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Diff for /imach/src/imach.c between versions 1.251 and 1.255

version 1.251, 2016/09/15 15:01:13 version 1.255, 2017/03/08 16:02:28
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.255  2017/03/08 16:02:28  brouard
     Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
   
     Revision 1.254  2017/03/08 07:13:00  brouard
     Summary: Fixing data parameter line
   
     Revision 1.253  2016/12/15 11:59:41  brouard
     Summary: 0.99 in progress
   
     Revision 1.252  2016/09/15 21:15:37  brouard
     *** empty log message ***
   
   Revision 1.251  2016/09/15 15:01:13  brouard    Revision 1.251  2016/09/15 15:01:13  brouard
   Summary: not working    Summary: not working
   
Line 128 Line 140
   Author: Nicolas Brouard    Author: Nicolas Brouard
   
   Revision 1.210  2015/11/18 17:41:20  brouard    Revision 1.210  2015/11/18 17:41:20  brouard
   Summary: Start working on projected prevalences    Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
   
   Revision 1.209  2015/11/17 22:12:03  brouard  
   Summary: Adding ftolpl parameter    Summary: Adding ftolpl parameter
   Author: N Brouard    Author: N Brouard
   
Line 2393  void powell(double p[], double **xi, int Line 2403  void powell(double p[], double **xi, int
             flatd++;              flatd++;
         }          }
         if(flatd >0){          if(flatd >0){
           printf("%d flat directions\n",flatd);            printf("%d flat directions: ",flatd);
           fprintf(ficlog,"%d flat directions\n",flatd);            fprintf(ficlog,"%d flat directions :",flatd);
           for (j=1;j<=n;j++) {             for (j=1;j<=n;j++) { 
             if(flatdir[j]>0){              if(flatdir[j]>0){
               printf("%d ",j);                printf("%d ",j);
Line 4188  void pstamp(FILE *fichier) Line 4198  void pstamp(FILE *fichier)
   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
   int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
   
     /* y=a+bx regression */
     double   sumx = 0.0;                        /* sum of x                      */
     double   sumx2 = 0.0;                       /* sum of x**2                   */
     double   sumxy = 0.0;                       /* sum of x * y                  */
     double   sumy = 0.0;                        /* sum of y                      */
     double   sumy2 = 0.0;                       /* sum of y**2                   */
     double   sume2; /* sum of square or residuals */
     double yhat;
     
     double denom=0;
     int i;
     int ne=*no;
     
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       sumx  += x[i];       
       sumx2 += x[i]*x[i];  
       sumxy += x[i] * y[i];
       sumy  += y[i];      
       sumy2 += y[i]*y[i]; 
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     
     denom = (ne * sumx2 - sumx*sumx);
     if (denom == 0) {
       // vertical, slope m is infinity
       *b = INFINITY;
       *a = 0;
       if (r) *r = 0;
       return 1;
     }
     
     *b = (ne * sumxy  -  sumx * sumy) / denom;
     *a = (sumy * sumx2  -  sumx * sumxy) / denom;
     if (r!=NULL) {
       *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
         sqrt((sumx2 - sumx*sumx/ne) *
              (sumy2 - sumy*sumy/ne));
     }
     *no=ne;
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       yhat = y[i] - *a -*b* x[i];
       sume2  += yhat * yhat ;       
       
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     *sb = sqrt(sume2/(ne-2)/(sumx2 - sumx * sumx /ne));
     *sa= *sb * sqrt(sumx2/ne);
     
     return 0; 
   }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \  void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies as well as proposing some starting values */  {  /* Some frequencies as well as proposing some starting values */
       
   int i, m, jk, j1, bool, z1,j, k, iv, jj=0;    int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0;
   int iind=0, iage=0;    int iind=0, iage=0;
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
     double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */
     int no;
   double *meanq;    double *meanq;
   double **meanqt;    double **meanqt;
   double *pp, **prop, *posprop, *pospropt;    double *pp, **prop, *posprop, *pospropt;
Line 4251  Title=%s <br>Datafile=%s Firstpass=%d La Line 4328  Title=%s <br>Datafile=%s Firstpass=%d La
   }    }
   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
       
     y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   j1=0;    j1=0;
       
Line 4268  Title=%s <br>Datafile=%s Firstpass=%d La Line 4347  Title=%s <br>Datafile=%s Firstpass=%d La
   dateintsum=0;    dateintsum=0;
   k2cpt=0;    k2cpt=0;
   
   for (j = 0; j <= cptcoveff; j+=cptcoveff){   /* j= 0 constant model */    if(cptcoveff == 0 )
       nl=1;  /* Constant model only */
     else
       nl=2;
     for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
       if(nj==1)
         j=0;  /* First pass for the constant */
       else
         j=cptcoveff; /* Other passes for the covariate values */
     first=1;      first=1;
     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */      for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
       posproptt=0.;        posproptt=0.;
Line 4514  Title=%s <br>Datafile=%s Firstpass=%d La Line 4601  Title=%s <br>Datafile=%s Firstpass=%d La
               if(first==1){                if(first==1){
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);                  printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
               }                }
                 /* printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
             }              }
             if(jk!=0 && m!=0)              if(jk!=0 && m!=0)
Line 4560  Title=%s <br>Datafile=%s Firstpass=%d La Line 4648  Title=%s <br>Datafile=%s Firstpass=%d La
         for(i=1,jk=1; i <=nlstate; i++){          for(i=1,jk=1; i <=nlstate; i++){
           for(k=1; k <=(nlstate+ndeath); k++){            for(k=1; k <=(nlstate+ndeath); k++){
             if (k != i) {              if (k != i) {
               printf("%d%d ",i,k);  
               fprintf(ficlog,"%d%d ",i,k);  
               for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */                for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */
                 if(jj==1){  /* Constant case */                  if(jj==1){  /* Constant case (in fact cste + age) */
                   if(j1==1){ /* All dummy covariates to zero */                    if(j1==1){ /* All dummy covariates to zero */
                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */                      freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */                      freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
                       printf("%d%d ",i,k);
                       fprintf(ficlog,"%d%d ",i,k);
                       printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
                       fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                       pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                     }
                   }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
                     for(iage=iagemin; iage <= iagemax+3; iage++){
                       x[iage]= (double)iage;
                       y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
                       /* printf("i=%d, k=%d, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */
                   }                    }
                   printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));                    linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
                   fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));                    pstart[jk]=b;
                   pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);                    pstart[jk-1]=a;
                 }else if( (log(j1-1)/log(2)+1 == jj -2 -nagesqr)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */                   }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ 
                     printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                   pstart[jk]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));                    pstart[jk]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
                     printf("%d%d ",i,k);
                     fprintf(ficlog,"%d%d ",i,k);
                   printf("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));                    printf("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
                 }else if(jj==2 || nagesqr==1){ /* age or age*age parameter */  
                   ;  
                 }else{ /* Other cases, like quantitative fixed or varying covariates */                  }else{ /* Other cases, like quantitative fixed or varying covariates */
                   ;                    ;
                 }                  }
Line 4583  Title=%s <br>Datafile=%s Firstpass=%d La Line 4682  Title=%s <br>Datafile=%s Firstpass=%d La
                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */                  /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                 jk++;                   jk++; 
               } /* end jj */                } /* end jj */
               printf("\n");  
               fprintf(ficlog,"\n");  
             } /* end k!= i */              } /* end k!= i */
           } /* end k */            } /* end k */
         } /* end i, jk */          } /* end i, jk */
Line 4599  Title=%s <br>Datafile=%s Firstpass=%d La Line 4696  Title=%s <br>Datafile=%s Firstpass=%d La
             printf("%d%d ",i,k);              printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);              fprintf(ficlog,"%d%d ",i,k);
             for(jj=1; jj <=ncovmodel; jj++){              for(jj=1; jj <=ncovmodel; jj++){
               if(jj==1){                pstart[jk]=p[jk]; /* Setting pstart to p values by default */
                 if(jj==1){ /* Age has to be done */
                   pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                 printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));                  printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                 fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));                  fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
               }                }
Line 4630  Title=%s <br>Datafile=%s Firstpass=%d La Line 4729  Title=%s <br>Datafile=%s Firstpass=%d La
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
     } /* end j=0 */      } /* end j=0 */
   } /* end j */    } /* end j */
   
     if(mle == -2){  /* We want to use these values as starting values */
       for(i=1, jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j!=i){
             /*ca[0]= k+'a'-1;ca[1]='\0';*/
             printf("%1d%1d",i,j);
             fprintf(ficparo,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               /*    printf(" %lf",param[i][j][k]); */
               /*    fprintf(ficparo," %lf",param[i][j][k]); */
               p[jk]=pstart[jk];
               printf(" %f ",pstart[jk]);
               fprintf(ficparo," %f ",pstart[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficparo,"\n");
           }
         }
       }
     } /* end mle=-2 */
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
       
   fclose(ficresp);    fclose(ficresp);
Line 4637  Title=%s <br>Datafile=%s Firstpass=%d La Line 4758  Title=%s <br>Datafile=%s Firstpass=%d La
   fclose(ficresphtmfr);    fclose(ficresphtmfr);
   free_vector(meanq,1,nqfveff);    free_vector(meanq,1,nqfveff);
   free_matrix(meanqt,1,lastpass,1,nqtveff);    free_matrix(meanqt,1,lastpass,1,nqtveff);
     free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
   free_vector(pospropt,1,nlstate);    free_vector(pospropt,1,nlstate);
   free_vector(posprop,1,nlstate);    free_vector(posprop,1,nlstate);
Line 6288  void printinghtml(char fileresu[], char Line 6411  void printinghtml(char fileresu[], char
   
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++) /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */     for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
      if(TKresult[nres]!= k1)       if(m != 1 && TKresult[nres]!= k1)
        continue;         continue;
   
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
Line 6339  divided by h: <sub>h</sub>P<sub>ij</sub> Line 6462  divided by h: <sub>h</sub>P<sub>ij</sub>
      }       }
      /* Period (stable) prevalence in each health state */       /* Period (stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d some years earlier, knowing that we will be in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(backcast==1){       if(backcast==1){
        /* Period (stable) back prevalence in each health state */         /* Period (stable) back prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability to be in state %d at a younger age, knowing that we will be in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
        }         }
      }       }
Line 6420  See page 'Matrix of variance-covariance Line 6543  See page 'Matrix of variance-covariance
   
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
      if(TKresult[nres]!= k1)       if(m != 1 && TKresult[nres]!= k1)
        continue;         continue;
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
Line 6516  void printinggnuplot(char fileresu[], ch Line 6639  void printinggnuplot(char fileresu[], ch
     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */      for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
         if(TKresult[nres]!= k1)          if(m != 1 && TKresult[nres]!= k1)
           continue;            continue;
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
Line 6598  void printinggnuplot(char fileresu[], ch Line 6721  void printinggnuplot(char fileresu[], ch
   /*2 eme*/    /*2 eme*/
   for (k1=1; k1<= m ; k1 ++){      for (k1=1; k1<= m ; k1 ++){  
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
Line 6658  void printinggnuplot(char fileresu[], ch Line 6781  void printinggnuplot(char fileresu[], ch
   /*3eme*/    /*3eme*/
   for (k1=1; k1<= m ; k1 ++){    for (k1=1; k1<= m ; k1 ++){
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
   
       for (cpt=1; cpt<= nlstate ; cpt ++) {        for (cpt=1; cpt<= nlstate ; cpt ++) {
Line 6707  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6830  plot [%.f:%.f] \"%s\" every :::%d::%d u
   /* Survival functions (period) from state i in state j by initial state i */    /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */    for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
Line 6753  set ter svg size 640, 480\nunset log y\n Line 6876  set ter svg size 640, 480\nunset log y\n
   /* Survival functions (period) from state i in state j by final state j */    /* Survival functions (period) from state i in state j by final state j */
   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */    for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
Line 6807  set ter svg size 640, 480\nunset log y\n Line 6930  set ter svg size 640, 480\nunset log y\n
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */    for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     if(TKresult[nres]!= k1)      if(m != 1 && TKresult[nres]!= k1)
       continue;        continue;
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
               
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
Line 6833  set ter svg size 640, 480\nunset log y\n Line 6956  set ter svg size 640, 480\nunset log y\n
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
       k=3; /* Offset */        k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){ /* State of origin */
         if(i==1)          if(i==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else          else
           fprintf(ficgp,", '' ");            fprintf(ficgp,", '' ");
         l=(nlstate+ndeath)*(i-1)+1;          l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
         for (j=2; j<= nlstate ; j ++)          for (j=2; j<= nlstate ; j ++)
           fprintf(ficgp,"+$%d",k+l+j-1);            fprintf(ficgp,"+$%d",k+l+j-1);
Line 6854  set ter svg size 640, 480\nunset log y\n Line 6977  set ter svg size 640, 480\nunset log y\n
     /* CV back preval stable (period) for each covariate */      /* CV back preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
Line 6879  set ter svg size 640, 480\nunset log y\n Line 7002  set ter svg size 640, 480\nunset log y\n
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */          k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){          for (i=1; i<= nlstate ; i ++){ /* State of origin */
           if(i==1)            if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
           else            else
             fprintf(ficgp,", '' ");              fprintf(ficgp,", '' ");
           /* l=(nlstate+ndeath)*(i-1)+1; */            /* l=(nlstate+ndeath)*(i-1)+1; */
           l=(nlstate+ndeath)*(cpt-1)+1;            l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */            fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
           /* for (j=2; j<= nlstate ; j ++) */            /* for (j=2; j<= nlstate ; j ++) */
           /*    fprintf(ficgp,"+$%d",k+l+j-1); */            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
Line 6905  set ter svg size 640, 480\nunset log y\n Line 7028  set ter svg size 640, 480\nunset log y\n
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
Line 7036  set ter svg size 640, 480\nunset log y\n Line 7159  set ter svg size 640, 480\nunset log y\n
     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
     for(jk=1; jk <=m; jk++)  /* For each combination of covariate */      for(jk=1; jk <=m; jk++)  /* For each combination of covariate */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= jk)        if(m != 1 && TKresult[nres]!= jk)
         continue;          continue;
       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);        fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
Line 7398  set ter svg size 640, 480\nunset log y\n Line 7521  set ter svg size 640, 480\nunset log y\n
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++) /* For each resultline */
   for(k=1; k<=i1;k++){    for(k=1; k<=i1;k++){
     if(TKresult[nres]!= k)      if(i1 != 1 && TKresult[nres]!= k)
       continue;        continue;
     if(invalidvarcomb[k]){      if(invalidvarcomb[k]){
       printf("\nCombination (%d) projection ignored because no cases \n",k);         printf("\nCombination (%d) projection ignored because no cases \n",k); 
Line 8349  int decoderesult ( char resultline[], in Line 8472  int decoderesult ( char resultline[], in
   if (strlen(resultsav) >1){    if (strlen(resultsav) >1){
     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
   }    }
     if(j == 0){ /* Resultline but no = */
       TKresult[nres]=0; /* Combination for the nresult and the model */
       return (0);
     }
       
   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
Line 9285  int prevalence_limit(double *p, double * Line 9413  int prevalence_limit(double *p, double *
   
   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */    for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
   
       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
Line 9382  int back_prevalence_limit(double *p, dou Line 9510  int back_prevalence_limit(double *p, dou
       
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)       if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
       fprintf(ficresplb,"#******");        fprintf(ficresplb,"#******");
Line 9441  int back_prevalence_limit(double *p, dou Line 9569  int back_prevalence_limit(double *p, dou
         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);          fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
       } /* Age */        } /* Age */
       /* was end of cptcod */        /* was end of cptcod */
         /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
     } /* end of any combination */      } /* end of any combination */
   } /* end of nres */      } /* end of nres */  
   /* hBijx(p, bage, fage); */    /* hBijx(p, bage, fage); */
Line 9485  int hPijx(double *p, int bage, int fage) Line 9614  int hPijx(double *p, int bage, int fage)
                 /*      k=k+1;  */                  /*      k=k+1;  */
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){      for(k=1; k<=i1;k++){
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
Line 9557  int hPijx(double *p, int bage, int fage) Line 9686  int hPijx(double *p, int bage, int fage)
       
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   pstamp(ficrespijb);    pstamp(ficrespijb);
   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");    fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
   i1= pow(2,cptcoveff);    i1= pow(2,cptcoveff);
   /* 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++){*\/ */
   /*    k=k+1;  */    /*    k=k+1;  */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficrespijb,"\n#****** ");        fprintf(ficrespijb,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
Line 9591  int hPijx(double *p, int bage, int fage) Line 9720  int hPijx(double *p, int bage, int fage)
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);          hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");          fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);              fprintf(ficrespijb," %1d-%1d",i,j);
Line 10007  int main(int argc, char *argv[]) Line 10136  int main(int argc, char *argv[])
     fclose (ficlog);      fclose (ficlog);
     goto end;      goto end;
     exit(0);      exit(0);
   } else if(mle==-2) { /* Guessing from means */  
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);  
     printf(" You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso);  
     fprintf(ficlog," You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso);  
      
   }  else if(mle==-5) { /* Main Wizard */    }  else if(mle==-5) { /* Main Wizard */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
Line 10997  Please run with mle=-1 to get a correct Line 11121  Please run with mle=-1 to get a correct
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                                   
     /* Other stuffs, more or less useful */          /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while(fgets(line, MAXLINE, ficpar)) {
       ungetc(c,ficpar);        /* If line starts with a # it is a comment */
       fgets(line, MAXLINE, ficpar);        if (line[0] == '#') {
       fputs(line,stdout);          numlinepar++;
       fputs(line,ficparo);          fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);  
           if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        if (num_filled != 7) {
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          goto end;
             }
     while((c=getc(ficpar))=='#' && c!= EOF){      /* fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); */
       ungetc(c,ficpar);        printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fgets(line, MAXLINE, ficpar);        fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fputs(line,stdout);        fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fputs(line,ficparo);        printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
         fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       }
   
       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);  
           
           
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
           
     fscanf(ficpar,"pop_based=%d\n",&popbased);      if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
     fprintf(ficlog,"pop_based=%d\n",popbased);        if (num_filled != 1) {
     fprintf(ficparo,"pop_based=%d\n",popbased);             printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     fprintf(ficres,"pop_based=%d\n",popbased);             fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
     while((c=getc(ficpar))=='#' && c!= EOF){        }
       ungetc(c,ficpar);        printf("pop_based=%d\n",popbased);
       fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"pop_based=%d\n",popbased);
       fputs(line,stdout);        fprintf(ficparo,"pop_based=%d\n",popbased);   
       fputs(line,ficres);        fprintf(ficres,"pop_based=%d\n",popbased);   
       fputs(line,ficparo);  
     }      }
     ungetc(c,ficpar);       
           while(fgets(line, MAXLINE, ficpar)) {
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);        /* If line starts with a # it is a comment */
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);        if (line[0] == '#') {
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);          numlinepar++;
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);          fputs(line,stdout);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);          fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
      /* while((c=getc(ficpar))=='#' && c!= EOF){ */
      /*    ungetc(c,ficpar); */
      /*    fgets(line, MAXLINE, ficpar); */
      /*    fputs(line,stdout); */
      /*    fputs(line,ficres); */
      /*    fputs(line,ficparo); */
      /*  } */
      /*  ungetc(c,ficpar); */
       
       /* fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj); */
       if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){
         if (num_filled != 8) {
           printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           goto end;
         }
        fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
        printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
        fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
        fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
       
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  
       fputs(line,stdout);  
       fputs(line,ficparo);  
       fputs(line,ficres);  
     }      }
     ungetc(c,ficpar);       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /*   fputs(line,ficres); */
       /* } */
       /* ungetc(c,ficpar); */
           
     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);      fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
     fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
     fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);        if (num_filled != 8) {
     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);          printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           goto end;
         }
         printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
         fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
         fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
         fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           }
     /* Results */      /* Results */
     nresult=0;      nresult=0;
     while(fgets(line, MAXLINE, ficpar)) {      while(fgets(line, MAXLINE, ficpar)) {
Line 11077  Please run with mle=-1 to get a correct Line 11260  Please run with mle=-1 to get a correct
     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){      while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
       if (num_filled == 0){        if (num_filled == 0){
         resultline[0]='\0';          resultline[0]='\0';
           printf("Warning %d: no result line should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
       break;        break;
       } else if (num_filled != 1){        } else if (num_filled != 1){
         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);          printf("ERROR %d: result line should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
       }        }
       nresult++; /* Sum of resultlines */        nresult++; /* Sum of resultlines */
       printf("Result %d: result=%s\n",nresult, resultline);        printf("Result %d: result=%s\n",nresult, resultline);
Line 11251  Please run with mle=-1 to get a correct Line 11435  Please run with mle=-1 to get a correct
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
Line 11324  Please run with mle=-1 to get a correct Line 11508  Please run with mle=-1 to get a correct
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       printf("\n#****** Result for:");        printf("\n#****** Result for:");
       fprintf(ficrest,"\n#****** Result for:");        fprintf(ficrest,"\n#****** Result for:");
Line 11465  Please run with mle=-1 to get a correct Line 11649  Please run with mle=-1 to get a correct
   
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){      for(k=1; k<=i1;k++){
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficresvpl,"\n#****** ");        fprintf(ficresvpl,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
Removed from v.1.251  
changed lines
  Added in v.1.255

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