1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
- dateintsum=dateintsum+k2;
- 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 = 1 to imx */
-
- /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- pstamp(ficresp);
- if (cptcovn>0) {
- fprintf(ficresp, "\n#********** Variable ");
- fprintf(ficresphtm, "\n
********** Variable ");
- fprintf(ficresphtmfr, "\n
********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++){
- fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- }
- fprintf(ficresp, "**********\n#");
- fprintf(ficresphtm, "**********
\n");
- fprintf(ficresphtmfr, "**********
\n");
- fprintf(ficlog, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(ficlog, "**********\n");
- }
- fprintf(ficresphtm,"");
- for(i=1; i<=nlstate;i++) {
- fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
- fprintf(ficresphtm, "| Age | Prev(%d) | N(%d) | N | ",i,i);
- }
- fprintf(ficresp, "\n");
- fprintf(ficresphtm, "\n");
-
- /* Header of frequency table by age */
- fprintf(ficresphtmfr,"");
- fprintf(ficresphtmfr,"| Age | ");
- for(jk=-1; jk <=nlstate+ndeath; jk++){
- for(m=-1; m <=nlstate+ndeath; m++){
- if(jk!=0 && m!=0)
- fprintf(ficresphtmfr,"%d%d | ",jk,m);
- }
- }
- fprintf(ficresphtmfr, "\n");
+ /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+ }
+ } /* end z1 */
+ } /* cptcovn > 0 */
+
+ if (bool==1){
+ /* for(m=firstpass; m<=lastpass; m++){ */
+ for(mi=1; mi=firstpass && m <=lastpass){
+ k2=anint[m][iind]+(mint[m][iind]/12.);
+ /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+ if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
+ if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
+ if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
+ prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+ if (m1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
+ dateintsum=dateintsum+k2;
+ k2cpt++;
+ /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
+ }
+ /*}*/
+ } /* end m */
+ } /* end bool */
+ } /* end iind = 1 to imx */
+ /* prop[s][age] is feeded for any initial and valid live state as well as
+ freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
+
+
+ /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+ pstamp(ficresp);
+ if (cptcovn>0) {
+ fprintf(ficresp, "\n#********** Variable ");
+ fprintf(ficresphtm, "\n
********** Variable ");
+ fprintf(ficresphtmfr, "\n
********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++){
+ fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ }
+ fprintf(ficresp, "**********\n#");
+ fprintf(ficresphtm, "**********
\n");
+ fprintf(ficresphtmfr, "**********
\n");
+ fprintf(ficlog, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficlog, "**********\n");
+ }
+ fprintf(ficresphtm,"");
+ for(i=1; i<=nlstate;i++) {
+ fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+ fprintf(ficresphtm, "| Age | Prev(%d) | N(%d) | N | ",i,i);
+ }
+ fprintf(ficresp, "\n");
+ fprintf(ficresphtm, "\n");
- /* For each age */
- for(i=iagemin; i <= iagemax+3; i++){
- fprintf(ficresphtm,"");
- if(i==iagemax+1){
- fprintf(ficlog,"1");
- fprintf(ficresphtmfr,"
| 0 | ");
- }else if(i==iagemax+2){
- fprintf(ficlog,"0");
- fprintf(ficresphtmfr,"
|---|
| Unknown | ");
- }else if(i==iagemax+3){
- fprintf(ficlog,"Total");
- fprintf(ficresphtmfr,"
|---|
| Total | ");
- }else{
- if(first==1){
- first=0;
- printf("See log file for details...\n");
- }
- fprintf(ficresphtmfr,"
|---|
| %d | ",i);
- fprintf(ficlog,"Age %d", i);
- }
- for(jk=1; jk <=nlstate ; jk++){
- for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
- pp[jk] += freq[jk][m][i];
- }
- for(jk=1; jk <=nlstate ; jk++){
- for(m=-1, pos=0; m <=0 ; m++)
- pos += freq[jk][m][i];
- if(pp[jk]>=1.e-10){
- if(first==1){
- printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
- }
- fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
- }else{
- if(first==1)
- printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
- fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
- }
- }
-
- for(jk=1; jk <=nlstate ; jk++){
- for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
- pp[jk] += freq[jk][m][i];
- }
- for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
- pos += pp[jk];
- posprop += prop[jk][i];
- }
- for(jk=1; jk <=nlstate ; jk++){
- if(pos>=1.e-5){
- if(first==1)
- printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- }else{
- if(first==1)
- printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- }
- if( i <= iagemax){
- if(pos>=1.e-5){
- fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
- fprintf(ficresphtm,"%d | %.5f | %.0f | %.0f | ",i,prop[jk][i]/posprop, prop[jk][i],posprop);
- /*probs[i][jk][j1]= pp[jk]/pos;*/
- /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
- }
- else{
- fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
- fprintf(ficresphtm,"%d | NaNq | %.0f | %.0f | ",i, prop[jk][i],posprop);
- }
- }
- }
-
- for(jk=-1; jk <=nlstate+ndeath; jk++){
- for(m=-1; m <=nlstate+ndeath; m++){
- if(freq[jk][m][i] !=0 ) { /* minimizing output */
- if(first==1){
- printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
- }
- fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
- }
- if(jk!=0 && m!=0)
- fprintf(ficresphtmfr,"%.0f | ",freq[jk][m][i]);
- }
- }
- fprintf(ficresphtmfr,"
|---|
\n ");
- if(i <= iagemax){
- fprintf(ficresp,"\n");
- fprintf(ficresphtm,"\n");
- }
- if(first==1)
- printf("Others in log...\n");
- fprintf(ficlog,"\n");
- } /* end loop i */
- fprintf(ficresphtm,"
\n");
- fprintf(ficresphtmfr,"
\n");
- /*}*/
- } /* end j1 */
- dateintmean=dateintsum/k2cpt;
-
- fclose(ficresp);
- fclose(ficresphtm);
- fclose(ficresphtmfr);
- free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
- free_vector(pp,1,nlstate);
- free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
- /* End of Freq */
-}
+ /* Header of frequency table by age */
+ fprintf(ficresphtmfr,"");
+ fprintf(ficresphtmfr,"| Age | ");
+ for(jk=-1; jk <=nlstate+ndeath; jk++){
+ for(m=-1; m <=nlstate+ndeath; m++){
+ if(jk!=0 && m!=0)
+ fprintf(ficresphtmfr,"%d%d | ",jk,m);
+ }
+ }
+ fprintf(ficresphtmfr, "\n");
+
+ /* For each age */
+ for(iage=iagemin; iage <= iagemax+3; iage++){
+ fprintf(ficresphtm,"");
+ if(iage==iagemax+1){
+ fprintf(ficlog,"1");
+ fprintf(ficresphtmfr,"
| 0 | ");
+ }else if(iage==iagemax+2){
+ fprintf(ficlog,"0");
+ fprintf(ficresphtmfr,"
|---|
| Unknown | ");
+ }else if(iage==iagemax+3){
+ fprintf(ficlog,"Total");
+ fprintf(ficresphtmfr,"
|---|
| Total | ");
+ }else{
+ if(first==1){
+ first=0;
+ printf("See log file for details...\n");
+ }
+ fprintf(ficresphtmfr,"
|---|
| %d | ",iage);
+ fprintf(ficlog,"Age %d", iage);
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+ pp[jk] += freq[jk][m][iage];
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pos=0; m <=0 ; m++)
+ pos += freq[jk][m][iage];
+ if(pp[jk]>=1.e-10){
+ if(first==1){
+ printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+ }
+ fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+ }else{
+ if(first==1)
+ printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+ fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+ }
+ }
+
+ for(jk=1; jk <=nlstate ; jk++){
+ /* posprop[jk]=0; */
+ for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+ pp[jk] += freq[jk][m][iage];
+ } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
+
+ for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
+ pos += pp[jk]; /* pos is the total number of transitions until this age */
+ posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
+ from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+ pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
+ from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ if(pos>=1.e-5){
+ if(first==1)
+ printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ }else{
+ if(first==1)
+ printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+ fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+ }
+ if( iage <= iagemax){
+ if(pos>=1.e-5){
+ fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+ fprintf(ficresphtm,"%d | %.5f | %.0f | %.0f | ",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+ /*probs[iage][jk][j1]= pp[jk]/pos;*/
+ /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
+ }
+ else{
+ fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
+ fprintf(ficresphtm,"%d | NaNq | %.0f | %.0f | ",iage, prop[jk][iage],pospropta);
+ }
+ }
+ pospropt[jk] +=posprop[jk];
+ } /* end loop jk */
+ /* pospropt=0.; */
+ for(jk=-1; jk <=nlstate+ndeath; jk++){
+ for(m=-1; m <=nlstate+ndeath; m++){
+ if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+ if(first==1){
+ printf(" %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)
+ fprintf(ficresphtmfr,"%.0f | ",freq[jk][m][iage]);
+ }
+ } /* end loop jk */
+ posproptt=0.;
+ for(jk=1; jk <=nlstate; jk++){
+ posproptt += pospropt[jk];
+ }
+ fprintf(ficresphtmfr,"
|---|
\n ");
+ if(iage <= iagemax){
+ fprintf(ficresp,"\n");
+ fprintf(ficresphtm,"\n");
+ }
+ if(first==1)
+ printf("Others in log...\n");
+ fprintf(ficlog,"\n");
+ } /* end loop age iage */
+ fprintf(ficresphtm,"| Tot | ");
+ for(jk=1; jk <=nlstate ; jk++){
+ if(posproptt < 1.e-5){
+ fprintf(ficresphtm,"Nanq | %.0f | %.0f | ",pospropt[jk],posproptt);
+ }else{
+ fprintf(ficresphtm,"%.5f | %.0f | %.0f | ",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+ }
+ }
+ fprintf(ficresphtm,"
|---|
\n");
+ fprintf(ficresphtm,"
\n");
+ fprintf(ficresphtmfr,"
\n");
+ if(posproptt < 1.e-5){
+ fprintf(ficresphtm,"\n This combination (%d) is not valid and no result will be produced
",j1);
+ fprintf(ficresphtmfr,"\n This combination (%d) is not valid and no result will be produced
",j1);
+ fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
+ invalidvarcomb[j1]=1;
+ }else{
+ fprintf(ficresphtm,"\n This combination (%d) is valid and result will be produced.
",j1);
+ invalidvarcomb[j1]=0;
+ }
+ fprintf(ficresphtmfr,"\n");
+ } /* end selected combination of covariate j1 */
+ dateintmean=dateintsum/k2cpt;
+
+ fclose(ficresp);
+ fclose(ficresphtm);
+ fclose(ficresphtmfr);
+ free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+ free_vector(pospropt,1,nlstate);
+ free_vector(posprop,1,nlstate);
+ free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+ free_vector(pp,1,nlstate);
+ /* End of Freq */
+ }
/************ Prevalence ********************/
-void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
-{
- /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
- in each health status at the date of interview (if between dateprev1 and dateprev2).
- We still use firstpass and lastpass as another selection.
- */
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+ {
+ /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+ in each health status at the date of interview (if between dateprev1 and dateprev2).
+ We still use firstpass and lastpass as another selection.
+ */
- int i, m, jk, j1, bool, z1,j;
- int mi; /* Effective wave */
- int iage;
- double agebegin, ageend;
-
- double **prop;
- double posprop;
- double y2; /* in fractional years */
- int iagemin, iagemax;
- int first; /** to stop verbosity which is redirected to log file */
-
- iagemin= (int) agemin;
- iagemax= (int) agemax;
- /*pp=vector(1,nlstate);*/
- prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
- /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
- j1=0;
-
- /*j=cptcoveff;*/
- if (cptcovn<1) {j=1;ncodemax[1]=1;}
-
- first=1;
- for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
- for (i=1; i<=nlstate; i++)
- for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
- prop[i][iage]=0.0;
-
- for (i=1; i<=imx; i++) { /* Each individual */
- bool=1;
- if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
- for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
- if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
- bool=0;
- }
- if (bool==1) { /* For this combination of covariates values, this individual fits */
- /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
- for(mi=1; mi=firstpass && m <=lastpass){
- y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
- if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
- if(agev[m][i]==0) agev[m][i]=iagemax+1;
- if(agev[m][i]==1) agev[m][i]=iagemax+2;
- if((int)agev[m][i] iagemax+3+AGEMARGE){
- printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
- exit(1);
- }
- if (s[m][i]>0 && s[m][i]<=nlstate) {
- /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
- prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
- prop[s[m][i]][iagemax+3] += weight[i];
- } /* end valid statuses */
- } /* end selection of dates */
- } /* end selection of waves */
- } /* end effective waves */
- } /* end bool */
- }
- for(i=iagemin; i <= iagemax+3; i++){
- for(jk=1,posprop=0; jk <=nlstate ; jk++) {
- posprop += prop[jk][i];
- }
-
- for(jk=1; jk <=nlstate ; jk++){
- if( i <= iagemax){
- if(posprop>=1.e-5){
- probs[i][jk][j1]= prop[jk][i]/posprop;
- } else{
- if(first==1){
- first=0;
- printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
- }
- }
- }
- }/* end jk */
- }/* end i */
- /*} *//* end i1 */
- } /* end j1 */
-
- /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
- /*free_vector(pp,1,nlstate);*/
- free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-} /* End of prevalence */
+ int i, m, jk, j1, bool, z1,j;
+ int mi; /* Effective wave */
+ int iage;
+ double agebegin, ageend;
+
+ double **prop;
+ double posprop;
+ double y2; /* in fractional years */
+ int iagemin, iagemax;
+ int first; /** to stop verbosity which is redirected to log file */
+
+ iagemin= (int) agemin;
+ iagemax= (int) agemax;
+ /*pp=vector(1,nlstate);*/
+ prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+ /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+ j1=0;
+
+ /*j=cptcoveff;*/
+ if (cptcovn<1) {j=1;ncodemax[1]=1;}
+
+ first=1;
+ for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
+ for (i=1; i<=nlstate; i++)
+ for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
+ prop[i][iage]=0.0;
+
+ for (i=1; i<=imx; i++) { /* Each individual */
+ bool=1;
+ if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+ for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
+ if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
+ bool=0;
+ }
+ if (bool==1) { /* For this combination of covariates values, this individual fits */
+ /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
+ for(mi=1; mi=firstpass && m <=lastpass){
+ y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+ if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+ if(agev[m][i]==0) agev[m][i]=iagemax+1;
+ if(agev[m][i]==1) agev[m][i]=iagemax+2;
+ if((int)agev[m][i] iagemax+3+AGEMARGE){
+ printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
+ exit(1);
+ }
+ if (s[m][i]>0 && s[m][i]<=nlstate) {
+ /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
+ prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
+ prop[s[m][i]][iagemax+3] += weight[i];
+ } /* end valid statuses */
+ } /* end selection of dates */
+ } /* end selection of waves */
+ } /* end effective waves */
+ } /* end bool */
+ }
+ for(i=iagemin; i <= iagemax+3; i++){
+ for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+ posprop += prop[jk][i];
+ }
+
+ for(jk=1; jk <=nlstate ; jk++){
+ if( i <= iagemax){
+ if(posprop>=1.e-5){
+ probs[i][jk][j1]= prop[jk][i]/posprop;
+ } else{
+ if(first==1){
+ first=0;
+ printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
+ }
+ }
+ }
+ }/* end jk */
+ }/* end i */
+ /*} *//* end i1 */
+ } /* end j1 */
+
+ /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+ /*free_vector(pp,1,nlstate);*/
+ free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+ } /* End of prevalence */
/************* Waves Concatenation ***************/
@@ -4222,13 +4277,13 @@ void concatwav(int wav[], int **dh, int
}
/*********** Tricode ****************************/
-void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
+ void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
{
/**< Uses cptcovn+2*cptcovprod as the number of covariates */
/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
* Boring subroutine which should only output nbcode[Tvar[j]][k]
* Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
- * nbcode[Tvar[j]][1]=
+ * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);
*/
int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
@@ -4237,7 +4292,8 @@ void tricode(int *Tvar, int **nbcode, in
int modmincovj=0; /* Modality min of covariates j */
- cptcoveff=0;
+ /* cptcoveff=0; */
+ *cptcov=0;
for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
@@ -4347,7 +4403,8 @@ void tricode(int *Tvar, int **nbcode, in
}
}
/* ij--; */
- cptcoveff=ij; /*Number of total covariates*/
+ /* cptcoveff=ij; /\*Number of total covariates*\/ */
+ *cptcov=ij; /*Number of total covariates*/
}
@@ -4466,7 +4523,7 @@ void cvevsij(double ***eij, double x[],
{
/* Covariances of health expectancies eij and of total life expectancies according
- to initial status i, ei. .
+ to initial status i, ei. .
*/
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
int nhstepma, nstepma; /* Decreasing with age */
@@ -4572,47 +4629,47 @@ void cvevsij(double ***eij, double x[],
decrease memory allocation */
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){
- xp[i] = x[i] + (i==theta ?delti[theta]:0);
- xm[i] = x[i] - (i==theta ?delti[theta]:0);
+ xp[i] = x[i] + (i==theta ?delti[theta]:0);
+ xm[i] = x[i] - (i==theta ?delti[theta]:0);
}
hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
for(j=1; j<= nlstate; j++){
- for(i=1; i<=nlstate; i++){
- for(h=0; h<=nhstepm-1; h++){
- gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
- gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
- }
- }
+ for(i=1; i<=nlstate; i++){
+ for(h=0; h<=nhstepm-1; h++){
+ gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+ gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+ }
+ }
}
for(ij=1; ij<= nlstate*nlstate; ij++)
- for(h=0; h<=nhstepm-1; h++){
- gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- }
+ for(h=0; h<=nhstepm-1; h++){
+ gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+ }
}/* End theta */
for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*nlstate;j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[h][j][theta]=gradg[h][theta][j];
+ for(theta=1; theta <=npar; theta++)
+ trgradg[h][j][theta]=gradg[h][theta][j];
- for(ij=1;ij<=nlstate*nlstate;ij++)
+ for(ij=1;ij<=nlstate*nlstate;ij++)
for(ji=1;ji<=nlstate*nlstate;ji++)
- varhe[ij][ji][(int)age] =0.;
+ varhe[ij][ji][(int)age] =0.;
- printf("%d|",(int)age);fflush(stdout);
- fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
- for(h=0;h<=nhstepm-1;h++){
+ printf("%d|",(int)age);fflush(stdout);
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+ for(h=0;h<=nhstepm-1;h++){
for(k=0;k<=nhstepm-1;k++){
- matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- for(ij=1;ij<=nlstate*nlstate;ij++)
- for(ji=1;ji<=nlstate*nlstate;ji++)
- varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+ matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+ for(ij=1;ij<=nlstate*nlstate;ij++)
+ for(ji=1;ji<=nlstate*nlstate;ji++)
+ varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
}
}
@@ -4620,22 +4677,22 @@ void cvevsij(double ***eij, double x[],
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
- for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+ for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+ eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
- /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+ /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
- }
+ }
fprintf(ficresstdeij,"%3.0f",age );
for(i=1; i<=nlstate;i++){
eip=0.;
vip=0.;
for(j=1; j<=nlstate;j++){
- eip += eij[i][j][(int)age];
- for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
- vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
- fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+ eip += eij[i][j][(int)age];
+ for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+ vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+ fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
}
fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
}
@@ -4644,13 +4701,13 @@ void cvevsij(double ***eij, double x[],
fprintf(ficrescveij,"%3.0f",age );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){
- cptj= (j-1)*nlstate+i;
- for(i2=1; i2<=nlstate;i2++)
- for(j2=1; j2<=nlstate;j2++){
- cptj2= (j2-1)*nlstate+i2;
- if(cptj2 <= cptj)
- fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
- }
+ cptj= (j-1)*nlstate+i;
+ for(i2=1; i2<=nlstate;i2++)
+ for(j2=1; j2<=nlstate;j2++){
+ cptj2= (j2-1)*nlstate+i2;
+ if(cptj2 <= cptj)
+ fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+ }
}
fprintf(ficrescveij,"\n");
@@ -5107,86 +5164,86 @@ void cvevsij(double ***eij, double x[],
/************ Variance of one-step probabilities ******************/
void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
-{
- int i, j=0, k1, l1, tj;
- int k2, l2, j1, z1;
- int k=0, l;
- int first=1, first1, first2;
- double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
- double **dnewm,**doldm;
- double *xp;
- double *gp, *gm;
- double **gradg, **trgradg;
- double **mu;
- double age, cov[NCOVMAX+1];
- double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
- int theta;
- char fileresprob[FILENAMELENGTH];
- char fileresprobcov[FILENAMELENGTH];
- char fileresprobcor[FILENAMELENGTH];
- double ***varpij;
-
- strcpy(fileresprob,"PROB_");
- strcat(fileresprob,fileres);
- if((ficresprob=fopen(fileresprob,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprob);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
- }
- strcpy(fileresprobcov,"PROBCOV_");
- strcat(fileresprobcov,fileresu);
- if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprobcov);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
- }
- strcpy(fileresprobcor,"PROBCOR_");
- strcat(fileresprobcor,fileresu);
- if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprobcor);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
- }
- printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
- fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
- pstamp(ficresprob);
- fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
- fprintf(ficresprob,"# Age");
- pstamp(ficresprobcov);
- fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
- fprintf(ficresprobcov,"# Age");
- pstamp(ficresprobcor);
- fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
- fprintf(ficresprobcor,"# Age");
-
+ {
+ int i, j=0, k1, l1, tj;
+ int k2, l2, j1, z1;
+ int k=0, l;
+ int first=1, first1, first2;
+ double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+ double **dnewm,**doldm;
+ double *xp;
+ double *gp, *gm;
+ double **gradg, **trgradg;
+ double **mu;
+ double age, cov[NCOVMAX+1];
+ double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+ int theta;
+ char fileresprob[FILENAMELENGTH];
+ char fileresprobcov[FILENAMELENGTH];
+ char fileresprobcor[FILENAMELENGTH];
+ double ***varpij;
+
+ strcpy(fileresprob,"PROB_");
+ strcat(fileresprob,fileres);
+ if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", fileresprob);
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+ }
+ strcpy(fileresprobcov,"PROBCOV_");
+ strcat(fileresprobcov,fileresu);
+ if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", fileresprobcov);
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+ }
+ strcpy(fileresprobcor,"PROBCOR_");
+ strcat(fileresprobcor,fileresu);
+ if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", fileresprobcor);
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+ }
+ printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+ fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+ printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+ fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+ printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+ fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+ pstamp(ficresprob);
+ fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+ fprintf(ficresprob,"# Age");
+ pstamp(ficresprobcov);
+ fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+ fprintf(ficresprobcov,"# Age");
+ pstamp(ficresprobcor);
+ fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+ fprintf(ficresprobcor,"# Age");
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=(nlstate+ndeath);j++){
- fprintf(ficresprob," p%1d-%1d (SE)",i,j);
- fprintf(ficresprobcov," p%1d-%1d ",i,j);
- fprintf(ficresprobcor," p%1d-%1d ",i,j);
- }
- /* fprintf(ficresprob,"\n");
- fprintf(ficresprobcov,"\n");
- fprintf(ficresprobcor,"\n");
- */
- xp=vector(1,npar);
- dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
- first=1;
- fprintf(ficgp,"\n# Routine varprob");
- fprintf(fichtm,"\n Computing and drawing one step probabilities with their confidence intervals
\n");
- fprintf(fichtm,"\n");
- fprintf(fichtm,"\n this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.\n",optionfilehtmcov);
- fprintf(fichtmcov,"Current page is file %s
\n\nMatrix of variance-covariance of pairs of step probabilities
\n",optionfilehtmcov, optionfilehtmcov);
- fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated \
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=(nlstate+ndeath);j++){
+ fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+ fprintf(ficresprobcov," p%1d-%1d ",i,j);
+ fprintf(ficresprobcor," p%1d-%1d ",i,j);
+ }
+ /* fprintf(ficresprob,"\n");
+ fprintf(ficresprobcov,"\n");
+ fprintf(ficresprobcor,"\n");
+ */
+ xp=vector(1,npar);
+ dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+ varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+ first=1;
+ fprintf(ficgp,"\n# Routine varprob");
+ fprintf(fichtm,"\n Computing and drawing one step probabilities with their confidence intervals
\n");
+ fprintf(fichtm,"\n");
+
+ fprintf(fichtm,"\n this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.\n",optionfilehtmcov);
+ fprintf(fichtmcov,"Current page is file %s
\n\nMatrix of variance-covariance of pairs of step probabilities
\n",optionfilehtmcov, optionfilehtmcov);
+ fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated \
and drawn. It helps understanding how is the covariance between two incidences.\
They are expressed in year-1 in order to be less dependent of stepm.
\n");
- fprintf(fichtmcov,"\n
Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+ fprintf(fichtmcov,"\n
Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \
It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
standard deviations wide on each axis.
\
@@ -5194,251 +5251,252 @@ standard deviations wide on each axis. <
and made the appropriate rotation to look at the uncorrelated principal directions.
\
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
\n");
- cov[1]=1;
- /* tj=cptcoveff; */
- tj = (int) pow(2,cptcoveff);
- if (cptcovn<1) {tj=1;ncodemax[1]=1;}
- j1=0;
- for(j1=1; j1<=tj;j1++){
- /*for(i1=1; i1<=ncodemax[t];i1++){ */
- /*j1++;*/
- if (cptcovn>0) {
- fprintf(ficresprob, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(ficresprob, "**********\n#\n");
- fprintf(ficresprobcov, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(ficresprobcov, "**********\n#\n");
-
- fprintf(ficgp, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(ficgp, "**********\n#\n");
-
-
- fprintf(fichtmcov, "\n
********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(fichtmcov, "**********\n
");
-
- fprintf(ficresprobcor, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
- fprintf(ficresprobcor, "**********\n#");
- }
-
- gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
- trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- gp=vector(1,(nlstate)*(nlstate+ndeath));
- gm=vector(1,(nlstate)*(nlstate+ndeath));
- for (age=bage; age<=fage; age ++){
- cov[2]=age;
- if(nagesqr==1)
- cov[3]= age*age;
- for (k=1; k<=cptcovn;k++) {
- cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
- /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
- * 1 1 1 1 1
- * 2 2 1 1 1
- * 3 1 2 1 1
- */
- /* nbcode[1][1]=0 nbcode[1][2]=1;*/
- }
- /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
- for (k=1; k<=cptcovprod;k++)
- cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-
-
- for(theta=1; theta <=npar; theta++){
- for(i=1; i<=npar; i++)
- xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-
- pmij(pmmij,cov,ncovmodel,xp,nlstate);
-
- k=0;
- for(i=1; i<= (nlstate); i++){
- for(j=1; j<=(nlstate+ndeath);j++){
- k=k+1;
- gp[k]=pmmij[i][j];
- }
- }
-
- for(i=1; i<=npar; i++)
- xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-
- pmij(pmmij,cov,ncovmodel,xp,nlstate);
- k=0;
- for(i=1; i<=(nlstate); i++){
- for(j=1; j<=(nlstate+ndeath);j++){
- k=k+1;
- gm[k]=pmmij[i][j];
- }
- }
-
- for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
- gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
- }
-
- for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[j][theta]=gradg[theta][j];
-
- matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-
- pmij(pmmij,cov,ncovmodel,x,nlstate);
-
- k=0;
- for(i=1; i<=(nlstate); i++){
- for(j=1; j<=(nlstate+ndeath);j++){
- k=k+1;
- mu[k][(int) age]=pmmij[i][j];
- }
- }
- for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
- for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
- varpij[i][j][(int)age] = doldm[i][j];
-
- /*printf("\n%d ",(int)age);
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
- fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
- }*/
-
- fprintf(ficresprob,"\n%d ",(int)age);
- fprintf(ficresprobcov,"\n%d ",(int)age);
- fprintf(ficresprobcor,"\n%d ",(int)age);
-
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
- fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
- fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
- }
- i=0;
- for (k=1; k<=(nlstate);k++){
- for (l=1; l<=(nlstate+ndeath);l++){
- i++;
- fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
- fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
- for (j=1; j<=i;j++){
- /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
- fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
- fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
- }
- }
- }/* end of loop for state */
- } /* end of loop for age */
- free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
- free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
- free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
- free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-
- /* Confidence intervalle of pij */
- /*
- fprintf(ficgp,"\nunset parametric;unset label");
- fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
- fprintf(fichtm,"\n
Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname);
- fprintf(fichtm,"\n
![](\"pijgr%s.png\")
",optionfilefiname);
- fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
- fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
- */
-
- /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
- first1=1;first2=2;
- for (k2=1; k2<=(nlstate);k2++){
- for (l2=1; l2<=(nlstate+ndeath);l2++){
- if(l2==k2) continue;
- j=(k2-1)*(nlstate+ndeath)+l2;
- for (k1=1; k1<=(nlstate);k1++){
- for (l1=1; l1<=(nlstate+ndeath);l1++){
- if(l1==k1) continue;
- i=(k1-1)*(nlstate+ndeath)+l1;
- if(i<=j) continue;
- for (age=bage; age<=fage; age ++){
- if ((int)age %5==0){
- v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
- v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
- cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
- mu1=mu[i][(int) age]/stepm*YEARM ;
- mu2=mu[j][(int) age]/stepm*YEARM;
- c12=cv12/sqrt(v1*v2);
- /* Computing eigen value of matrix of covariance */
- lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
- lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
- if ((lc2 <0) || (lc1 <0) ){
- if(first2==1){
- first1=0;
- printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
- }
- fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
- /* lc1=fabs(lc1); */ /* If we want to have them positive */
- /* lc2=fabs(lc2); */
- }
+ cov[1]=1;
+ /* tj=cptcoveff; */
+ tj = (int) pow(2,cptcoveff);
+ if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+ j1=0;
+ for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates */
+ if (cptcovn>0) {
+ fprintf(ficresprob, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresprob, "**********\n#\n");
+ fprintf(ficresprobcov, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresprobcov, "**********\n#\n");
+
+ fprintf(ficgp, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficgp, "**********\n#\n");
+
+
+ fprintf(fichtmcov, "\n
********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(fichtmcov, "**********\n
");
+
+ fprintf(ficresprobcor, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresprobcor, "**********\n#");
+ if(invalidvarcomb[j1]){
+ fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
+ fprintf(fichtmcov,"\nCombination (%d) ignored because no cases
\n",j1);
+ continue;
+ }
+ }
+ gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+ trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ gp=vector(1,(nlstate)*(nlstate+ndeath));
+ gm=vector(1,(nlstate)*(nlstate+ndeath));
+ for (age=bage; age<=fage; age ++){
+ cov[2]=age;
+ if(nagesqr==1)
+ cov[3]= age*age;
+ for (k=1; k<=cptcovn;k++) {
+ cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
+ /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
+ * 1 1 1 1 1
+ * 2 2 1 1 1
+ * 3 1 2 1 1
+ */
+ /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+ }
+ /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+ for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+ for (k=1; k<=cptcovprod;k++)
+ cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+
+
+ for(theta=1; theta <=npar; theta++){
+ for(i=1; i<=npar; i++)
+ xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+
+ pmij(pmmij,cov,ncovmodel,xp,nlstate);
+
+ k=0;
+ for(i=1; i<= (nlstate); i++){
+ for(j=1; j<=(nlstate+ndeath);j++){
+ k=k+1;
+ gp[k]=pmmij[i][j];
+ }
+ }
+
+ for(i=1; i<=npar; i++)
+ xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+
+ pmij(pmmij,cov,ncovmodel,xp,nlstate);
+ k=0;
+ for(i=1; i<=(nlstate); i++){
+ for(j=1; j<=(nlstate+ndeath);j++){
+ k=k+1;
+ gm[k]=pmmij[i][j];
+ }
+ }
+
+ for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+ gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+ }
- /* Eigen vectors */
- v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
- /*v21=sqrt(1.-v11*v11); *//* error */
- v21=(lc1-v1)/cv12*v11;
- v12=-v21;
- v22=v11;
- tnalp=v21/v11;
- if(first1==1){
- first1=0;
- printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
- }
- fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
- /*printf(fignu*/
- /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
- /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
- if(first==1){
- first=0;
- fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
- fprintf(ficgp,"\nset parametric;unset label");
- fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
- fprintf(ficgp,"\nset ter svg size 640, 480");
- fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\
- :\
+ for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+ for(theta=1; theta <=npar; theta++)
+ trgradg[j][theta]=gradg[theta][j];
+
+ matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+ matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+
+ pmij(pmmij,cov,ncovmodel,x,nlstate);
+
+ k=0;
+ for(i=1; i<=(nlstate); i++){
+ for(j=1; j<=(nlstate+ndeath);j++){
+ k=k+1;
+ mu[k][(int) age]=pmmij[i][j];
+ }
+ }
+ for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+ for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+ varpij[i][j][(int)age] = doldm[i][j];
+
+ /*printf("\n%d ",(int)age);
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+ printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+ fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+ }*/
+
+ fprintf(ficresprob,"\n%d ",(int)age);
+ fprintf(ficresprobcov,"\n%d ",(int)age);
+ fprintf(ficresprobcor,"\n%d ",(int)age);
+
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+ fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+ fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+ fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+ }
+ i=0;
+ for (k=1; k<=(nlstate);k++){
+ for (l=1; l<=(nlstate+ndeath);l++){
+ i++;
+ fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+ fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+ for (j=1; j<=i;j++){
+ /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
+ fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+ fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+ }
+ }
+ }/* end of loop for state */
+ } /* end of loop for age */
+ free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+ free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+ free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+ free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+
+ /* Confidence intervalle of pij */
+ /*
+ fprintf(ficgp,"\nunset parametric;unset label");
+ fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+ fprintf(fichtm,"\n
Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname);
+ fprintf(fichtm,"\n
",optionfilefiname);
+ fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+ fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+ */
+
+ /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+ first1=1;first2=2;
+ for (k2=1; k2<=(nlstate);k2++){
+ for (l2=1; l2<=(nlstate+ndeath);l2++){
+ if(l2==k2) continue;
+ j=(k2-1)*(nlstate+ndeath)+l2;
+ for (k1=1; k1<=(nlstate);k1++){
+ for (l1=1; l1<=(nlstate+ndeath);l1++){
+ if(l1==k1) continue;
+ i=(k1-1)*(nlstate+ndeath)+l1;
+ if(i<=j) continue;
+ for (age=bage; age<=fage; age ++){
+ if ((int)age %5==0){
+ v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+ v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+ cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+ mu1=mu[i][(int) age]/stepm*YEARM ;
+ mu2=mu[j][(int) age]/stepm*YEARM;
+ c12=cv12/sqrt(v1*v2);
+ /* Computing eigen value of matrix of covariance */
+ lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+ lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+ if ((lc2 <0) || (lc1 <0) ){
+ if(first2==1){
+ first1=0;
+ printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+ }
+ fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+ /* lc1=fabs(lc1); */ /* If we want to have them positive */
+ /* lc2=fabs(lc2); */
+ }
+
+ /* Eigen vectors */
+ v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+ /*v21=sqrt(1.-v11*v11); *//* error */
+ v21=(lc1-v1)/cv12*v11;
+ v12=-v21;
+ v22=v11;
+ tnalp=v21/v11;
+ if(first1==1){
+ first1=0;
+ printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+ }
+ fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+ /*printf(fignu*/
+ /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+ /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+ if(first==1){
+ first=0;
+ fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
+ fprintf(ficgp,"\nset parametric;unset label");
+ fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+ fprintf(ficgp,"\nset ter svg size 640, 480");
+ fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\
+ : \
%s_%d%1d%1d-%1d%1d.svg, ",k1,l1,k2,l2,\
- subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
- subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
- fprintf(fichtmcov,"\n
![](\"%s_%d%1d%1d-%1d%1d.svg\")
",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
- fprintf(fichtmcov,"\n
Correlation at age %d (%.3f),",(int) age, c12);
- fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
- fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
- fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
- fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
- mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
- }else{
- first=0;
- fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
- fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
- fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
- fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
- mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
- }/* if first */
- } /* age mod 5 */
- } /* end loop age */
- fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
- first=1;
- } /*l12 */
- } /* k12 */
- } /*l1 */
- }/* k1 */
- /* } */ /* loop covariates */
- }
- free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
- free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
- free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
- free_vector(xp,1,npar);
- fclose(ficresprob);
- fclose(ficresprobcov);
- fclose(ficresprobcor);
- fflush(ficgp);
- fflush(fichtmcov);
-}
+ subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
+ subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+ fprintf(fichtmcov,"\n
",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+ fprintf(fichtmcov,"\n
Correlation at age %d (%.3f),",(int) age, c12);
+ fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+ fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+ fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+ fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
+ mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
+ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ }else{
+ first=0;
+ fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+ fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+ fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+ fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
+ mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
+ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ }/* if first */
+ } /* age mod 5 */
+ } /* end loop age */
+ fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+ first=1;
+ } /*l12 */
+ } /* k12 */
+ } /*l1 */
+ }/* k1 */
+ } /* loop on combination of covariates j1 */
+ free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+ free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+ free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+ free_vector(xp,1,npar);
+ fclose(ficresprob);
+ fclose(ficresprobcov);
+ fclose(ficresprobcor);
+ fflush(ficgp);
+ fflush(fichtmcov);
+ }
/******************* Printing html file ***********/
@@ -5481,14 +5539,15 @@ void printinghtml(char fileresu[], char
%s
\n", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
}
-fprintf(fichtm," \n- Graphs
");
+ fprintf(fichtm," \n
- Graphs
");
+
+ m=pow(2,cptcoveff);
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- m=pow(2,cptcoveff);
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+ jj1=0;
+ for(k1=1; k1<=m;k1++){
- jj1=0;
- for(k1=1; k1<=m;k1++){
- /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+ /* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;
if (cptcovn > 0) {
fprintf(fichtm,"
************ Results for covariates");
@@ -5497,6 +5556,11 @@ fprintf(fichtm," \n- Graphs
printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
}
fprintf(fichtm," ************\n
");
+ if(invalidvarcomb[k1]){
+ fprintf(fichtm,"\nCombination (%d) ignored because no cases
\n",k1);
+ printf("\nCombination (%d) ignored because no cases \n",k1);
+ continue;
+ }
}
/* aij, bij */
fprintf(fichtm,"
- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: %s_%d-1.svg
\
@@ -5506,7 +5570,7 @@ fprintf(fichtm," \n- Graphs
![](\"%s_%d-2.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Quasi-incidences */
fprintf(fichtm,"
\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
divided by h: hPij/h : %s_%d-3.svg
\
![](\"%s_%d-3.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
@@ -5518,7 +5582,7 @@ divided by h: hPij
/* State specific survival functions (period) */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"
\n- Survival functions from state %d in each live state and total.\
- Or probability to survive in various states (1 to %d) being in state %d at different ages.\
+ Or probability to survive in various states (1 to %d) being in state %d at different ages. \
%s%d_%d.svg
![](\"%s_%d-%d.svg\")
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
}
/* Period (stable) prevalence in each health state */
@@ -5526,30 +5590,30 @@ divided by h: hPij
fprintf(fichtm,"
\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. %s_%d-%d.svg
\
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
}
- if(backcast==1){
- /* Period (stable) back prevalence in each health state */
- for(cpt=1; cpt<=nlstate;cpt++){
- fprintf(fichtm,"
\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. %s_%d-%d.svg
\
+ if(backcast==1){
+ /* Period (stable) back prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\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. %s_%d-%d.svg
\
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
+ }
}
- }
- if(prevfcast==1){
- /* Projection of prevalence up to period (stable) prevalence in each health state */
- for(cpt=1; cpt<=nlstate;cpt++){
- fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
\
+ if(prevfcast==1){
+ /* Projection of prevalence up to period (stable) prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
\
", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
- }
- }
-
+ }
+ }
+
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n
- 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): %s_%d%d.svg
\
![](\"%s_%d%d.svg\")
",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
}
- /* } /\* end i1 *\/ */
- }/* End k1 */
- fprintf(fichtm,"
");
+ /* } /\* end i1 *\/ */
+ }/* End k1 */
+ fprintf(fichtm,"
");
- fprintf(fichtm,"\
+ fprintf(fichtm,"\
\n
- \n\
- Parameter file with estimated parameters and covariance matrix: %s
\
- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).
\
@@ -5561,32 +5625,32 @@ variances but at the covariance matrix.
covariance matrix of the one-step probabilities. \
See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
- fprintf(fichtm," - Standard deviation of one-step probabilities: %s
\n",
- subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
- fprintf(fichtm,"\
+ fprintf(fichtm," - Standard deviation of one-step probabilities: %s
\n",
+ subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
+ fprintf(fichtm,"\
- Variance-covariance of one-step probabilities: %s
\n",
- subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
+ subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
- fprintf(fichtm,"\
+ fprintf(fichtm,"\
- Correlation matrix of one-step probabilities: %s
\n",
- subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
- fprintf(fichtm,"\
+ subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
+ fprintf(fichtm,"\
- Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \
%s
\n ",
estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
- fprintf(fichtm,"\
+ fprintf(fichtm,"\
- (a) Health expectancies by health status at initial age (eij) and standard errors (in parentheses) (b) life expectancies and standard errors (ei.=ei1+ei2+...)(estepm=%2d months): \
%s
\n",
estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
- fprintf(fichtm,"\
+ fprintf(fichtm,"\
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): %s
\n",
- estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
- fprintf(fichtm,"\
+ estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
+ fprintf(fichtm,"\
- Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): %s
\n",
- estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
- fprintf(fichtm,"\
+ estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
+ fprintf(fichtm,"\
- Standard deviation of period (stable) prevalences: %s
\n",\
- subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+ subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
/* if(popforecast==1) fprintf(fichtm,"\n */
/* - Prevalences forecasting: f%s
\n */
@@ -5594,21 +5658,26 @@ See page 'Matrix of variance-covariance
/*
",fileres,fileres,fileres,fileres); */
/* else */
/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)
\n",popforecast, stepm, model); */
- fflush(fichtm);
- fprintf(fichtm," - Graphs
");
+ fflush(fichtm);
+ fprintf(fichtm,"
- Graphs
");
- m=pow(2,cptcoveff);
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+ m=pow(2,cptcoveff);
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- jj1=0;
- for(k1=1; k1<=m;k1++){
- /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+ jj1=0;
+ for(k1=1; k1<=m;k1++){
+ /* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;
if (cptcovn > 0) {
fprintf(fichtm,"
************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
fprintf(fichtm," ************\n
");
+
+ if(invalidvarcomb[k1]){
+ fprintf(fichtm,"\nCombination (%d) ignored because no cases
\n",k1);
+ continue;
+ }
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n
- Observed (cross-sectional) and period (incidence based) \
@@ -5621,16 +5690,17 @@ true period expectancies (those weighted
drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: %s_%d.svg\n
\
![](\"%s_%d.svg\")
",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
- /* } /\* end i1 *\/ */
- }/* End k1 */
- fprintf(fichtm,"
");
- fflush(fichtm);
+ /* } /\* end i1 *\/ */
+ }/* End k1 */
+ fprintf(fichtm,"
");
+ fflush(fichtm);
}
/******************* Gnuplot file **************/
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
char dirfileres[132],optfileres[132];
+ char gplotcondition[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
int lv=0, vlv=0, kl=0;
int ng=0;
@@ -5680,7 +5750,7 @@ true period expectancies (those weighted
strcpy(optfileres,"vpl");
/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
- for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
+ for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
@@ -5690,9 +5760,13 @@ true period expectancies (those weighted
/* 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 */
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
- fprintf(ficgp," V%d=%d ",k,vlv);
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
@@ -5732,10 +5806,10 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
/*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
if(k==cptcoveff){
- fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, k,kl+1+1,nbcode[Tvaraff[k]][lv], \
- 4+(cpt-1), cpt );
+ fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+ 6+(cpt-1), cpt );
}else{
- fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, k,kl+1+1,nbcode[Tvaraff[k]][lv]);
+ fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
kl++;
}
} /* end covariate */
@@ -5745,6 +5819,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
} /* cpt */
/*2 eme*/
for (k1=1; k1<= m ; k1 ++) {
+
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
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 */
@@ -5752,9 +5827,13 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];
- fprintf(ficgp," V%d=%d ",k,vlv);
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
@@ -5792,6 +5871,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
/*3eme*/
for (k1=1; k1<= m ; k1 ++) {
+
for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
@@ -5800,9 +5880,13 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];
- fprintf(ficgp," V%d=%d ",k,vlv);
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
/* k=2+nlstate*(2*cpt-2); */
k=2+(nlstate+1)*(cpt-1);
@@ -5826,99 +5910,117 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
}
}
+ /* 4eme */
/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
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 */
- /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
- /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
- /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
- vlv= nbcode[Tvaraff[k]][lv];
- fprintf(ficgp," V%d=%d ",k,vlv);
+ 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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
+ /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
+ vlv= nbcode[Tvaraff[k]][lv];
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
-
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
+
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-set ter svg size 640, 480\n\
-unset log y\n\
+set ter svg size 640, 480\n \
+unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;
for (i=1; i<= nlstate ; i ++){
- if(i==1){
- fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
- }else{
- fprintf(ficgp,", '' ");
- }
- l=(nlstate+ndeath)*(i-1)+1;
- fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
- for (j=2; j<= nlstate+ndeath ; j ++)
- fprintf(ficgp,"+$%d",k+l+j-1);
- fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+ if(i==1){
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+ }else{
+ fprintf(ficgp,", '' ");
+ }
+ l=(nlstate+ndeath)*(i-1)+1;
+ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+ for (j=2; j<= nlstate+ndeath ; j ++)
+ fprintf(ficgp,"+$%d",k+l+j-1);
+ fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
} /* nlstate */
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
-
+
+/* 5eme */
/* Survival functions (period) from state i in state j by final state j */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
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);
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 */
- /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
- /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
- /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
- vlv= nbcode[Tvaraff[k]][lv];
- fprintf(ficgp," V%d=%d ",k,vlv);
+ 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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
+ /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
+ vlv= nbcode[Tvaraff[k]][lv];
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
-
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
+
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-set ter svg size 640, 480\n\
-unset log y\n\
+set ter svg size 640, 480\n \
+unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
- if(j==1)
- fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
- else
- fprintf(ficgp,", '' ");
- l=(nlstate+ndeath)*(cpt-1) +j;
- fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
- /* for (i=2; i<= nlstate+ndeath ; i ++) */
- /* fprintf(ficgp,"+$%d",k+l+i-1); */
- fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+ if(j==1)
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+ else
+ fprintf(ficgp,", '' ");
+ l=(nlstate+ndeath)*(cpt-1) +j;
+ fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+ /* for (i=2; i<= nlstate+ndeath ; i ++) */
+ /* fprintf(ficgp,"+$%d",k+l+i-1); */
+ fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
} /* nlstate */
fprintf(ficgp,", '' ");
fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
- l=(nlstate+ndeath)*(cpt-1) +j;
- if(j < nlstate)
- fprintf(ficgp,"$%d +",k+l);
- else
- fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+ l=(nlstate+ndeath)*(cpt-1) +j;
+ if(j < nlstate)
+ fprintf(ficgp,"$%d +",k+l);
+ else
+ fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
}
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
-
+
+/* 6eme */
/* CV preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+
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 */
- 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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
- /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
- vlv= nbcode[Tvaraff[k]][lv];
- fprintf(ficgp," V%d=%d ",k,vlv);
+ 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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
+ /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
+ vlv= nbcode[Tvaraff[k]][lv];
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
@@ -5927,60 +6029,68 @@ unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){
- if(i==1)
- fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
- else
- fprintf(ficgp,", '' ");
- l=(nlstate+ndeath)*(i-1)+1;
- fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
- for (j=2; j<= nlstate ; j ++)
- fprintf(ficgp,"+$%d",k+l+j-1);
- fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+ if(i==1)
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+ else
+ fprintf(ficgp,", '' ");
+ l=(nlstate+ndeath)*(i-1)+1;
+ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+ for (j=2; j<= nlstate ; j ++)
+ fprintf(ficgp,"+$%d",k+l+j-1);
+ fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
} /* nlstate */
fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
+
+
+/* 7eme */
if(backcast == 1){
/* CV back preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
- fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
- 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 */
- /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
- /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
- /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
- vlv= nbcode[Tvaraff[k]][lv];
- fprintf(ficgp," V%d=%d ",k,vlv);
- }
- fprintf(ficgp,"\n#\n");
-
- fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-set ter svg size 640, 480\n \
-unset log y\n \
+ fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+ 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 */
+ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
+ /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
+ /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
+ vlv= nbcode[Tvaraff[k]][lv];
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+ }
+ fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
+
+ fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+set ter svg size 640, 480\n \
+unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);
- k=3; /* Offset */
- for (i=1; i<= nlstate ; i ++){
- if(i==1)
- fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
- else
- fprintf(ficgp,", '' ");
- /* l=(nlstate+ndeath)*(i-1)+1; */
- l=(nlstate+ndeath)*(cpt-1)+1;
- /* 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",k1,k+l+(cpt-1)+i-1); /* a vérifier */
- /* for (j=2; j<= nlstate ; j ++) */
- /* fprintf(ficgp,"+$%d",k+l+j-1); */
- /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
- fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
- } /* nlstate */
- fprintf(ficgp,"\nset out\n");
+ k=3; /* Offset */
+ for (i=1; i<= nlstate ; i ++){
+ if(i==1)
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+ else
+ fprintf(ficgp,", '' ");
+ /* l=(nlstate+ndeath)*(i-1)+1; */
+ l=(nlstate+ndeath)*(cpt-1)+1;
+ /* 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",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+ /* for (j=2; j<= nlstate ; j ++) */
+ /* fprintf(ficgp,"+$%d",k+l+j-1); */
+ /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
+ fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+ } /* nlstate */
+ fprintf(ficgp,"\nset out\n");
} /* end cpt state*/
} /* end covariate */
} /* End if backcast */
+ /* 8eme */
if(prevfcast==1){
/* Projection from cross-sectional to stable (period) for each covariate */
@@ -5993,9 +6103,13 @@ plot [%.f:%.f] ", ageminpar, agemaxpar)
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];
- fprintf(ficgp," V%d=%d ",k,vlv);
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
@@ -6034,42 +6148,33 @@ plot [%.f:%.f] ", ageminpar, agemaxpar)
/*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
}
- fprintf(ficgp," u %d:((",ioffset);
+ fprintf(ficgp," u %d:(",ioffset);
kl=0;
- for (k=1; k<=cptcoveff; k++){ /* For each covariate */
+ strcpy(gplotcondition,"(");
+ for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
- vlv= nbcode[Tvaraff[k]][lv];
+ vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
kl++;
- /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
- /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
- /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
- /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
- if(k==cptcoveff){
- if(i==nlstate+1){
- if(cptcoveff ==1){
- fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
- ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
- }else{
- fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
- ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
- }
- }else{
- if(cptcoveff ==1){
- fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
- ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
- }else{
- fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \
- ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
- }
- }
- }else{ /* k < cptcoveff */
- fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[k]][lv]);
- kl++;
- }
- } /* end covariate */
+ sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+ kl++;
+ if(k 1)
+ sprintf(gplotcondition+strlen(gplotcondition)," && ");
+ }
+ strcpy(gplotcondition+strlen(gplotcondition),")");
+ /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+ /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+ /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+ /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+ if(i==nlstate+1){
+ fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+ }else{
+ fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+ }
} /* end if covariate */
} /* nlstate */
fprintf(ficgp,"\nset out\n");
@@ -6222,152 +6327,157 @@ plot [%.f:%.f] ", ageminpar, agemaxpar)
/*************** Moving average **************/
/* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
-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, cpt, cptcod;
- int modcovmax =1;
- int mobilavrange, mob;
- int iage=0;
-
- double sum=0.;
- double age;
- double *sumnewp, *sumnewm;
- double *agemingood, *agemaxgood; /* Currently identical for all covariates */
-
-
- modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
- a covariate has 2 modalities, should be equal to ncovcombmax */
-
- sumnewp = vector(1,modcovmax);
- sumnewm = vector(1,modcovmax);
- agemingood = vector(1,modcovmax);
- agemaxgood = vector(1,modcovmax);
-
- for (cptcod=1;cptcod<=modcovmax;cptcod++){
- sumnewm[cptcod]=0.;
- sumnewp[cptcod]=0.;
- agemingood[cptcod]=0;
- agemaxgood[cptcod]=0;
- }
- if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+ int i, cpt, cptcod;
+ int modcovmax =1;
+ int mobilavrange, mob;
+ int iage=0;
+
+ double sum=0.;
+ double age;
+ double *sumnewp, *sumnewm;
+ double *agemingood, *agemaxgood; /* Currently identical for all covariates */
+
+
+ /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
+ /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
+
+ sumnewp = vector(1,ncovcombmax);
+ sumnewm = vector(1,ncovcombmax);
+ agemingood = vector(1,ncovcombmax);
+ agemaxgood = vector(1,ncovcombmax);
+
+ for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+ sumnewm[cptcod]=0.;
+ sumnewp[cptcod]=0.;
+ agemingood[cptcod]=0;
+ agemaxgood[cptcod]=0;
+ }
+ if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
- if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
- if(mobilav==1) mobilavrange=5; /* default */
- else mobilavrange=mobilav;
- for (age=bage; age<=fage; age++)
- for (i=1; i<=nlstate;i++)
- for (cptcod=1;cptcod<=modcovmax;cptcod++)
- mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
- /* We keep the original values on the extreme ages bage, fage and for
- fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
- we use a 5 terms etc. until the borders are no more concerned.
- */
- for (mob=3;mob <=mobilavrange;mob=mob+2){
- for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
- for (i=1; i<=nlstate;i++){
- for (cptcod=1;cptcod<=modcovmax;cptcod++){
- mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
- for (cpt=1;cpt<=(mob-1)/2;cpt++){
- mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
- mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
- }
- mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
- }
- }
- }/* end age */
- }/* end mob */
- }else
- return -1;
- for (cptcod=1;cptcod<=modcovmax;cptcod++){
- /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
- agemingood[cptcod]=fage-(mob-1)/2;
- for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
- sumnewm[cptcod]=0.;
- for (i=1; i<=nlstate;i++){
- sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
- }
- if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
- agemingood[cptcod]=age;
- }else{ /* bad */
- for (i=1; i<=nlstate;i++){
- mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
- } /* i */
- } /* end bad */
- }/* age */
- sum=0.;
- for (i=1; i<=nlstate;i++){
- sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
- }
- if(fabs(sum - 1.) > 1.e-3) { /* bad */
- printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
- /* for (i=1; i<=nlstate;i++){ */
- /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
- /* } /\* i *\/ */
- } /* end bad */
- /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
- /* From youngest, finding the oldest wrong */
- agemaxgood[cptcod]=bage+(mob-1)/2;
- for (age=bage+(mob-1)/2; age<=fage; age++){
- sumnewm[cptcod]=0.;
- for (i=1; i<=nlstate;i++){
- sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
- }
- if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
- agemaxgood[cptcod]=age;
- }else{ /* bad */
- for (i=1; i<=nlstate;i++){
- mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
- } /* i */
- } /* end bad */
- }/* age */
- sum=0.;
- for (i=1; i<=nlstate;i++){
- sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
- }
- if(fabs(sum - 1.) > 1.e-3) { /* bad */
- printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
- /* for (i=1; i<=nlstate;i++){ */
- /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
- /* } /\* i *\/ */
- } /* end bad */
-
- for (age=bage; age<=fage; age++){
- printf("%d %d ", cptcod, (int)age);
- sumnewp[cptcod]=0.;
- sumnewm[cptcod]=0.;
- for (i=1; i<=nlstate;i++){
- sumnewp[cptcod]+=probs[(int)age][i][cptcod];
- sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
- /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
- }
- /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
- }
- /* printf("\n"); */
- /* } */
- /* brutal averaging */
- for (i=1; i<=nlstate;i++){
- for (age=1; age<=bage; age++){
- mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
- /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
- }
- for (age=fage; age<=AGESUP; age++){
- mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
- /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
- }
- } /* end i status */
- for (i=nlstate+1; i<=nlstate+ndeath;i++){
- for (age=1; age<=AGESUP; age++){
- /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
- mobaverage[(int)age][i][cptcod]=0.;
- }
- }
- }/* end cptcod */
- free_vector(sumnewm,1, modcovmax);
- free_vector(sumnewp,1, modcovmax);
- free_vector(agemaxgood,1, modcovmax);
- free_vector(agemingood,1, modcovmax);
- return 0;
-}/* End movingaverage */
+ if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+ if(mobilav==1) mobilavrange=5; /* default */
+ else mobilavrange=mobilav;
+ for (age=bage; age<=fage; age++)
+ for (i=1; i<=nlstate;i++)
+ for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
+ mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+ /* We keep the original values on the extreme ages bage, fage and for
+ fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+ we use a 5 terms etc. until the borders are no more concerned.
+ */
+ for (mob=3;mob <=mobilavrange;mob=mob+2){
+ for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+ for (i=1; i<=nlstate;i++){
+ for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+ mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+ for (cpt=1;cpt<=(mob-1)/2;cpt++){
+ mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+ mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+ }
+ mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+ }
+ }
+ }/* end age */
+ }/* end mob */
+ }else
+ return -1;
+ for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+ /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
+ if(invalidvarcomb[cptcod]){
+ printf("\nCombination (%d) ignored because no cases \n",cptcod);
+ continue;
+ }
+
+ agemingood[cptcod]=fage-(mob-1)/2;
+ for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
+ sumnewm[cptcod]=0.;
+ for (i=1; i<=nlstate;i++){
+ sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+ }
+ if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+ agemingood[cptcod]=age;
+ }else{ /* bad */
+ for (i=1; i<=nlstate;i++){
+ mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+ } /* i */
+ } /* end bad */
+ }/* age */
+ sum=0.;
+ for (i=1; i<=nlstate;i++){
+ sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+ }
+ if(fabs(sum - 1.) > 1.e-3) { /* bad */
+ printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
+ /* for (i=1; i<=nlstate;i++){ */
+ /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+ /* } /\* i *\/ */
+ } /* end bad */
+ /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+ /* From youngest, finding the oldest wrong */
+ agemaxgood[cptcod]=bage+(mob-1)/2;
+ for (age=bage+(mob-1)/2; age<=fage; age++){
+ sumnewm[cptcod]=0.;
+ for (i=1; i<=nlstate;i++){
+ sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+ }
+ if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+ agemaxgood[cptcod]=age;
+ }else{ /* bad */
+ for (i=1; i<=nlstate;i++){
+ mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+ } /* i */
+ } /* end bad */
+ }/* age */
+ sum=0.;
+ for (i=1; i<=nlstate;i++){
+ sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+ }
+ if(fabs(sum - 1.) > 1.e-3) { /* bad */
+ printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
+ /* for (i=1; i<=nlstate;i++){ */
+ /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+ /* } /\* i *\/ */
+ } /* end bad */
+
+ for (age=bage; age<=fage; age++){
+ printf("%d %d ", cptcod, (int)age);
+ sumnewp[cptcod]=0.;
+ sumnewm[cptcod]=0.;
+ for (i=1; i<=nlstate;i++){
+ sumnewp[cptcod]+=probs[(int)age][i][cptcod];
+ sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+ /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
+ }
+ /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
+ }
+ /* printf("\n"); */
+ /* } */
+ /* brutal averaging */
+ for (i=1; i<=nlstate;i++){
+ for (age=1; age<=bage; age++){
+ mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+ /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+ }
+ for (age=fage; age<=AGESUP; age++){
+ mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+ /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+ }
+ } /* end i status */
+ for (i=nlstate+1; i<=nlstate+ndeath;i++){
+ for (age=1; age<=AGESUP; age++){
+ /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
+ mobaverage[(int)age][i][cptcod]=0.;
+ }
+ }
+ }/* end cptcod */
+ free_vector(sumnewm,1, ncovcombmax);
+ free_vector(sumnewp,1, ncovcombmax);
+ free_vector(agemaxgood,1, ncovcombmax);
+ free_vector(agemingood,1, ncovcombmax);
+ return 0;
+ }/* End movingaverage */
/************** Forecasting ******************/
@@ -6921,7 +7031,7 @@ double gompertz(double x[])
double A,B,L=0.0,sump=0.,num=0.;
int i,n=0; /* n is the size of the sample */
- for (i=0;i<=imx-1 ; i++) {
+ for (i=1;i<=imx ; i++) {
sump=sump+weight[i];
/* sump=sump+1;*/
num=num+1;
@@ -7765,10 +7875,11 @@ int prevalence_limit(double *p, double *
i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ for(k=1; k<=i1;k++){
+ /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
+ /* k=k+1; */
/* to clean */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
fprintf(ficrespl,"#******");
@@ -7782,6 +7893,12 @@ int prevalence_limit(double *p, double *
fprintf(ficrespl,"******\n");
printf("******\n");
fprintf(ficlog,"******\n");
+ if(invalidvarcomb[k]){
+ printf("\nCombination (%d) ignored because no cases \n",k);
+ fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
+ fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+ continue;
+ }
fprintf(ficrespl,"#Age ");
for(j=1;j<=cptcoveff;j++) {
@@ -7795,11 +7912,11 @@ int prevalence_limit(double *p, double *
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
fprintf(ficrespl,"%.0f ",age );
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)]);
tot=0.;
for(i=1; i<=nlstate;i++){
- tot += prlim[i][i];
- fprintf(ficrespl," %.5f", prlim[i][i]);
+ tot += prlim[i][i];
+ fprintf(ficrespl," %.5f", prlim[i][i]);
}
fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
} /* Age */
@@ -7844,11 +7961,12 @@ int back_prevalence_limit(double *p, dou
i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}
-
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+
+ for(k=1; k<=i1;k++){
+ /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
+ /* k=k+1; */
/* to clean */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
fprintf(ficresplb,"#******");
@@ -7862,6 +7980,12 @@ int back_prevalence_limit(double *p, dou
fprintf(ficresplb,"******\n");
printf("******\n");
fprintf(ficlog,"******\n");
+ if(invalidvarcomb[k]){
+ printf("\nCombination (%d) ignored because no cases \n",k);
+ fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+ fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+ continue;
+ }
fprintf(ficresplb,"#Age ");
for(j=1;j<=cptcoveff;j++) {
@@ -8015,6 +8139,10 @@ int hPijx(double *p, int bage, int fage)
for(j=1;j<=cptcoveff;j++)
fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrespijb,"******\n");
+ if(invalidvarcomb[k]){
+ fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+ continue;
+ }
/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
@@ -8432,16 +8560,14 @@ int main(int argc, char *argv[])
fclose (ficlog);
goto end;
exit(0);
- }
- else if(mle==-3) { /* Main Wizard */
+ } else if(mle==-5) { /* Main Wizard */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
matcov=matrix(1,npar,1,npar);
hess=matrix(1,npar,1,npar);
- }
- else{
+ } else{ /* Begin of mle != -1 or -5 */
/* Read guessed parameters */
/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){
@@ -8456,37 +8582,37 @@ int main(int argc, char *argv[])
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
for(i=1; i <=nlstate; i++){
- j=0;
+ j=0;
for(jj=1; jj <=nlstate+ndeath; jj++){
- if(jj==i) continue;
- j++;
- fscanf(ficpar,"%1d%1d",&i1,&j1);
- if ((i1 != i) || (j1 != jj)){
- printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+ if(jj==i) continue;
+ j++;
+ fscanf(ficpar,"%1d%1d",&i1,&j1);
+ if ((i1 != i) || (j1 != jj)){
+ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
It might be a problem of design; if ncovcol and the model are correct\n \
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
- exit(1);
- }
- fprintf(ficparo,"%1d%1d",i1,j1);
- if(mle==1)
- printf("%1d%1d",i,jj);
- fprintf(ficlog,"%1d%1d",i,jj);
- for(k=1; k<=ncovmodel;k++){
- fscanf(ficpar," %lf",¶m[i][j][k]);
- if(mle==1){
- printf(" %lf",param[i][j][k]);
- fprintf(ficlog," %lf",param[i][j][k]);
- }
- else
- fprintf(ficlog," %lf",param[i][j][k]);
- fprintf(ficparo," %lf",param[i][j][k]);
- }
- fscanf(ficpar,"\n");
- numlinepar++;
- if(mle==1)
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficparo,"\n");
+ exit(1);
+ }
+ fprintf(ficparo,"%1d%1d",i1,j1);
+ if(mle==1)
+ printf("%1d%1d",i,jj);
+ fprintf(ficlog,"%1d%1d",i,jj);
+ for(k=1; k<=ncovmodel;k++){
+ fscanf(ficpar," %lf",¶m[i][j][k]);
+ if(mle==1){
+ printf(" %lf",param[i][j][k]);
+ fprintf(ficlog," %lf",param[i][j][k]);
+ }
+ else
+ fprintf(ficlog," %lf",param[i][j][k]);
+ fprintf(ficparo," %lf",param[i][j][k]);
+ }
+ fscanf(ficpar,"\n");
+ numlinepar++;
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficparo,"\n");
}
}
fflush(ficlog);
@@ -8507,35 +8633,35 @@ run imach with mle=-1 to get a correct t
for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){
- fscanf(ficpar,"%1d%1d",&i1,&j1);
- if ( (i1-i) * (j1-j) != 0){
- printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
- exit(1);
- }
- printf("%1d%1d",i,j);
- fprintf(ficparo,"%1d%1d",i1,j1);
- fprintf(ficlog,"%1d%1d",i1,j1);
- for(k=1; k<=ncovmodel;k++){
- fscanf(ficpar,"%le",&delti3[i][j][k]);
- printf(" %le",delti3[i][j][k]);
- fprintf(ficparo," %le",delti3[i][j][k]);
- fprintf(ficlog," %le",delti3[i][j][k]);
- }
- fscanf(ficpar,"\n");
- numlinepar++;
- printf("\n");
- fprintf(ficparo,"\n");
- fprintf(ficlog,"\n");
+ fscanf(ficpar,"%1d%1d",&i1,&j1);
+ if ( (i1-i) * (j1-j) != 0){
+ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+ exit(1);
+ }
+ printf("%1d%1d",i,j);
+ fprintf(ficparo,"%1d%1d",i1,j1);
+ fprintf(ficlog,"%1d%1d",i1,j1);
+ for(k=1; k<=ncovmodel;k++){
+ fscanf(ficpar,"%le",&delti3[i][j][k]);
+ printf(" %le",delti3[i][j][k]);
+ fprintf(ficparo," %le",delti3[i][j][k]);
+ fprintf(ficlog," %le",delti3[i][j][k]);
+ }
+ fscanf(ficpar,"\n");
+ numlinepar++;
+ printf("\n");
+ fprintf(ficparo,"\n");
+ fprintf(ficlog,"\n");
}
}
fflush(ficlog);
-
+
/* Reads covariance matrix */
delti=delti3[1][1];
-
-
+
+
/* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-
+
/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
@@ -8546,47 +8672,48 @@ run imach with mle=-1 to get a correct t
fputs(line,ficlog);
}
ungetc(c,ficpar);
-
+
matcov=matrix(1,npar,1,npar);
hess=matrix(1,npar,1,npar);
for(i=1; i <=npar; i++)
for(j=1; j <=npar; j++) matcov[i][j]=0.;
-
+
/* Scans npar lines */
for(i=1; i <=npar; i++){
count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
if(count != 3){
- printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
- fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
- exit(1);
- }else
- if(mle==1)
- printf("%1d%1d%1d",i1,j1,jk);
+ exit(1);
+ }else{
+ if(mle==1)
+ printf("%1d%1d%1d",i1,j1,jk);
+ }
fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
for(j=1; j <=i; j++){
- fscanf(ficpar," %le",&matcov[i][j]);
- if(mle==1){
- printf(" %.5le",matcov[i][j]);
- }
- fprintf(ficlog," %.5le",matcov[i][j]);
- fprintf(ficparo," %.5le",matcov[i][j]);
+ fscanf(ficpar," %le",&matcov[i][j]);
+ if(mle==1){
+ printf(" %.5le",matcov[i][j]);
+ }
+ fprintf(ficlog," %.5le",matcov[i][j]);
+ fprintf(ficparo," %.5le",matcov[i][j]);
}
fscanf(ficpar,"\n");
numlinepar++;
if(mle==1)
- printf("\n");
+ printf("\n");
fprintf(ficlog,"\n");
fprintf(ficparo,"\n");
}
/* End of read covariance matrix npar lines */
for(i=1; i <=npar; i++)
for(j=i+1;j<=npar;j++)
- matcov[i][j]=matcov[j][i];
+ matcov[i][j]=matcov[j][i];
if(mle==1)
printf("\n");
@@ -8614,10 +8741,19 @@ Please run with mle=-1 to get a correct
annais=vector(1,n);
moisdc=vector(1,n);
andc=vector(1,n);
+ weight=vector(1,n);
agedc=vector(1,n);
cod=ivector(1,n);
- weight=vector(1,n);
- for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+ for(i=1;i<=n;i++){
+ num[i]=0;
+ moisnais[i]=0;
+ annais[i]=0;
+ moisdc[i]=0;
+ andc[i]=0;
+ agedc[i]=0;
+ cod[i]=0;
+ weight[i]=1.0; /* Equal weights, 1 by default */
+ }
mint=matrix(1,maxwav,1,n);
anint=matrix(1,maxwav,1,n);
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
@@ -8714,12 +8850,19 @@ Please run with mle=-1 to get a correct
free_vector(andc,1,n);
/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;
Ndum =ivector(-1,NCOVMAX);
- if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
- tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+ cptcoveff=0;
+ if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
+ tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+ }
+
+ ncovcombmax=pow(2,cptcoveff);
+ invalidvarcomb=ivector(1, ncovcombmax);
+ for(i=1;i 0) */
-
-
m=pow(2,cptcoveff);
/**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
@@ -8806,40 +8945,9 @@ Please run with mle=-1 to get a correct
* 2211
* V1=1+1, V2=0+1, V3=1+1, V4=1+1
* V3=2
+ * codtabm and decodtabm are identical
*/
- /* /\* for(h=1; h <=100 ;h++){ *\/ */
- /* /\* printf("h=%2d ", h); *\/ */
- /* /\* for(k=1; k <=10; k++){ *\/ */
- /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
- /* /\* codtab[h][k]=codtabm(h,k); *\/ */
- /* /\* } *\/ */
- /* /\* printf("\n"); *\/ */
- /* } */
- /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
- /* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/ */
- /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
- /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
- /* h++; */
- /* if (h>m) */
- /* h=1; */
- /* codtab[h][k]=j; */
- /* /\* codtab[12][3]=1; *\/ */
- /* /\*codtab[h][Tvar[k]]=j;*\/ */
- /* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
- /* } */
- /* } */
- /* } */
- /* } */
- /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
- codtab[1][2]=1;codtab[2][2]=2; */
- /* for(i=1; i <=m ;i++){ */
- /* for(k=1; k <=cptcovn; k++){ */
- /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
- /* } */
- /* printf("\n"); */
- /* } */
- /* scanf("%d",i);*/
free_ivector(Ndum,-1,NCOVMAX);
@@ -8914,9 +9022,10 @@ Title=%s
Datafile=%s Firstpass=%d La
#endif
- /* Calculates basic frequencies. Computes observed prevalence at single age
+ /* Calculates basic frequencies. Computes observed prevalence at single age
+ and for any valid combination of covariates
and prints on file fileres'p'. */
- freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
firstpass, lastpass, stepm, weightopt, model);
fprintf(fichtm,"\n");
@@ -8925,10 +9034,10 @@ Youngest age at first (selected) pass %.
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
\n",\
imx,agemin,agemax,jmin,jmax,jmean);
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
/* For Powell, parameters are in a vector p[] starting at p[1]
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
@@ -8938,6 +9047,9 @@ Interval (in months) between two waves:
/* For mortality only */
if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);
+ for(i=1;i<=NDIM;i++)
+ for(j=1;j<=NDIM;j++)
+ ximort[i][j]=0.;
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);
ageexmed=vector(1,n);
@@ -9086,14 +9198,14 @@ Interval (in months) between two waves:
for(i=1; i <=NDIM; i++)
for(j=i+1;j<=NDIM;j++)
- matcov[i][j]=matcov[j][i];
+ matcov[i][j]=matcov[j][i];
printf("\nCovariance matrix\n ");
fprintf(ficlog,"\nCovariance matrix\n ");
for(i=1; i <=NDIM; i++) {
for(j=1;j<=NDIM;j++){
- printf("%f ",matcov[i][j]);
- fprintf(ficlog,"%f ",matcov[i][j]);
+ printf("%f ",matcov[i][j]);
+ fprintf(ficlog,"%f ",matcov[i][j]);
}
printf("\n "); fprintf(ficlog,"\n ");
}
@@ -9134,6 +9246,8 @@ Interval (in months) between two waves:
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+ ageminpar=50;
+ agemaxpar=100;
if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
@@ -9141,8 +9255,11 @@ Please run with mle=-1 to get a correct
fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
- }else
+ }else{
+ printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+ fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ }
printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
stepm, weightopt,\
model,imx,p,matcov,agemortsup);
@@ -9150,11 +9267,11 @@ Please run with mle=-1 to get a correct
free_vector(lsurv,1,AGESUP);
free_vector(lpop,1,AGESUP);
free_vector(tpop,1,AGESUP);
-#ifdef GSL
+ free_matrix(ximort,1,NDIM,1,NDIM);
free_ivector(cens,1,n);
free_vector(agecens,1,n);
free_ivector(dcwave,1,n);
- free_matrix(ximort,1,NDIM,1,NDIM);
+#ifdef GSL
#endif
} /* Endof if mle==-3 mortality only */
/* Standard */
@@ -9191,20 +9308,20 @@ Please run with mle=-1 to get a correct
fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){
- if (k != i) {
- printf("%d%d ",i,k);
- fprintf(ficlog,"%d%d ",i,k);
- fprintf(ficres,"%1d%1d ",i,k);
- for(j=1; j <=ncovmodel; j++){
- printf("%12.7f ",p[jk]);
- fprintf(ficlog,"%12.7f ",p[jk]);
- fprintf(ficres,"%12.7f ",p[jk]);
- jk++;
- }
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficres,"\n");
- }
+ if (k != i) {
+ printf("%d%d ",i,k);
+ fprintf(ficlog,"%d%d ",i,k);
+ fprintf(ficres,"%1d%1d ",i,k);
+ for(j=1; j <=ncovmodel; j++){
+ printf("%12.7f ",p[jk]);
+ fprintf(ficlog,"%12.7f ",p[jk]);
+ fprintf(ficres,"%12.7f ",p[jk]);
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ }
}
}
if(mle != 0){
@@ -9214,42 +9331,42 @@ Please run with mle=-1 to get a correct
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
for(i=1,jk=1; i <=nlstate; i++){
- for(k=1; k <=(nlstate+ndeath); k++){
- if (k != i) {
- printf("%d%d ",i,k);
- fprintf(ficlog,"%d%d ",i,k);
- for(j=1; j <=ncovmodel; j++){
- printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
- fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
- jk++;
- }
- printf("\n");
- fprintf(ficlog,"\n");
- }
- }
+ for(k=1; k <=(nlstate+ndeath); k++){
+ if (k != i) {
+ printf("%d%d ",i,k);
+ fprintf(ficlog,"%d%d ",i,k);
+ for(j=1; j <=ncovmodel; j++){
+ printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+ fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ }
+ }
}
} /* end of hesscov and Wald tests */
-
+
/* */
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
for(i=1,jk=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath; j++){
- if (j!=i) {
- fprintf(ficres,"%1d%1d",i,j);
- printf("%1d%1d",i,j);
- fprintf(ficlog,"%1d%1d",i,j);
- for(k=1; k<=ncovmodel;k++){
- printf(" %.5e",delti[jk]);
- fprintf(ficlog," %.5e",delti[jk]);
- fprintf(ficres," %.5e",delti[jk]);
- jk++;
- }
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficres,"\n");
- }
+ if (j!=i) {
+ fprintf(ficres,"%1d%1d",i,j);
+ printf("%1d%1d",i,j);
+ fprintf(ficlog,"%1d%1d",i,j);
+ for(k=1; k<=ncovmodel;k++){
+ printf(" %.5e",delti[jk]);
+ fprintf(ficlog," %.5e",delti[jk]);
+ fprintf(ficres," %.5e",delti[jk]);
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ }
}
}
@@ -9273,83 +9390,83 @@ Please run with mle=-1 to get a correct
for(itimes=1;itimes<=2;itimes++){
jj=0;
for(i=1; i <=nlstate; i++){
- for(j=1; j <=nlstate+ndeath; j++){
- if(j==i) continue;
- for(k=1; k<=ncovmodel;k++){
- jj++;
- ca[0]= k+'a'-1;ca[1]='\0';
- if(itimes==1){
- if(mle>=1)
- printf("#%1d%1d%d",i,j,k);
- fprintf(ficlog,"#%1d%1d%d",i,j,k);
- fprintf(ficres,"#%1d%1d%d",i,j,k);
- }else{
- if(mle>=1)
- printf("%1d%1d%d",i,j,k);
- fprintf(ficlog,"%1d%1d%d",i,j,k);
- fprintf(ficres,"%1d%1d%d",i,j,k);
- }
- ll=0;
- for(li=1;li <=nlstate; li++){
- for(lj=1;lj <=nlstate+ndeath; lj++){
- if(lj==li) continue;
- for(lk=1;lk<=ncovmodel;lk++){
- ll++;
- if(ll<=jj){
- cb[0]= lk +'a'-1;cb[1]='\0';
- if(ll=1)
- printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- }else{
- if(mle>=1)
- printf(" %.5e",matcov[jj][ll]);
- fprintf(ficlog," %.5e",matcov[jj][ll]);
- fprintf(ficres," %.5e",matcov[jj][ll]);
- }
- }else{
- if(itimes==1){
- if(mle>=1)
- printf(" Var(%s%1d%1d)",ca,i,j);
- fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
- fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
- }else{
- if(mle>=1)
- printf(" %.7e",matcov[jj][ll]);
- fprintf(ficlog," %.7e",matcov[jj][ll]);
- fprintf(ficres," %.7e",matcov[jj][ll]);
- }
- }
- }
- } /* end lk */
- } /* end lj */
- } /* end li */
- if(mle>=1)
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficres,"\n");
- numlinepar++;
- } /* end k*/
- } /*end j */
+ for(j=1; j <=nlstate+ndeath; j++){
+ if(j==i) continue;
+ for(k=1; k<=ncovmodel;k++){
+ jj++;
+ ca[0]= k+'a'-1;ca[1]='\0';
+ if(itimes==1){
+ if(mle>=1)
+ printf("#%1d%1d%d",i,j,k);
+ fprintf(ficlog,"#%1d%1d%d",i,j,k);
+ fprintf(ficres,"#%1d%1d%d",i,j,k);
+ }else{
+ if(mle>=1)
+ printf("%1d%1d%d",i,j,k);
+ fprintf(ficlog,"%1d%1d%d",i,j,k);
+ fprintf(ficres,"%1d%1d%d",i,j,k);
+ }
+ ll=0;
+ for(li=1;li <=nlstate; li++){
+ for(lj=1;lj <=nlstate+ndeath; lj++){
+ if(lj==li) continue;
+ for(lk=1;lk<=ncovmodel;lk++){
+ ll++;
+ if(ll<=jj){
+ cb[0]= lk +'a'-1;cb[1]='\0';
+ if(ll=1)
+ printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ }else{
+ if(mle>=1)
+ printf(" %.5e",matcov[jj][ll]);
+ fprintf(ficlog," %.5e",matcov[jj][ll]);
+ fprintf(ficres," %.5e",matcov[jj][ll]);
+ }
+ }else{
+ if(itimes==1){
+ if(mle>=1)
+ printf(" Var(%s%1d%1d)",ca,i,j);
+ fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+ fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+ }else{
+ if(mle>=1)
+ printf(" %.7e",matcov[jj][ll]);
+ fprintf(ficlog," %.7e",matcov[jj][ll]);
+ fprintf(ficres," %.7e",matcov[jj][ll]);
+ }
+ }
+ }
+ } /* end lk */
+ } /* end lj */
+ } /* end li */
+ if(mle>=1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ numlinepar++;
+ } /* end k*/
+ } /*end j */
} /* end i */
} /* end itimes */
fflush(ficlog);
fflush(ficres);
- 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(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); */
@@ -9360,17 +9477,17 @@ Please run with mle=-1 to get a correct
estepm=0;
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("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
- fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\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 */
-
+
+ if (num_filled != 6) {
+ printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
+ fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\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 (fage <= 2) {
@@ -9381,7 +9498,7 @@ Please run with mle=-1 to get a correct
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
fprintf(ficres,"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 */
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
@@ -9444,27 +9561,27 @@ Please run with mle=-1 to get a correct
/* day and month of proj2 are not used but only year anproj2.*/
- /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+ /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
- printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
- fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
- }else
+ }else{
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
-
- printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
- model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
- jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
-
- /*------------ free_vector -------------*/
- /* chdir(path); */
-
+ }
+ printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
+ model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
+ jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+
+ /*------------ free_vector -------------*/
+ /* chdir(path); */
+
/* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
@@ -9475,11 +9592,11 @@ Please run with mle=-1 to get a correct
/*free_matrix(covar,1,NCOVMAX,1,n);*/
fclose(ficparo);
fclose(ficres);
-
-
+
+
/* Other results (useful)*/
-
-
+
+
/*--------------- Prevalence limit (period or stable prevalence) --------------*/
/*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
prlim=matrix(1,nlstate,1,nlstate);
@@ -9491,7 +9608,7 @@ Please run with mle=-1 to get a correct
hPijx(p, bage, fage);
fclose(ficrespij);
- ncovcombmax= pow(2,cptcoveff);
+ /* ncovcombmax= pow(2,cptcoveff); */
/*-------------- Variance of one-step probabilities---*/
k=1;
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
@@ -9577,7 +9694,7 @@ Please run with mle=-1 to get a correct
for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficreseij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {
- fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}
fprintf(ficreseij,"******\n");
@@ -9671,57 +9788,57 @@ Please run with mle=-1 to get a correct
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
- oldm=oldms;savm=savms; /* ZZ Segmentation fault */
- cptcod= 0; /* To be deleted */
- printf("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 */
- 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)
- 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);
- else
- fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
- fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
- for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
- fprintf(ficrest,"\n");
- /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
- epj=vector(1,nlstate+1);
- 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");
- for(age=bage; age <=fage ;age++){
- prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
- if (vpopbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][k];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][k];
- }
- }
+ oldm=oldms;savm=savms; /* ZZ Segmentation fault */
+ cptcod= 0; /* To be deleted */
+ printf("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 */
+ 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)
+ 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);
+ else
+ fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+ fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
+ for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+ fprintf(ficrest,"\n");
+ /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+ epj=vector(1,nlstate+1);
+ 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");
+ for(age=bage; age <=fage ;age++){
+ prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
+ if (vpopbased==1) {
+ if(mobilav ==0){
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=probs[(int)age][i][k];
+ }else{ /* mobilav */
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=mobaverage[(int)age][i][k];
+ }
+ }
- 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++) {
- epj[j] += prlim[i][i]*eij[i][j][(int)age];
- /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
- /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
- }
- epj[nlstate+1] +=epj[j];
- }
- /* printf(" age %4.0f \n",age); */
+ 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++) {
+ epj[j] += prlim[i][i]*eij[i][j][(int)age];
+ /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+ /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
+ }
+ epj[nlstate+1] +=epj[j];
+ }
+ /* printf(" age %4.0f \n",age); */
- for(i=1, vepp=0.;i <=nlstate;i++)
- for(j=1;j <=nlstate;j++)
- vepp += vareij[i][j][(int)age];
- fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
- for(j=1;j <=nlstate;j++){
- fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
- }
- fprintf(ficrest,"\n");
- }
+ for(i=1, vepp=0.;i <=nlstate;i++)
+ for(j=1;j <=nlstate;j++)
+ vepp += vareij[i][j][(int)age];
+ fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+ for(j=1;j <=nlstate;j++){
+ fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+ }
+ fprintf(ficrest,"\n");
+ }
} /* End vpopbased */
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
@@ -9781,10 +9898,10 @@ Please run with mle=-1 to get a correct
if (mobilav!=0 ||mobilavproj !=0)
free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
- } /* mle==-3 arrives here for freeing */
- /* endfree:*/
free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+ } /* mle==-3 arrives here for freeing */
+ /* endfree:*/
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
@@ -9801,6 +9918,7 @@ Please run with mle=-1 to get a correct
free_ivector(Tvar,1,NCOVMAX);
free_ivector(Tprod,1,NCOVMAX);
free_ivector(Tvaraff,1,NCOVMAX);
+ free_ivector(invalidvarcomb,1,ncovcombmax);
free_ivector(Tage,1,NCOVMAX);
free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
![%s_%d-1.svg](\"%s_%d-1.svg\"){kind=link}
![%s%d_%d.svg](\"%s%d_%d.svg\"){kind=link}