/* $Id$
$State$
$Log$
+ Revision 1.204 2015/10/01 16:20:26 brouard
+ Summary: Some new graphs of contribution to likelihood
+
Revision 1.203 2015/09/30 17:45:14 brouard
Summary: looking at better estimation of the hessian
}
/* got dirc from getcwd*/
printf(" DIRC = %s \n",dirc);
- } else { /* strip direcotry from path */
+ } else { /* strip directory from path */
ss++; /* after this, the filename */
l2 = strlen( ss ); /* length of filename */
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
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]); */
if(globpr){
- fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f\
+ fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \
- num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+ num[i], agexact, 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]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){
llt +=ll[k]*gipmx/gsw;
printf("Problem with resultfile: %s\n", fileresilk);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
}
- fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
- fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+ fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+ fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %weight 2wlli out sav ");
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
for(k=1; k<=nlstate; k++)
fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
*fretone=(*funcone)(p);
if(*globpri !=0){
fclose(ficresilk);
- fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
- fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
+ if (mle ==0)
+ fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
+ else if(mle >=1)
+ fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
+ fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+
+ fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
<img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
- fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
+
fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
<img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
- fflush(fichtm);
-
- for (k=1; k<= nlstate ; k++) {
- fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
+ fflush(fichtm);
+
+ for (k=1; k<= nlstate ; k++) {
+
fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
-
- }
- }
+ }
+ }
return;
}
/************ 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[])
{
- /* Variance of prevalence limit */
+ /* 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 **dnewm,**doldm;
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] =0.;
+ if((int)age==67 ||(int)age== 66 ){
+ matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+ }else{
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+ }
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
}
for(cpt=1; cpt<=nlstate;cpt++) {
- fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
+ fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
}
/* } /\* end i1 *\/ */
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
-<img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
+prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
+<img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\
- observed and cahotic prevalences: %s_%d.svg<br>\
-<img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
+ observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
+<img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
/* } /\* end i1 *\/ */
}/* End k1 */
fprintf(fichtm,"</ul>");
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
/* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
- fprintf(ficgp,"\nset ter png size 640, 480");
+ fprintf(ficgp,"\nset ter pngcairo size 640, 480");
/* nice for mle=4 plot by number of matrix products.
replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
/* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
- fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
+ fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
- fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
+ fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
for (i=1; i<= nlstate ; i ++) {
fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
- fprintf(ficgp,"unset log;\n plot \"%s\"",subdirf(fileresilk));
- fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable \\\n",i,1,i,1);
+ fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
+ fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
for (j=2; j<= nlstate+ndeath ; j ++) {
- fprintf(ficgp,", \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable ",i,j,i,j);
+ fprintf(ficgp,",\\\n \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
}
fprintf(ficgp,";\nset out; unset ylabel;\n");
}
printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
if(argc <=1){
printf("\nEnter the parameter file name: ");
- fgets(pathr,FILENAMELENGTH,stdin);
+ if(!fgets(pathr,FILENAMELENGTH,stdin)){
+ printf("ERROR Empty parameter file name\n");
+ goto end;
+ }
i=strlen(pathr);
if(pathr[i-1]=='\n')
pathr[i-1]='\0';
i=strlen(pathr);
- if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+ if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
pathr[i-1]='\0';
- for (tok = pathr; tok != NULL; ){
+ }
+ i=strlen(pathr);
+ if( i==0 ){
+ printf("ERROR Empty parameter file name\n");
+ goto end;
+ }
+ for (tok = pathr; tok != NULL; ){
printf("Pathr |%s|\n",pathr);
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
printf("val= |%s| pathr=%s\n",val,pathr);
free_matrix(ximort,1,NDIM,1,NDIM);
#endif
} /* Endof if mle==-3 mortality only */
- /* Standard maximisation */
- else{ /* For mle !=- 3 */
- globpr=0;/* debug */
- /* Computes likelihood for initial parameters */
+ /* Standard */
+ else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
+ globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+ /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);
printf("\n");
- globpr=1; /* again, to print the contributions */
+ if(mle>=1){ /* Could be 1 or 2, Real Maximization */
+ /* mlikeli uses func not funcone */
+ mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+ }
+ if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
+ globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+ /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+ }
+ globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);
printf("\n");
- if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
- mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
- }
/*--------- results files --------------*/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
}
fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
+ /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
/* printf(" age %4.0f ",age); */
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
for(i=1, epj[j]=0.;i <=nlstate;i++) {
git://henry.ined.fr / .git / commitdiff