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Diff for /imach/src/imach.c between versions 1.245 and 1.247

version 1.245, 2016/09/02 07:25:01 version 1.247, 2016/09/02 11:11:21
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.247  2016/09/02 11:11:21  brouard
     *** empty log message ***
   
     Revision 1.246  2016/09/02 08:49:22  brouard
     *** empty log message ***
   
   Revision 1.245  2016/09/02 07:25:01  brouard    Revision 1.245  2016/09/02 07:25:01  brouard
   *** empty log message ***    *** empty log message ***
   
Line 2581  Earliest age to start was %d-%d=%d, ncvl Line 2587  Earliest age to start was %d-%d=%d, ncvl
   /* 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;
     int first=0;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
Line 2706  Earliest age to start was %d-%d=%d, ncvl Line 2713  Earliest age to start was %d-%d=%d, ncvl
     }      }
   } /* age loop */    } /* age loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\    if(first){
       first=1;
       printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
   Oldest 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);
     }
     fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
 Oldest 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);  Oldest 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); */    /* 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(min,1,nlstate);
Line 3593  double funcone( double *x) Line 3605  double funcone( double *x)
       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
         /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]          /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           and mw[mi+1][i]. dh depends on stepm.*/            and mw[mi+1][i]. dh depends on stepm.*/
         newm=savm;          newm=savm;
         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
         cov[2]=agexact;          cov[2]=agexact;
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= agexact*agexact;            cov[3]= agexact*agexact;
Line 3649  double funcone( double *x) Line 3662  double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\          fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
Line 4007  double hessij( double x[], double **hess Line 4020  double hessij( double x[], double **hess
       kmax=kmax+10;        kmax=kmax+10;
     }      }
     if(kmax >=10 || firstime ==1){      if(kmax >=10 || firstime ==1){
       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);        printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);        fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could 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);
     }      }
Line 6401  void printinggnuplot(char fileresu[], ch Line 6414  void printinggnuplot(char fileresu[], ch
         if(TKresult[nres]!= k1)          if(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); */
         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */            lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
Line 6410  void printinggnuplot(char fileresu[], ch Line 6423  void printinggnuplot(char fileresu[], ch
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */            vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */            /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
           printf(" V%d=%d ",Tvaraff[k],vlv);            /* printf(" V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                 }       
         printf("\n#\n");          /* printf("\n#\n"); */
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 9874  int main(int argc, char *argv[]) Line 9887  int main(int argc, char *argv[])
   delti=delti3[1][1];    delti=delti3[1][1];
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
   /* We could also provide initial parameters values giving by simple logistic regression 
    * only one way, that is without matrix product. We will have nlstate maximizations */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
Line 10646  Please run with mle=-1 to get a correct Line 10665  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2, Real Maximization */      if(mle>=1){ /* Could be 1 or 2, Real Maximization */
       /* mlikeli uses func not funcone */        /* mlikeli uses func not funcone */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }      }
     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */      if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
Removed from v.1.245  
changed lines
  Added in v.1.247

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