[BACK]Return to imach.c CVS log [TXT] [DIR] Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.205 and 1.210

version 1.205, 2015/10/23 15:50:53 version 1.210, 2015/11/18 17:41:20
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.210  2015/11/18 17:41:20  brouard
     Summary: Start working on projected prevalences
   
     Revision 1.209  2015/11/17 22:12:03  brouard
     Summary: Adding ftolpl parameter
     Author: N Brouard
   
     We had difficulties to get smoothed confidence intervals. It was due
     to the period prevalence which wasn't computed accurately. The inner
     parameter ftolpl is now an outer parameter of the .imach parameter
     file after estepm. If ftolpl is small 1.e-4 and estepm too,
     computation are long.
   
     Revision 1.208  2015/11/17 14:31:57  brouard
     Summary: temporary
   
     Revision 1.207  2015/10/27 17:36:57  brouard
     *** empty log message ***
   
     Revision 1.206  2015/10/24 07:14:11  brouard
     *** empty log message ***
   
   Revision 1.205  2015/10/23 15:50:53  brouard    Revision 1.205  2015/10/23 15:50:53  brouard
   Summary: 0.98r3 some clarification for graphs on likelihood contributions    Summary: 0.98r3 some clarification for graphs on likelihood contributions
   
Line 1960  double **prevalim(double **prlim, int nl Line 1982  double **prevalim(double **prlim, int nl
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      matrix by transitions matrix until convergence is reached with precision ftolpl */       matrix by transitions matrix until convergence is reached with precision ftolpl */
       /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
     /* Wx is row vector: population in state 1, population in state 2, population dead */
     /* or prevalence in state 1, prevalence in state 2, 0 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
     /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
     /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
     /*  0,                   0                  , 1} */
     /*
      * and after some iteration: */
     /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
     /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     /* {0.51571254859325999, 0.4842874514067399, */
     /*  0.51326036147820708, 0.48673963852179264} */
     /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();    double **out, cov[NCOVMAX+1], **pmij();
   double **newm;    double **newm;
   double agefin, delaymax=100 ; /* Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
       
     min=vector(1,nlstate);
     max=vector(1,nlstate);
     meandiff=vector(1,nlstate);
   
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 2006  double **prevalim(double **prlim, int nl Line 2049  double **prevalim(double **prlim, int nl
           
     savm=oldm;      savm=oldm;
     oldm=newm;      oldm=newm;
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){      for(j=1; j<=nlstate; j++){
       min=1.;        max[j]=0.;
       max=0.;        min[j]=1.;
       for(i=1; i<=nlstate; i++) {      }
         sumnew=0;      for(i=1;i<=nlstate;i++){
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        sumnew=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         for(j=1; j<=nlstate; j++){ 
         prlim[i][j]= newm[i][j]/(1-sumnew);          prlim[i][j]= newm[i][j]/(1-sumnew);
         max=FMAX(max,prlim[i][j]);          max[j]=FMAX(max[j],prlim[i][j]);
         min=FMIN(min,prlim[i][j]);          min[j]=FMIN(min[j],prlim[i][j]);
         /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */  
       }        }
       maxmin=(max-min)/(max+min)*2;      }
       maxmax=FMAX(maxmax,maxmin);  
       maxmax=0.;
       for(j=1; j<=nlstate; j++){
         meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
         maxmax=FMAX(maxmax,meandiff[j]);
         /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
     } /* j loop */      } /* j loop */
     *ncvyear= (int)age- (int)agefin;      *ncvyear= (int)age- (int)agefin;
     /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */      /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */        /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
         free_vector(max,1,nlstate);
         free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* age loop */
   printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\      /* After some age loop it doesn't converge */
 Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);    printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
 /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */  Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
     free_vector(min,1,nlstate);
     free_vector(max,1,nlstate);
     free_vector(meandiff,1,nlstate);
     
   return prlim; /* should not reach here */    return prlim; /* should not reach here */
 }  }
   
Line 2647  void likelione(FILE *ficres,double p[], Line 2704  void likelione(FILE *ficres,double p[],
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     }      }
     fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");      fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %weight 2wlli out sav ");      fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(k=1; k<=nlstate; k++)       for(k=1; k<=nlstate; k++) 
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
Line 2662  void likelione(FILE *ficres,double p[], Line 2719  void likelione(FILE *ficres,double p[],
     else if(mle >=1)      else if(mle >=1)
       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       
       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \  
 <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  
       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \  
 <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  
       fflush(fichtm);  
               
       for (k=1; k<= nlstate ; k++) {      for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \        fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
 <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);  <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
       }      }
       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
   <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
   <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fflush(fichtm);
   }    }
   return;    return;
 }  }
Line 2937  double hessij( double x[], double **hess Line 2994  double hessij( double x[], double **hess
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k, kmax=1;    int k, kmax=1;
   double v1, v2, cv12, lc1, lc2;    double v1, v2, cv12, lc1, lc2;
   
     int firstime=0;
       
   fx=func(x);    fx=func(x);
   for (k=1; k<=kmax; k=k+10) {    for (k=1; k<=kmax; k=k+10) {
Line 2958  double hessij( double x[], double **hess Line 3017  double hessij( double x[], double **hess
     k4=func(p2)-fx;      k4=func(p2)-fx;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */      res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
     if(k1*k2*k3*k4 <0.){      if(k1*k2*k3*k4 <0.){
         firstime=1;
       kmax=kmax+10;        kmax=kmax+10;
       if(kmax >=10){      }
       if(kmax >=10 || firstime ==1){
       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);        printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);        fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }  
     }      }
 #ifdef DEBUGHESSIJ  #ifdef DEBUGHESSIJ
     v1=hess[thetai][thetai];      v1=hess[thetai][thetai];
Line 3164  void  freqsummary(char fileres[], int ia Line 3224  void  freqsummary(char fileres[], int ia
       k2cpt=0;        k2cpt=0;
       for (i=1; i<=imx; i++) {        for (i=1; i<=imx; i++) {
         bool=1;          bool=1;
         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */          if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           for (z1=1; z1<=cptcoveff; z1++)                   for (z1=1; z1<=cptcoveff; z1++)       
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
Line 3174  void  freqsummary(char fileres[], int ia Line 3234  void  freqsummary(char fileres[], int ia
                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
             }               } 
         }          } /* cptcovn > 0 */
     
         if (bool==1){          if (bool==1){
           for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){
Line 3188  void  freqsummary(char fileres[], int ia Line 3248  void  freqsummary(char fileres[], int ia
                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               }                }
                               
               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
                 dateintsum=dateintsum+k2;                  dateintsum=dateintsum+k2;
                 k2cpt++;                  k2cpt++;
                   /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
               }                }
               /*}*/                /*}*/
           }            } /* end m */
         }          } /* end bool */
       } /* end i */        } /* end i = 1 to imx */
                 
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       pstamp(ficresp);        pstamp(ficresp);
Line 3281  void  freqsummary(char fileres[], int ia Line 3342  void  freqsummary(char fileres[], int ia
         if(first==1)          if(first==1)
           printf("Others in log...\n");            printf("Others in log...\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
       }        } /* end loop i */
       /*}*/        /*}*/
   }    } /* end j1 */
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
     
   fclose(ficresp);    fclose(ficresp);
Line 3970  void cvevsij(double ***eij, double x[], Line 4031  void cvevsij(double ***eij, double x[],
 }  }
   
 /************ Variance ******************/  /************ Variance ******************/
  void varevsij(char optionfilefiname[], 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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])   void varevsij(char optionfilefiname[], 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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
 {  {
   /* 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);*/
Line 4024  void cvevsij(double ***eij, double x[], Line 4085  void cvevsij(double ***eij, double x[],
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   pstamp(ficresprobmorprev);    pstamp(ficresprobmorprev);
   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
Line 4035  void cvevsij(double ***eij, double x[], Line 4095  void cvevsij(double ***eij, double x[],
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   }      }  
   fprintf(ficresprobmorprev,"\n");    fprintf(ficresprobmorprev,"\n");
     
   fprintf(ficgp,"\n# Routine varevsij");    fprintf(ficgp,"\n# Routine varevsij");
   fprintf(ficgp,"\nunset title \n");    fprintf(ficgp,"\nunset title \n");
 /* fprintf(fichtm, "#Local time at start: %s", strstart);*/  /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
Line 4072  void cvevsij(double ***eij, double x[], Line 4133  void cvevsij(double ***eij, double x[],
   /* For example we decided to compute the life expectancy with the smallest unit */    /* 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 agelim. 
      Look at function hpijx to understand why (it is linked to memory size questions) */       Look at function hpijx to understand why because of memory size limitations, 
   /* 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 every two years of age and if       means that if the survival funtion is printed every 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 
Line 4095  void cvevsij(double ***eij, double x[], Line 4156  void cvevsij(double ***eij, double x[],
       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         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);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
   
       if (popbased==1) {        if (popbased==1) {
         if(mobilav ==0){          if(mobilav ==0){
Line 4108  void cvevsij(double ***eij, double x[], Line 4169  void cvevsij(double ***eij, double x[],
         }          }
       }        }
       
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
       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++)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
       /* This for computing probability of death (h=1 means        /* Next for computing probability of death (h=1 means
          computed over hstepm matrices product = hstepm*stepm months)            computed over hstepm matrices product = hstepm*stepm months) 
          as a weighted average of prlim.           as a weighted average of prlim.
       */        */
Line 4126  void cvevsij(double ***eij, double x[], Line 4188  void cvevsij(double ***eij, double x[],
   
       for(i=1; i<=npar; i++) /* Computes gradient x - delta */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         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);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
     
       if (popbased==1) {        if (popbased==1) {
         if(mobilav ==0){          if(mobilav ==0){
Line 4139  void cvevsij(double ***eij, double x[], Line 4201  void cvevsij(double ***eij, double x[],
         }          }
       }        }
   
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   
       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.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++)
Line 4201  void cvevsij(double ***eij, double x[], Line 4265  void cvevsij(double ***eij, double x[],
         varppt[j][i]=doldmp[j][i];          varppt[j][i]=doldmp[j][i];
     /* end ppptj */      /* end ppptj */
     /*  x centered again */      /*  x centered again */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);    
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
     
     if (popbased==1) {      if (popbased==1) {
       if(mobilav ==0){        if(mobilav ==0){
Line 4218  void cvevsij(double ***eij, double x[], Line 4282  void cvevsij(double ***eij, double x[],
        computed over hstepm (estepm) matrices product = hstepm*stepm months)          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
        as a weighted average of prlim.         as a weighted average of prlim.
     */      */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     for(j=nlstate+1;j<=nlstate+ndeath;j++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       for(i=1,gmp[j]=0.;i<= nlstate; i++)         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
Line 4280  void cvevsij(double ***eij, double x[], Line 4345  void cvevsij(double ***eij, double x[],
 }  /* end varevsij */  }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ Variance of prevlim ******************/
  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyear, int ij, char strstart[])   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
 {  {
   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   /*  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);*/
Line 4290  void cvevsij(double ***eij, double x[], Line 4355  void cvevsij(double ***eij, double x[],
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
     double **mgm, **mgp;
   double age,agelim;    double age,agelim;
   int theta;    int theta;
       
Line 4312  void cvevsij(double ***eij, double x[], Line 4378  void cvevsij(double ***eij, double x[],
     if (stepm >= YEARM) hstepm=1;      if (stepm >= YEARM) hstepm=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     gradg=matrix(1,npar,1,nlstate);      gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
     gp=vector(1,nlstate);      gp=vector(1,nlstate);
     gm=vector(1,nlstate);      gm=vector(1,nlstate);
   
Line 4319  void cvevsij(double ***eij, double x[], Line 4387  void cvevsij(double ***eij, double x[],
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
               mgp[theta][i] = prlim[i][i];
         }
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
           mgm[theta][i] = prlim[i][i];
         }
       for(i=1;i<=nlstate;i++)        for(i=1;i<=nlstate;i++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
     } /* End theta */      } /* End theta */
   
     trgradg =matrix(1,nlstate,1,npar);      trgradg =matrix(1,nlstate,1,npar);
Line 4338  void cvevsij(double ***eij, double x[], Line 4415  void cvevsij(double ***eij, double x[],
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       for(theta=1; theta <=npar; theta++)        for(theta=1; theta <=npar; theta++)
         trgradg[j][theta]=gradg[theta][j];          trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] =0.;        varpl[i][(int)age] =0.;
     if((int)age==67 ||(int)age== 66 ){      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     }else{      }else{
Line 4357  void cvevsij(double ***eij, double x[], Line 4452  void cvevsij(double ***eij, double x[],
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
     free_vector(gp,1,nlstate);      free_vector(gp,1,nlstate);
     free_vector(gm,1,nlstate);      free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
     free_matrix(gradg,1,npar,1,nlstate);      free_matrix(gradg,1,npar,1,nlstate);
     free_matrix(trgradg,1,nlstate,1,npar);      free_matrix(trgradg,1,nlstate,1,npar);
   } /* End age */    } /* End age */
Line 4768  divided by h: hPij/h : <a href=\"%s_%d-3 Line 4865  divided by h: hPij/h : <a href=\"%s_%d-3
      }       }
      /* State specific survival functions (period) */       /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\         fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.\   Or probability to survive in various states (1 to %d) being in state %d at different ages.\
  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);   <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
      }       }
Line 4880  void printinggnuplot(char fileresu[], ch Line 4977  void printinggnuplot(char fileresu[], ch
     /*#endif */      /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
   
     /* Projected Prevalences */
   /* plot "NAGI0w_V1V2_monthlyb2b-proj/F_NAGI0w_V1V2_monthlyb2b-proj.txt" u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0))? $7/(1-$13):1/0) t 'p11' w line */
   /* replot ""  u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0))? $8/(1-$14):1/0) t 'p21' w line */
   /* replot ""  u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0)&&($9!=0))? $9/(1-$15):1/0) t 'p.1' w line */
   
   /* Contribution to likelihood */    /* Contribution to likelihood */
   /* Plot the probability implied in the likelihood */    /* Plot the probability implied in the likelihood */
     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");      fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
Line 6487  void syscompilerinfo(int logged) Line 6589  void syscompilerinfo(int logged)
   
  }   }
   
  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   int i, j, k, i1 ;    int i, j, k, i1 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
Line 6543  void syscompilerinfo(int logged) Line 6645  void syscompilerinfo(int logged)
                   
         for (age=agebase; age<=agelim; age++){          for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
           fprintf(ficrespl,"%.0f ",age );            fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)            for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);              fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 6552  void syscompilerinfo(int logged) Line 6654  void syscompilerinfo(int logged)
             tot +=  prlim[i][i];              tot +=  prlim[i][i];
             fprintf(ficrespl," %.5f", prlim[i][i]);              fprintf(ficrespl," %.5f", prlim[i][i]);
           }            }
           fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);            fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
         } /* Age */          } /* Age */
         /* was end of cptcod */          /* was end of cptcod */
     } /* cptcov */      } /* cptcov */
Line 6645  int main(int argc, char *argv[]) Line 6747  int main(int argc, char *argv[])
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;    int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   int ncvyearnp=0;    int ncvyear=0; /* Number of years needed for the period prevalence to converge */
   int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */  
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
   int num_filled;    int num_filled;
Line 6906  int main(int argc, char *argv[]) Line 7007  int main(int argc, char *argv[])
   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \    if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){                          &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
     if (num_filled != 8) {      if (num_filled != 8) {
       printf("Not 8\n");        printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         printf("but line=%s\n",line);
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);      printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
   }    }
   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
   ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
   /* Third parameter line */    /* Third parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
Line 7847  Please run with mle=-1 to get a correct Line 7949  Please run with mle=-1 to get a correct
           
     fflush(ficlog);      fflush(ficlog);
     fflush(ficres);      fflush(ficres);
             while(fgets(line, MAXLINE, ficpar)) {
     while((c=getc(ficpar))=='#' && c!= EOF){      /* If line starts with a # it is a comment */
       ungetc(c,ficpar);      if (line[0] == '#') {
       fgets(line, MAXLINE, ficpar);        numlinepar++;
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
     }        fputs(line,ficlog);
     ungetc(c,ficpar);        continue;
       }else
         break;
     }
   
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /* } */
       /* ungetc(c,ficpar); */
           
     estepm=0;      estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
   
       if (num_filled != 6) {
         printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
         printf("but line=%s\n",line);
         goto end;
       }
       printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
     }
     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
     /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
   
       /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
     if (estepm==0 || estepm < stepm) estepm=stepm;      if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {      if (fage <= 2) {
       bage = ageminpar;        bage = ageminpar;
Line 7956  Please run with mle=-1 to get a correct Line 8081  Please run with mle=-1 to get a correct
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, ncvyear);      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
 #ifdef FREEEXIT2  #ifdef FREEEXIT2
Line 8019  Please run with mle=-1 to get a correct Line 8144  Please run with mle=-1 to get a correct
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }      }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
Line 8039  Please run with mle=-1 to get a correct Line 8164  Please run with mle=-1 to get a correct
       /*}*/        /*}*/
     }      }
     fclose(ficreseij);      fclose(ficreseij);
       printf("done evsij\n");fflush(stdout);
       fprintf(ficlog,"done evsij\n");fflush(ficlog);
   
     /*---------- Health expectancies and variances ------------*/      /*---------- Health expectancies and variances ------------*/
   
Line 8050  Please run with mle=-1 to get a correct Line 8176  Please run with mle=-1 to get a correct
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }      }
     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
   
   
     strcpy(fileresstde,"STDE_");      strcpy(fileresstde,"STDE_");
Line 8060  Please run with mle=-1 to get a correct Line 8186  Please run with mle=-1 to get a correct
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
     }      }
     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"CVE_");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileresu);      strcat(filerescve,fileresu);
Line 8069  Please run with mle=-1 to get a correct Line 8195  Please run with mle=-1 to get a correct
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
     }      }
     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"V_");      strcpy(fileresv,"V_");
     strcat(fileresv,fileresu);      strcat(fileresv,fileresu);
Line 8078  Please run with mle=-1 to get a correct Line 8204  Please run with mle=-1 to get a correct
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"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' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
         
         fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }        }
         fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
         
         fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
         
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);          printf(" cvevsij %d, ",k);
         /*        fprintf(ficlog, " cvevsij %d, ",k);
          */        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
         /* goto endfree; */        printf(" end cvevsij \n ");
          fprintf(ficlog, " end cvevsij \n ");
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        
         pstamp(ficrest);        /*
          */
         /* goto endfree; */
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        
           oldm=oldms;savm=savms; /* ZZ Segmentation fault */        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           cptcod= 0; /* To be deleted */        pstamp(ficrest);
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */        
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");        
           if(vpopbased==1)        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           else          cptcod= 0; /* To be deleted */
             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");          printf("varevsij %d \n",vpopbased);
           fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          fprintf(ficlog, "varevsij %d \n",vpopbased);
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
           fprintf(ficrest,"\n");          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
           /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */          if(vpopbased==1)
           epj=vector(1,nlstate+1);            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
           for(age=bage; age <=fage ;age++){          else
             prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */            fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             if (vpopbased==1) {          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
               if(mobilav ==0){          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                 for(i=1; i<=nlstate;i++)          fprintf(ficrest,"\n");
                   prlim[i][i]=probs[(int)age][i][k];          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
               }else{ /* mobilav */           epj=vector(1,nlstate+1);
                 for(i=1; i<=nlstate;i++)          printf("Computing age specific period (stable) prevalences in each health state \n");
                   prlim[i][i]=mobaverage[(int)age][i][k];          fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
               }          for(age=bage; age <=fage ;age++){
             }            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
                     if (vpopbased==1) {
             fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);              if(mobilav ==0){
             /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */                for(i=1; i<=nlstate;i++)
             /* printf(" age %4.0f ",age); */                  prlim[i][i]=probs[(int)age][i][k];
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              }else{ /* mobilav */ 
               for(i=1, epj[j]=0.;i <=nlstate;i++) {                for(i=1; i<=nlstate;i++)
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];                  prlim[i][i]=mobaverage[(int)age][i][k];
                 /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/  
                 /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */  
               }  
               epj[nlstate+1] +=epj[j];  
             }              }
             /* printf(" age %4.0f \n",age); */            }
             
             for(i=1, vepp=0.;i <=nlstate;i++)            fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
               for(j=1;j <=nlstate;j++)            /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
                 vepp += vareij[i][j][(int)age];            /* printf(" age %4.0f ",age); */
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(j=1;j <=nlstate;j++){              for(i=1, epj[j]=0.;i <=nlstate;i++) {
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
             }              }
             fprintf(ficrest,"\n");              epj[nlstate+1] +=epj[j];
             }
             /* printf(" age %4.0f \n",age); */
             
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }            }
             fprintf(ficrest,"\n");
         }          }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        } /* End vpopbased */
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
         printf("done \n");fflush(stdout);
         fprintf(ficlog,"done\n");fflush(ficlog);
         
       /*}*/        /*}*/
     }      } /* End k */
     free_vector(weight,1,n);      free_vector(weight,1,n);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,1,n);
Line 8180  Please run with mle=-1 to get a correct Line 8318  Please run with mle=-1 to get a correct
     fclose(ficrescveij);      fclose(ficrescveij);
     fclose(ficresvij);      fclose(ficresvij);
     fclose(ficrest);      fclose(ficrest);
       printf("done Health expectancies\n");fflush(stdout);
       fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
     fclose(ficpar);      fclose(ficpar);
       
     /*------- Variance of period (stable) prevalence------*/         /*------- Variance of period (stable) prevalence------*/   
Line 8190  Please run with mle=-1 to get a correct Line 8330  Please run with mle=-1 to get a correct
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);      printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
       fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
Line 8203  Please run with mle=-1 to get a correct Line 8344  Please run with mle=-1 to get a correct
               
         varpl=matrix(1,nlstate,(int) bage, (int) fage);          varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);          varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       /*}*/        /*}*/
     }      }
   
     fclose(ficresvpl);      fclose(ficresvpl);
       printf("done variance-covariance of period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
   
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Removed from v.1.205  
changed lines
  Added in v.1.210

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>