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Diff for /imach/src/imach.c between versions 1.208 and 1.210

version 1.208, 2015/11/17 14:31:57 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    Revision 1.208  2015/11/17 14:31:57  brouard
   Summary: temporary    Summary: temporary
   
Line 1988  double **prevalim(double **prlim, int nl Line 2001  double **prevalim(double **prlim, int nl
   /* If we start from prlim again, prlim tends to a constant matrix */    /* 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. ; /* 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 2032  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(i=1; i<=nlstate; i++) { */      for(j=1; j<=nlstate; j++){
       /*        sumnew=0.; */        meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
       /*        sumnew+=prlim[i][j]; */        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); */
       /* prmimj = sumnew/(float)nlstate; /\* Means of various prevalence limits. */  
     } /* j loop */      } /* j loop */
     *ncvyear= (int)age- (int)agefin;      *ncvyear= (int)age- (int)agefin;
     /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, 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 */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g within %.0f years. \n\    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\
 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);  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);
   /* printf(" age= %d newm\n",(int)age); */  
   /* for(i=1; i<=nlstate+ndeath; i++) { */  
   /*   for(j=1;j<=nlstate+ndeath;j++){ */  
   /*     printf(" %lf", newm[i][j]); */  
   /*   } */  
   /*   printf("\n"); */  
   /* } */  
   /* printf("\n"); */  
   /* printf("prlim\n"); */  
   /* for(i=1; i<=nlstate; i++) { */  
   /*   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); */  
   /*     printf(" %lf", prlim[i][j]); */  
   /*   } */  
   /*   printf("\n"); */  
   /* } */  
   /* printf("\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); */    /* 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 3219  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 3229  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 3243  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 3336  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 4025  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 4128  void cvevsij(double ***eij, double x[], Line 4134  void cvevsij(double ***eij, double x[],
   /* 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 agelim.        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
Line 4150  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 4163  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 4181  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 4194  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 4256  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 4273  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 4335  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 4367  void cvevsij(double ***eij, double x[], Line 4377  void cvevsij(double ***eij, double x[],
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if (stepm >= YEARM) hstepm=1;      if (stepm >= YEARM) hstepm=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=matrix(1,npar,1,nlstate);      gradg=matrix(1,npar,1,nlstate);
     mgp=matrix(1,npar,1,nlstate);      mgp=matrix(1,npar,1,nlstate);
     mgm=matrix(1,npar,1,nlstate);      mgm=matrix(1,npar,1,nlstate);
Line 4378  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);
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Missing or not useful because 1 year */         if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);          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++){        for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
         mgp[theta][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 )
           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++){        for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
         mgm[theta][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 4400  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==68 ||(int)age== 69 ){      /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       printf("\nmgm mgp %d ",(int)age);      /*   printf("\nmgm mgp %d ",(int)age); */
       for(j=1; j<=nlstate;j++){      /*   for(j=1; j<=nlstate;j++){ */
         printf("%d ",j);      /*  printf(" %d ",j); */
         for(theta=1; theta <=npar; theta++)      /*  for(theta=1; theta <=npar; theta++) */
           printf("%d %lf %lf",theta,mgm[theta][j],mgp[theta][j]);      /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
         printf("\n ");      /*  printf("\n "); */
       }      /*   } */
     }      /* } */
     if((int)age==68 ||(int)age== 69 ){      /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       printf("\n gradg %d ",(int)age);      /*   printf("\n gradg %d ",(int)age); */
       for(j=1; j<=nlstate;j++){      /*   for(j=1; j<=nlstate;j++){ */
         printf("%d ",j);      /*  printf("%d ",j); */
         for(theta=1; theta <=npar; theta++)      /*  for(theta=1; theta <=npar; theta++) */
           printf("%d %lf ",theta,gradg[theta][j]);      /*    printf("%d %lf ",theta,gradg[theta][j]); */
         printf("\n ");      /*  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==68 ||(int)age== 69 ){      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 4962  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 6569  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 6625  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 6634  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 6727  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 6988  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 7929  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 8038  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 8208  Please run with mle=-1 to get a correct Line 8251  Please run with mle=-1 to get a correct
         cptcod= 0; /* To be deleted */          cptcod= 0; /* To be deleted */
         printf("varevsij %d \n",vpopbased);          printf("varevsij %d \n",vpopbased);
         fprintf(ficlog, "varevsij %d \n",vpopbased);          fprintf(ficlog, "varevsij %d \n",vpopbased);
         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 */          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 ");          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)          if(vpopbased==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);            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);
Line 8222  Please run with mle=-1 to get a correct Line 8265  Please run with mle=-1 to get a correct
         printf("Computing age specific period (stable) prevalences in each health state \n");          printf("Computing age specific period (stable) prevalences in each health state \n");
         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");          fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
         for(age=bage; age <=fage ;age++){          for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
           if (vpopbased==1) {            if (vpopbased==1) {
             if(mobilav ==0){              if(mobilav ==0){
               for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
Line 8301  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);
       /*}*/        /*}*/
     }      }
Removed from v.1.208  
changed lines
  Added in v.1.210

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