; i<=(nlstate+ndeath); i++){
           for(j=1; j<=(nlstate+ndeath);j++){
             k=k+1;
             gm[k]=pmmij[i][j];
           }
         }
        
          for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
       }
   
        for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
         for(theta=1; theta <=npar; theta++)
         trgradg[j][theta]=gradg[theta][j];
    
        matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
        matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
   
        pmij(pmmij,cov,ncovmodel,x,nlstate);
   
        k=0;
        for(i=1; i<=(nlstate+ndeath); i++){
          for(j=1; j<=(nlstate+ndeath);j++){
            k=k+1;
            gm[k]=pmmij[i][j];
           }
        }
        
        /*printf("\n%d ",(int)age);
        for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
          
   
          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        }*/
   
     fprintf(ficresprob,"\n%d ",(int)age);
   
     for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
       if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
   if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
     }
   
       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   }
    free_vector(xp,1,npar);
   fclose(ficresprob);
    exit(0);
   }
   
 /***********************************************/  /***********************************************/
 /**************** Main Program *****************/  /**************** Main Program *****************/
Line 1653  int main() Line 1876  int main()
   char line[MAXLINE], linepar[MAXLINE];    char line[MAXLINE], linepar[MAXLINE];
   char title[MAXLINE];    char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
   char filerest[FILENAMELENGTH];    char filerest[FILENAMELENGTH];
   char fileregp[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 */
   int c,  h , cpt,l;    int c,  h , cpt,l;
   int ju,jl, mi;    int ju,jl, mi;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
      int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm, nhstepm;
     int *popage;/*boolprev=0 if date and zero if wave*/
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
   
   double bage, fage, age, agelim, agebase;    double bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
Line 1677  int main() Line 1904  int main()
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;    double *epj, vepp;
     double kk1, kk2;
     double *popeffectif,*popcount;
     double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
     double yp,yp1,yp2;
   
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
   char z[1]="c", occ;    char z[1]="c", occ;
 #include <sys/time.h>  #include <sys/time.h>
 #include <time.h>  #include <time.h>
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
   /* long total_usecs;    /* long total_usecs;
   struct timeval start_time, end_time;    struct timeval start_time, end_time;
     
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   
   
   printf("\nIMACH, Version 0.64b");    printf("\nIMACH, Version 0.7");
   printf("\nEnter the parameter file name: ");    printf("\nEnter the parameter file name: ");
   
 #ifdef windows  #ifdef windows
Line 1738  split(pathtot, path,optionfile); Line 1972  split(pathtot, path,optionfile);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);
   while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
      
   covar=matrix(0,NCOVMAX,1,n);    covar=matrix(0,NCOVMAX,1,n);
   cptcovn=0;    cptcovn=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
Line 1772  split(pathtot, path,optionfile); Line 2014  split(pathtot, path,optionfile);
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
     
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
   
   p=param[1][1];    p=param[1][1];
     
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
Line 1862  split(pathtot, path,optionfile); Line 2105  split(pathtot, path,optionfile);
     tab=ivector(1,NCOVMAX);      tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);      ncodemax=ivector(1,8);
   
     i=1;      i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {      while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {        if ((i >= firstobs) && (i <=lastobs)) {
                 
Line 1884  split(pathtot, path,optionfile); Line 2127  split(pathtot, path,optionfile);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }          }
         num[i]=atol(stra);          num[i]=atol(stra);
          
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/          /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
             printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;          i=i+1;
       }        }
     }      }
       /* printf("ii=%d", ij);
     /*scanf("%d",i);*/         scanf("%d",i);*/
   imx=i-1; /* Number of individuals */    imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }
   
       for (i=1; i<=imx; i++)
       if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/
   
   /* Calculation of the number of parameter from char model*/    /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15);    Tvar=ivector(1,15);
   Tprod=ivector(1,15);    Tprod=ivector(1,15);
Line 1975  split(pathtot, path,optionfile); Line 2228  split(pathtot, path,optionfile);
     }      }
     /*-calculation of age at interview from date of interview and age at death -*/      /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);      agev=matrix(1,maxwav,1,imx);
   
      for (i=1; i<=imx; i++)
        for(m=2; (m<= maxwav); m++)
          if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
            anint[m][i]=9999;
            s[m][i]=-1;
          }
         
     for (i=1; i<=imx; i++)  {      for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
Line 2031  printf("Total number of individuals= %d, Line 2291  printf("Total number of individuals= %d,
     free_imatrix(outcome,1,maxwav+1,1,n);      free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);      free_vector(moisnais,1,n);
     free_vector(annais,1,n);      free_vector(annais,1,n);
     free_matrix(mint,1,maxwav,1,n);      /* free_matrix(mint,1,maxwav,1,n);
     free_matrix(anint,1,maxwav,1,n);         free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);      free_vector(moisdc,1,n);
     free_vector(andc,1,n);      free_vector(andc,1,n);
   
Line 2064  printf("Total number of individuals= %d, Line 2324  printf("Total number of individuals= %d,
        }         }
      }       }
    }     }
   
   
    /*for(i=1; i <=m ;i++){  
      for(k=1; k <=cptcovn; k++){  
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);  
      }  
      printf("\n");  
    }  
    scanf("%d",i);*/  
         
    /* Calculates basic frequencies. Computes observed prevalence at single age     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */         and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);  
   
      
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
           
     /* For Powell, parameters are in a vector p[] starting at p[1]      /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */         so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      p=param[1][1]; /* *(*(*(param +1)+1)+0) */
Line 2093  printf("Total number of individuals= %d, Line 2345  printf("Total number of individuals= %d,
     }      }
         
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);
       
   
    jk=1;     jk=1;
    fprintf(ficres,"# Parameters\n");     fprintf(ficres,"# Parameters\n");
    printf("# Parameters\n");     printf("# Parameters\n");
Line 2135  printf("Total number of individuals= %d, Line 2388  printf("Total number of individuals= %d,
           fprintf(ficres,"\n");            fprintf(ficres,"\n");
         }          }
       }        }
       }       }
         
     k=1;      k=1;
     fprintf(ficres,"# Covariance\n");      fprintf(ficres,"# Covariance\n");
Line 2171  printf("Total number of individuals= %d, Line 2424  printf("Total number of individuals= %d,
       fage = agemax;        fage = agemax;
     }      }
   
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy.\n");
   
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
    
       while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
        
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
         dateprev1=anprev1+mprev1/12.+jprev1/365.;
 /*------------ gnuplot -------------*/     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
      fprintf(ficparo,"pop_based=%d\n",popbased);  
      fprintf(ficres,"pop_based=%d\n",popbased);  
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
   fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   
    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);
   
    /*------------ gnuplot -------------*/
 chdir(pathcd);  chdir(pathcd);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    if((ficgp=fopen("graph.plt","w"))==NULL) {
     printf("Problem with file graph.gp");goto end;      printf("Problem with file graph.gp");goto end;
Line 2279  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2574  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
       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);        fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
     }      }
   }    }  
   
   /* proba elementaires */    /* proba elementaires */
    for(i=1,jk=1; i <=nlstate; i++){     for(i=1,jk=1; i <=nlstate; i++){
Line 2338  ij=1; Line 2633  ij=1;
   }    }
         
   fclose(ficgp);    fclose(ficgp);
     /* end gnuplot */
         
 chdir(path);  chdir(path);
     free_matrix(agev,1,maxwav,1,imx);     
     free_ivector(wav,1,imx);      free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  
      
     free_imatrix(s,1,maxwav+1,1,n);  
      
      
     free_ivector(num,1,n);      free_ivector(num,1,n);
     free_vector(agedc,1,n);      free_vector(agedc,1,n);
     free_vector(weight,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
     fclose(ficres);      fclose(ficres);
Line 2381  chdir(path); Line 2672  chdir(path);
     printf("Problem with %s \n",optionfilehtm);goto end;      printf("Problem with %s \n",optionfilehtm);goto end;
   }    }
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">   fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
 Total number of observations=%d <br>  Total number of observations=%d <br>
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
Line 2395  Interval (in months) between two waves: Line 2686  Interval (in months) between two waves:
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
           - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
   <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
   
  fprintf(fichtm," <li>Graphs</li><p>");   fprintf(fichtm," <li>Graphs</li><p>");
   
Line 2480  fclose(fichtm); Line 2773  fclose(fichtm);
       }        }
     }      }
   fclose(ficrespl);    fclose(ficrespl);
   
   /*------------- h Pij x at various ages ------------*/    /*------------- h Pij x at various ages ------------*/
     
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
Line 2489  fclose(fichtm); Line 2783  fclose(fichtm);
   printf("Computing pij: result on file '%s' \n", filerespij);    printf("Computing pij: result on file '%s' \n", filerespij);
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=24) stepsize=2;    /*if (stepm<=24) stepsize=2;*/
   
   agelim=AGESUP;    agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */    hstepm=stepsize*YEARM; /* Every year of age */
Line 2528  fclose(fichtm); Line 2822  fclose(fichtm);
     }      }
   }    }
   
     /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
   
   fclose(ficrespij);    fclose(ficrespij);
   
     if(stepm == 1) {
     /*---------- Forecasting ------------------*/
     calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
     /*printf("calage= %f", calagedate);*/
    
     prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
   
     strcpy(fileresf,"f");
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
   
     free_matrix(mint,1,maxwav,1,n);
     free_matrix(anint,1,maxwav,1,n);
     free_matrix(agev,1,maxwav,1,imx);
     /* Mobile average */
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav==1) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
             mobaverage[(int)agedeb][i][cptcod]=0.;
      
       for (agedeb=bage+4; agedeb<=fage; agedeb++){
         for (i=1; i<=nlstate;i++){
           for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
             for (cpt=0;cpt<=4;cpt++){
               mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
             }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
           }
         }
       }  
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   
     agelim=AGESUP;
     /*hstepm=stepsize*YEARM; *//* Every year of age */
     hstepm=1;
     hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */
     yp1=modf(dateintmean,&yp);
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
   
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL)    {
         printf("Problem with population file : %s\n",popfile);goto end;
       }
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
   
       i=1;  
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
         {
           i=i+1;
         }
       imx=i;
      
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# StartingAge FinalAge");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
         if (popforecast==1)  fprintf(ficresf," [Population]");
      
         for (cpt=0; cpt<4;cpt++) {
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);  
   
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
           nhstepm = nhstepm/hstepm;
           /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
          
           for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
             }
             for(j=1; j<=nlstate+ndeath;j++) {
               kk1=0.;kk2=0;
               for(i=1; i<=nlstate;i++) {        
                 if (mobilav==1)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                 else {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/
                 }
   
                 if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
               }
            
               if (h==(int)(calagedate+12*cpt)){
                 fprintf(ficresf," %.3f", kk1);
                
                 if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
               }
             }
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }
         }
       }
     }
     if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_imatrix(s,1,maxwav+1,1,n);
     free_vector(weight,1,n);
     fclose(ficresf);
     }/* End forecasting */
     else{
       erreur=108;
       printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);
     }
   
   /*---------- Health expectancies and variances ------------*/    /*---------- Health expectancies and variances ------------*/
   
   strcpy(filerest,"t");    strcpy(filerest,"t");
Line 2589  fclose(fichtm); Line 3032  fclose(fichtm);
       epj=vector(1,nlstate+1);        epj=vector(1,nlstate+1);
       for(age=bage; age <=fage ;age++){        for(age=bage; age <=fage ;age++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][k];
           }
          
         fprintf(ficrest," %.0f",age);          fprintf(ficrest," %.0f",age);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(i=1, epj[j]=0.;i <=nlstate;i++) {
Line 2608  fclose(fichtm); Line 3056  fclose(fichtm);
     }      }
   }    }
                 
          
   
   
  fclose(ficreseij);   fclose(ficreseij);
  fclose(ficresvij);   fclose(ficresvij);
   fclose(ficrest);    fclose(ficrest);
Line 2653  strcpy(fileresvpl,"vpl"); Line 3104  strcpy(fileresvpl,"vpl");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
   free_matrix(matcov,1,npar,1,npar);    free_matrix(matcov,1,npar,1,npar);
   free_vector(delti,1,npar);    free_vector(delti,1,npar);
     
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
   printf("End of Imach\n");    if(erreur >0)
       printf("End of Imach with error %d\n",erreur);
     else   printf("End of Imach\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
   /*printf("Total time was %d uSec.\n", total_usecs);*/    /*printf("Total time was %d uSec.\n", total_usecs);*/
   /*------ End -----------*/    /*------ End -----------*/
   
   
  end:   end:
 #ifdef windows  #ifdef windows
  chdir(pathcd);   chdir(pathcd);
 #endif  #endif
  /*system("wgnuplot graph.plt");*/   
  system("../gp37mgw/wgnuplot graph.plt");   system("..\\gp37mgw\\wgnuplot graph.plt");
   
 #ifdef windows  #ifdef windows
   while (z[0] != 'q') {    while (z[0] != 'q') {
Removed from v.1.10  
changed lines
  Added in v.1.21

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