********** Variable ");
+ fprintf(ficresphtmfr, "\n
********** Variable ");
+ fprintf(ficlog, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++){
+ if(!FixedV[Tvaraff[z1]]){
+ printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ }else{
+ printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ }
+ }
+ printf( "**********\n#");
+ fprintf(ficresp, "**********\n#");
+ fprintf(ficresphtm, "**********
\n");
+ fprintf(ficresphtmfr, "**********
\n");
+ fprintf(ficlog, "**********\n");
+ }
+ /*
+ Printing means of quantitative variables if any
+ */
+ for (z1=1; z1<= nqfveff; z1++) {
+ fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
+ fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
+ if(weightopt==1){
+ printf(" Weighted mean and standard deviation of");
+ fprintf(ficlog," Weighted mean and standard deviation of");
+ fprintf(ficresphtmfr," Weighted mean and standard deviation of");
+ }
+ /* mu = \frac{w x}{\sum w}
+ var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
+ */
+ printf(" fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+ fprintf(ficlog," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+ fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); + } + /* for (z1=1; z1<= nqtveff; z1++) { */ + /* for(m=1;m<=lastpass;m++){ */ + /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f
\n", z1, m, meanqt[m][z1]); */ + /* } */ + /* } */ + + fprintf(ficresphtm,"
| Age | Prev(%d) | N(%d) | N | ",i,i); + } + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n"); + fprintf(ficresphtm, "\n"); + + /* Header of frequency table by age */ + fprintf(ficresphtmfr,"
|---|
| Age | "); + for(s2=-1; s2 <=nlstate+ndeath; s2++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(s2!=0 && m!=0) + fprintf(ficresphtmfr,"%d%d | ",s2,m); + } + } + fprintf(ficresphtmfr, "\n"); + + /* For each age */ + for(iage=iagemin; iage <= iagemax+3; iage++){ + fprintf(ficresphtm,"||||||||
|---|---|---|---|---|---|---|---|---|---|
| 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(s1=1; s1 <=nlstate ; s1++){ + for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++) + pp[s1] += freq[s1][m][iage]; + } + for(s1=1; s1 <=nlstate ; s1++){ + for(m=-1, pos=0; m <=0 ; m++) + pos += freq[s1][m][iage]; + if(pp[s1]>=1.e-10){ + if(first==1){ + printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]); + } + fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]); + }else{ + if(first==1) + printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1); + fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1); + } + } + + for(s1=1; s1 <=nlstate ; s1++){ + /* posprop[s1]=0; */ + for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */ + pp[s1] += freq[s1][m][iage]; + } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */ + + for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){ + pos += pp[s1]; /* pos is the total number of transitions until this age */ + posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state + from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state + from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + } + + /* Writing ficresp */ + if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + if( iage <= iagemax){ + fprintf(ficresp," %d",iage); + } + }else if( nj==2){ + if( iage <= iagemax){ + fprintf(ficresp," %d",iage); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + } + } + for(s1=1; s1 <=nlstate ; s1++){ + if(pos>=1.e-5){ + if(first==1) + printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos); + fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos); + }else{ + if(first==1) + printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1); + fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1); + } + if( iage <= iagemax){ + if(pos>=1.e-5){ + if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + }else if( nj==2){ + fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + } + fprintf(ficresphtm,"%d | %.5f | %.0f | %.0f | ",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + /*probs[iage][s1][j1]= pp[s1]/pos;*/ + /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/ + } else{ + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta); + fprintf(ficresphtm,"%d | NaNq | %.0f | %.0f | ",iage, prop[s1][iage],pospropta); + } + } + pospropt[s1] +=posprop[s1]; + } /* end loop s1 */ + /* pospropt=0.; */ + for(s1=-1; s1 <=nlstate+ndeath; s1++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(freq[s1][m][iage] !=0 ) { /* minimizing output */ + if(first==1){ + printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); + } + /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */ + fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]); + } + if(s1!=0 && m!=0) + fprintf(ficresphtmfr,"%.0f | ",freq[s1][m][iage]); + } + } /* end loop s1 */ + posproptt=0.; + for(s1=1; s1 <=nlstate; s1++){ + posproptt += pospropt[s1]; + } + fprintf(ficresphtmfr,"
| Tot | "); + for(s1=1; s1 <=nlstate ; s1++){ + if(posproptt < 1.e-5){ + fprintf(ficresphtm,"Nanq | %.0f | %.0f | ",pospropt[s1],posproptt); + }else{ + fprintf(ficresphtm,"%.5f | %.0f | %.0f | ",pospropt[s1]/posproptt,pospropt[s1],posproptt); + } + } + fprintf(ficresphtm,"
This combination (%d) is not valid and no result will be produced
",j1); + fprintf(ficresphtmfr,"\nThis combination (%d) is not valid and no result will be produced
",j1); + fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1); + printf("# This combination (%d) is not valid and no result will be produced\n",j1); + invalidvarcomb[j1]=1; + }else{ + fprintf(ficresphtm,"\nThis combination (%d) is valid and result will be produced.
",j1); + invalidvarcomb[j1]=0; + } + fprintf(ficresphtmfr,"\n"); + fprintf(ficlog,"\n"); + if(j!=0){ + printf("#Freqsummary: Starting values for combination j1=%d:\n", j1); + for(i=1,s1=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */ + if(jj==1){ /* Constant case (in fact cste + age) */ + if(j1==1){ /* All dummy covariates to zero */ + freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */ + freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */ + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3])); + fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]); + } + }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */ + for(iage=iagemin; iage <= iagemax+3; iage++){ + x[iage]= (double)iage; + y[iage]= log(freq[i][k][iage]/freq[i][i][iage]); + /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */ + } + /* Some are not finite, but linreg will ignore these ages */ + no=0; + linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */ + pstart[s1]=b; + pstart[s1-1]=a; + }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj) && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ + printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]); + printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]); + pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])); + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4])); + }else{ /* Other cases, like quantitative fixed or varying covariates */ + ; + } + /* printf("%12.7f )", param[i][jj][k]); */ + /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */ + s1++; + } /* end jj */ + } /* end k!= i */ + } /* end k */ + } /* end i, s1 */ + } /* end j !=0 */ + } /* end selected combination of covariate j1 */ + if(j==0){ /* We can estimate starting values from the occurences in each case */ + printf("#Freqsummary: Starting values for the constants:\n"); + fprintf(ficlog,"\n"); + for(i=1,s1=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(jj=1; jj <=ncovmodel; jj++){ + pstart[s1]=p[s1]; /* Setting pstart to p values by default */ + if(jj==1){ /* Age has to be done */ + pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]); + printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + } + /* printf("%12.7f )", param[i][jj][k]); */ + /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */ + s1++; + } + printf("\n"); + fprintf(ficlog,"\n"); + } + } + } /* end of state i */ + printf("#Freqsummary\n"); + fprintf(ficlog,"\n"); + for(s1=-1; s1 <=nlstate+ndeath; s1++){ + for(s2=-1; s2 <=nlstate+ndeath; s2++){ + /* param[i]|j][k]= freq[s1][s2][iagemax+3] */ + printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); + fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); + /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */ + /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */ + /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */ + /* } */ + } + } /* end loop s1 */ + + printf("\n"); + fprintf(ficlog,"\n"); + } /* end j=0 */ + } /* end j */ + + if(mle == -2){ /* We want to use these values as starting values */ + for(i=1, jk=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath; j++){ + if(j!=i){ + /*ca[0]= k+'a'-1;ca[1]='\0';*/ + printf("%1d%1d",i,j); + fprintf(ficparo,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + /* printf(" %lf",param[i][j][k]); */ + /* fprintf(ficparo," %lf",param[i][j][k]); */ + p[jk]=pstart[jk]; + printf(" %f ",pstart[jk]); + fprintf(ficparo," %f ",pstart[jk]); + jk++; + } + printf("\n"); + fprintf(ficparo,"\n"); + } + } + } + } /* end mle=-2 */ + dateintmean=dateintsum/k2cpt; + date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); + + fclose(ficresp); + fclose(ficresphtm); + fclose(ficresphtmfr); + free_vector(idq,1,nqfveff); + free_vector(meanq,1,nqfveff); + free_vector(stdq,1,nqfveff); + free_matrix(meanqt,1,lastpass,1,nqtveff); + free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_vector(pospropt,1,nlstate); + free_vector(posprop,1,nlstate); + free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_vector(pp,1,nlstate); + /* End of freqsummary */ +} + +/* Simple linear regression */ +int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) { + + /* y=a+bx regression */ + double sumx = 0.0; /* sum of x */ + double sumx2 = 0.0; /* sum of x**2 */ + double sumxy = 0.0; /* sum of x * y */ + double sumy = 0.0; /* sum of y */ + double sumy2 = 0.0; /* sum of y**2 */ + double sume2 = 0.0; /* sum of square or residuals */ + double yhat; + + double denom=0; + int i; + int ne=*no; + + for ( i=ifi, ne=0;i<=ila;i++) { + if(!isfinite(x[i]) || !isfinite(y[i])){ + /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */ + continue; + } + ne=ne+1; + sumx += x[i]; + sumx2 += x[i]*x[i]; + sumxy += x[i] * y[i]; + sumy += y[i]; + sumy2 += y[i]*y[i]; + denom = (ne * sumx2 - sumx*sumx); + /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */ + } + + denom = (ne * sumx2 - sumx*sumx); + if (denom == 0) { + // vertical, slope m is infinity + *b = INFINITY; + *a = 0; + if (r) *r = 0; + return 1; + } + + *b = (ne * sumxy - sumx * sumy) / denom; + *a = (sumy * sumx2 - sumx * sumxy) / denom; + if (r!=NULL) { + *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */ + sqrt((sumx2 - sumx*sumx/ne) * + (sumy2 - sumy*sumy/ne)); + } + *no=ne; + for ( i=ifi, ne=0;i<=ila;i++) { + if(!isfinite(x[i]) || !isfinite(y[i])){ + /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */ + continue; + } + ne=ne+1; + yhat = y[i] - *a -*b* x[i]; + sume2 += yhat * yhat ; + + denom = (ne * sumx2 - sumx*sumx); + /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */ + } + *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne)); + *sa= *sb * sqrt(sumx2/ne); + + return 0; +} + +/************ 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. + */ + + int i, m, jk, j1, bool, z1,j, iv; + 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+4+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=0; + 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+4+AGEMARGE; iage++) + prop[i][iage]=0.0; + printf("Prevalence combination of varying and fixed dummies %d\n",j1); + /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */ + fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1); + + for (i=1; i<=imx; i++) { /* Each individual */ + bool=1; + /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */ + for(mi=1; miComputing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)
%s
\n",digitp); + + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + pstamp(ficresvij); + fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); + if(popbased==1) + fprintf(ficresvij,"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(ficresvij,"the age specific period (stable) prevalences in each health state \n"); + fprintf(ficresvij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++) + fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); + fprintf(ficresvij,"\n"); + + xp=vector(1,npar); + dnewm=matrix(1,nlstate,1,npar); + doldm=matrix(1,nlstate,1,nlstate); + dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar); + doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + + gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath); + gpp=vector(nlstate+1,nlstate+ndeath); + gmp=vector(nlstate+1,nlstate+ndeath); + trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ + + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelim. + Look at function hpijx to understand why because of memory size limitations, + we decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed every two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ + agelim = AGESUP; + for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ + nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate); + gp=matrix(0,nhstepm,1,nlstate); + gm=matrix(0,nhstepm,1,nlstate); + + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ + xp[i] = x[i] + (i==theta ?delti[theta]:0); + } + /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and + * returns into prlim . + */ + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres); + + /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */ + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h. + */ + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */ + /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability + * at horizon h in state j including mortality. + */ + for(j=1; j<= nlstate; j++){ + for(h=0; h<=nhstepm; h++){ + for(i=1, gp[h][j]=0.;i<=nlstate;i++) + gp[h][j] += prlim[i][i]*p3mat[i][j][h]; + } + } + /* Next for computing shifted+ probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 . + */ + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gpp[j]=0.; i<= nlstate; i++) + gpp[j] += prlim[i][i]*p3mat[i][j][1]; + } + + /* Again with minus shift */ + + for(i=1; i<=npar; i++) /* Computes gradient x - delta */ + xp[i] = x[i] - (i==theta ?delti[theta]:0); + + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); + + for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */ + for(h=0; h<=nhstepm; h++){ + for(i=1, gm[h][j]=0.;i<=nlstate;i++) + gm[h][j] += prlim[i][i]*p3mat[i][j][h]; + } + } + /* This for computing probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.; i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end shifting computations */ + + /**< Computing gradient matrix at horizon h + */ + for(j=1; j<= nlstate; j++) /* vareij */ + for(h=0; h<=nhstepm; h++){ + gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; + } + /**< Gradient of overall mortality p.3 (or p.j) + */ + for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */ + gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; + } + + } /* End theta */ + + /* We got the gradient matrix for each theta and state j */ + trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ + + for(h=0; h<=nhstepm; h++) /* veij */ + for(j=1; j<=nlstate;j++) + for(theta=1; theta <=npar; theta++) + trgradg[h][j][theta]=gradg[h][theta][j]; + + for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ + for(theta=1; theta <=npar; theta++) + trgradgp[j][theta]=gradgp[theta][j]; + /**< as well as its transposed matrix + */ + + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ + for(i=1;i<=nlstate;i++) + for(j=1;j<=nlstate;j++) + vareij[i][j][(int)age] =0.; + + /* Computing trgradg by matcov by gradg at age and summing over h + * and k (nhstepm) formula 15 of article + * Lievre-Brouard-Heathcote + */ + + for(h=0;h<=nhstepm;h++){ + for(k=0;k<=nhstepm;k++){ + matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]); + for(i=1;i<=nlstate;i++) + for(j=1;j<=nlstate;j++) + vareij[i][j][(int)age] += doldm[i][j]*hf*hf; + } + } + + /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of + * p.j overall mortality formula 49 but computed directly because + * we compute the grad (wix pijx) instead of grad (pijx),even if + * wix is independent of theta. + */ + matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); + matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); + for(j=nlstate+1;j<=nlstate+ndeath;j++) + for(i=nlstate+1;i<=nlstate+ndeath;i++) + varppt[j][i]=doldmp[j][i]; + /* end ppptj */ + /* x centered again */ + + prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres); + + if (popbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][ij]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][ij]; + } + } + + /* This for computing probability of death (h=1 means + computed over hstepm (estepm) matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ + hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres); + for(j=nlstate+1;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.;i<= nlstate; i++) + gmp[j] += prlim[i][i]*p3mat[i][j][1]; + } + /* end probability of death */ + + fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j])); + for(i=1; i<=nlstate;i++){ + fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); + } + } + fprintf(ficresprobmorprev,"\n"); + + fprintf(ficresvij,"%.0f ",age ); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++){ + fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); + } + fprintf(ficresvij,"\n"); + free_matrix(gp,0,nhstepm,1,nlstate); + free_matrix(gm,0,nhstepm,1,nlstate); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate); + free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar); + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } /* End age */ + free_vector(gpp,nlstate+1,nlstate+ndeath); + free_vector(gmp,nlstate+1,nlstate+ndeath); + free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); + free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ + /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */ + fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480"); + /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ + fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); + fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); + /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ + /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ + /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ + fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); + fprintf(fichtm,"\n
File (multiple files are possible if covariates are present): %s\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); + fprintf(fichtm,"\n
Probability is computed over estepm=%d months.
![](\"%s%s.svg\")
\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); + /* fprintf(fichtm,"\n
Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year
![](\"varmuptjgr%s%s.svg\")
\n", stepm,YEARM,digitp,digit); + */ + /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */ + fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit); + + free_vector(xp,1,npar); + free_matrix(doldm,1,nlstate,1,nlstate); + free_matrix(dnewm,1,nlstate,1,npar); + free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); + free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ + fclose(ficresprobmorprev); + fflush(ficgp); + fflush(fichtm); + } /* end varevsij */ + +/************ Variance of prevlim ******************/ + void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres) { - fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); -} + /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ -/************ Frequencies ********************/ -void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[]) -{ /* Some frequencies */ - - int i, m, jk, k1,i1, j1, bool, z1,z2,j; - int first; - double ***freq; /* Frequencies */ - double *pp, **prop; - double pos,posprop, k2, dateintsum=0,k2cpt=0; - char fileresp[FILENAMELENGTH]; - - pp=vector(1,nlstate); - prop=matrix(1,nlstate,iagemin,iagemax+3); - strcpy(fileresp,"p"); - strcat(fileresp,fileres); - if((ficresp=fopen(fileresp,"w"))==NULL) { - printf("Problem with prevalence resultfile: %s\n", fileresp); - fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); - exit(0); - } - freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); - j1=0; + double **dnewmpar,**doldm; + int i, j, nhstepm, hstepm; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double **mgm, **mgp; + double age,agelim; + int theta; - j=cptcoveff; - if (cptcovn<1) {j=1;ncodemax[1]=1;} - - first=1; + pstamp(ficresvpl); + fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n"); + fprintf(ficresvpl,"# Age "); + if(nresult >=1) + fprintf(ficresvpl," Result# "); + for(i=1; i<=nlstate;i++) + fprintf(ficresvpl," %1d-%1d",i,i); + fprintf(ficresvpl,"\n"); - for(k1=1; k1<=j;k1++){ - for(i1=1; i1<=ncodemax[k1];i1++){ - j1++; - /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); - scanf("%d", i);*/ - for (i=-5; i<=nlstate+ndeath; i++) - for (jk=-5; jk<=nlstate+ndeath; jk++) - for(m=iagemin; m <= iagemax+3; m++) - freq[i][jk][m]=0; + xp=vector(1,npar); + dnewmpar=matrix(1,nlstate,1,npar); + doldm=matrix(1,nlstate,1,nlstate); + + hstepm=1*YEARM; /* Every year of age */ + hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ + agelim = AGESUP; + for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ + nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + if (stepm >= YEARM) hstepm=1; + nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ + gradg=matrix(1,npar,1,nlstate); + mgp=matrix(1,npar,1,nlstate); + mgm=matrix(1,npar,1,nlstate); + gp=vector(1,nlstate); + gm=vector(1,nlstate); - for (i=1; i<=nlstate; i++) - for(m=iagemin; m <= iagemax+3; m++) - prop[i][m]=0; - - dateintsum=0; - k2cpt=0; - for (i=1; i<=imx; i++) { - bool=1; - if (cptcovn>0) { - for (z1=1; z1<=cptcoveff; z1++) - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) - bool=0; - } - if (bool==1){ - for(m=firstpass; m<=lastpass; m++){ - k2=anint[m][i]+(mint[m][i]/12.); - /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ - if(agev[m][i]==0) agev[m][i]=iagemax+1; - if(agev[m][i]==1) agev[m][i]=iagemax+2; - if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; - if (m
Computing and drawing one step probabilities with their confidence intervals
Matrix of variance-covariance of one-step probabilities (drawings)
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. File %s\n\n
Matrix of variance-covariance of pairs of step probabilities
\n",optionfilehtmcov, optionfilehtmcov); + fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p\n"); + 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.
\ + Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\ + 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 each valid combination of covariates or only once*/ + for(nres=1;nres <=1; nres++){ /* For each resultline */ + /* for(nres=1;nres <=nresult; nres++){ /\* For each resultline *\/ */ + 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)]); */ + for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "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,"\n
Combination (%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)]; */ + for (k=1; k<=nsd;k++) { /* For single dummy covariates only */ + /* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */ + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[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;*/ + } + /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */ + /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */ + /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ + for (k=1; k<=cptcovage;k++){ /* For product with age */ + if(Dummy[Tage[k]]==2){ /* dummy with age */ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,k)]*cov[2]; + /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */ + } else if(Dummy[Tage[k]]==3){ /* quantitative with age */ + printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]); + exit(1); + /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; *\/ */ + /* cov[++k1]=Tqresult[nres][k]; */ + } + /* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */ + } + for (k=1; k<=cptcovprod;k++){/* For product without age */ + if(Dummy[Tvard[k][1]==0]){ + if(Dummy[Tvard[k][2]==0]){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * nbcode[Tvard[k][2]][codtabm(j1,k)]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + }else{ /* Should we use the mean of the quantitative variables? */ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * Tqresult[nres][k]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */ + } + }else{ + if(Dummy[Tvard[k][2]==0]){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,k)] * Tqinvresult[nres][Tvard[k][1]]; + /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */ + }else{ + cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; + /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */ + } + } + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + } +/* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/ + 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,"\nProbability 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); */
+ }
+
+ /* Eigen vectors */
+ if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
+ printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+ fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+ v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
+ }else
+ 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");
+
+ jj1=0;
+
+ fprintf(fichtm," \n ");
+
+ fprintf(fichtm," ");
- for (age=bage; age<=fage; age ++){
- nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
- /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- /* if (stepm >= YEARM) hstepm=1;*/
- nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
+ jj1=0;
- /* If stepm=6 months */
- /* Computed by stepm unit matrices, product of hstepma matrices, stored
- in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-
- hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
-
- printf("%d|",(int)age);fflush(stdout);
- fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-
- /* Computing expectancies */
- 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] += (p3mat[i][j][h]+p3mat[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]);*/
+ fprintf(fichtm," \n ");
+
+ fprintf(fichtm," ");
-
- m=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++;
- if (cptcovn > 0) {
- fprintf(fichtm," ");
+ fprintf(fichtm,"\nAge l The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\nParameters, 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",optionfilehtmcov);
+ fprintf(fichtm,"\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(fabs(lc1)),v12,sqrt(fabs(lc2)), \
+ mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
+ }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(fabs(lc2)), \
+ mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(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 nres */
+ } /* 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);
}
-/*********** Tricode ****************************/
-void tricode(int *Tvar, int **nbcode, int imx)
-{
-
- int Ndum[20],ij=1, k, j, i, maxncov=19;
- int cptcode=0;
- cptcoveff=0;
-
- for (k=0; k
", model); */
+ fprintf(fichtm,"Result files (first order: no variance)
\n");
+ fprintf(fichtm,"
\n",
+ jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
+ fprintf(fichtm,"
\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
+ fprintf(fichtm,"\
+ - Estimated transition probabilities over %d (stepm) months: %s
\n ",
+ stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
+ fprintf(fichtm,"\
+ - Estimated back transition probabilities over %d (stepm) months: %s
\n ",
+ stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
+ fprintf(fichtm,"\
+ - Period (forward) prevalence in each health state: %s
\n",
+ subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
+ fprintf(fichtm,"\
+ - Backward prevalence in each health state: %s
\n",
+ subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
+ fprintf(fichtm,"\
+ - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+ %s
\n",
+ estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
+ if(prevfcast==1){
+ fprintf(fichtm,"\
+ - Prevalence projections by age and states: \
+ %s
\n
");
- pstamp(ficreseij);
- fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
- fprintf(ficreseij,"# Age");
- for(i=1; i<=nlstate;i++){
- for(j=1; j<=nlstate;j++){
- fprintf(ficreseij," e%1d%1d ",i,j);
- }
- fprintf(ficreseij," e%1d. ",i);
- }
- fprintf(ficreseij,"\n");
+ fprintf(fichtm,"\
+\n");
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ jj1++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"\n
");
-/*********** Health Expectancies ****************/
+ jj1=0;
-void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
-{
- /* Health expectancies, no variances */
- int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
- int nhstepma, nstepma; /* Decreasing with age */
- double age, agelim, hf;
- double ***p3mat;
- double eip;
+ /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+ jj1++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"\n
************ Results for covariates");
+ for (cpt=1; cpt<=cptcoveff;cpt++){
+ fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+ printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+ /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+ /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
+ }
+
+ /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+ fprintf(fichtm," (model=%s) ************\n
",model);
+ 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: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: %s_%d-1-%d.svg
\
+![](\"%s_%d-1-%d.svg\")
",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
+ /* Pij */
+ fprintf(fichtm,"
\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s_%d-2-%d.svg
\
+![](\"%s_%d-2-%d.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
+ /* 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, \
+ 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-%d.svg
\
+![](\"%s_%d-3-%d.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
+ /* Survival functions (period) in state j */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
\
+![](\"%s_%d-%d-%d.svg\")
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+ }
+ /* State specific survival functions (period) */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Survival functions in state %d and in any other live state (total).\
+ And probability to be observed in various states (up to %d) being in state %d at different ages. \
+ %s_%d-%d-%d.svg
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+ }
+ /* Period (forward stable) prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. %s_%d-%d-%d.svg
\
+", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+ }
+ if(prevbcast==1){
+ /* Backward prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. %s_%d-%d-%d.svg
\
+", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
+ }
+ }
+ if(prevfcast==1){
+ /* Projection of prevalence up to period (forward 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 and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
+ fprintf(fichtm,"",
+ subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ }
+ }
+ if(prevbcast==1){
+ /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
+ from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
+ account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
+with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
+ fprintf(fichtm," ", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+ }
+ }
+
+ 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-%d.svg",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
+ fprintf(fichtm,"", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
+ }
+ /* } /\* end i1 *\/ */
+ }/* End k1 */
+ fprintf(fichtm," Result files (second order: variances)
\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).
\
+But because parameters are usually highly correlated (a higher incidence of disability \
+and a higher incidence of recovery can give very close observed transition) it might \
+be very useful to look not only at linear confidence intervals estimated from the \
+variances but at the covariance matrix. And instead of looking at the estimated coefficients \
+(parameters) of the logistic regression, it might be more meaningful to visualize the \
+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,"\
+ - Variance-covariance of one-step probabilities: %s
\n",
+ subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
+
+ fprintf(fichtm,"\
+ - Correlation matrix of one-step probabilities: %s
\n",
+ 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
\n",
+ estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
+ fprintf(fichtm,"\
+ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the forward (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,"\
+ - 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,"\
+ - Standard deviation of forward (period) prevalences: %s
\n",\
+ subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
-
- if(estepm < stepm){
- printf ("Problem %d lower than %d\n",estepm, stepm);
- }
- else hstepm=estepm;
- /* We compute the life expectancy from trapezoids spaced every estepm months
- * This is mainly to measure the difference between two models: for example
- * if stepm=24 months pijx are given only every 2 years and by summing them
- * we are calculating an estimate of the Life Expectancy assuming a linear
- * progression in between and thus overestimating or underestimating according
- * to the curvature of the survival function. If, for the same date, we
- * estimate the model with stepm=1 month, we can keep estepm to 24 months
- * to compare the new estimate of Life expectancy with the same linear
- * hypothesis. A more precise result, taking into account a more precise
- * curvature will be obtained if estepm is as small as stepm. */
+/* if(popforecast==1) fprintf(fichtm,"\n */
+/* - Prevalences forecasting: f%s
\n */
+/* - Population forecasting (if popforecast=1): pop%s
\n */
+/*
",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);
- /* For example we decided to compute the life expectancy with the smallest unit */
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- nhstepm is the number of hstepm from age to agelim
- nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
- and note for a fixed period like estepm months */
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- survival function given by stepm (the optimization length). Unfortunately it
- means that if the survival funtion is printed only each two years of age and if
- you sum them up and add 1 year (area under the trapezoids) you won't get the same
- results. So we changed our mind and took the option of the best precision.
- */
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+ m=pow(2,cptcoveff);
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- agelim=AGESUP;
- /* If stepm=6 months */
- /* Computed by stepm unit matrices, product of hstepm matrices, stored
- in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-
-/* nhstepm age range expressed in number of stepm */
- nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
- /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- /* if (stepm >= YEARM) hstepm=1;*/
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ fprintf(fichtm,"
");
+ fflush(fichtm);
+}
- double eip, vip;
+/******************* Gnuplot file **************/
+void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
- varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
- xp=vector(1,npar);
- xm=vector(1,npar);
- dnewm=matrix(1,nlstate*nlstate,1,npar);
- doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-
- pstamp(ficresstdeij);
- fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
- fprintf(ficresstdeij,"# Age");
- for(i=1; i<=nlstate;i++){
- for(j=1; j<=nlstate;j++)
- fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
- fprintf(ficresstdeij," e%1d. ",i);
- }
- fprintf(ficresstdeij,"\n");
+ char dirfileres[132],optfileres[132];
+ char gplotcondition[132], gplotlabel[132];
+ int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
+ int lv=0, vlv=0, kl=0;
+ int ng=0;
+ int vpopbased;
+ int ioffset; /* variable offset for columns */
+ int iyearc=1; /* variable column for year of projection */
+ int iagec=1; /* variable column for age of projection */
+ int nres=0; /* Index of resultline */
+ int istart=1; /* For starting graphs in projections */
- pstamp(ficrescveij);
- fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
- fprintf(ficrescveij,"# 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," %1d%1d,%1d%1d",i,j,i2,j2);
- }
- }
- fprintf(ficrescveij,"\n");
-
- if(estepm < stepm){
- printf ("Problem %d lower than %d\n",estepm, stepm);
- }
- else hstepm=estepm;
- /* We compute the life expectancy from trapezoids spaced every estepm months
- * This is mainly to measure the difference between two models: for example
- * if stepm=24 months pijx are given only every 2 years and by summing them
- * we are calculating an estimate of the Life Expectancy assuming a linear
- * progression in between and thus overestimating or underestimating according
- * to the curvature of the survival function. If, for the same date, we
- * estimate the model with stepm=1 month, we can keep estepm to 24 months
- * to compare the new estimate of Life expectancy with the same linear
- * hypothesis. A more precise result, taking into account a more precise
- * curvature will be obtained if estepm is as small as stepm. */
+/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+/* printf("Problem with file %s",optionfilegnuplot); */
+/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+/* } */
- /* For example we decided to compute the life expectancy with the smallest unit */
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- nhstepm is the number of hstepm from age to agelim
- nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
- and note for a fixed period like estepm months */
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- survival function given by stepm (the optimization length). Unfortunately it
- means that if the survival funtion is printed only each two years of age and if
- you sum them up and add 1 year (area under the trapezoids) you won't get the same
- results. So we changed our mind and took the option of the best precision.
- */
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+ /*#ifdef windows */
+ fprintf(ficgp,"cd \"%s\" \n",pathc);
+ /*#endif */
+ m=pow(2,cptcoveff);
- /* If stepm=6 months */
- /* nhstepm age range expressed in number of stepm */
- agelim=AGESUP;
- nstepm=(int) rint((agelim-bage)*YEARM/stepm);
- /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- /* if (stepm >= YEARM) hstepm=1;*/
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-
- p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
- trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
- gp=matrix(0,nhstepm,1,nlstate*nlstate);
- gm=matrix(0,nhstepm,1,nlstate*nlstate);
+ /* diagram of the model */
+ fprintf(ficgp,"\n#Diagram of the model \n");
+ fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
+ fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
+ fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+
+ fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+ fprintf(ficgp,"\n#show arrow\nunset label\n");
+ fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+ fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
+ fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
+ fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
+ fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
+
+ /* Contribution to likelihood */
+ /* Plot the probability implied in the likelihood */
+ fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
+ fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
+ /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
+ fprintf(ficgp,"\nset ter pngcairo size 640, 480");
+/* nice for mle=4 plot by number of matrix products.
+ replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
+/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
+ /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
+ fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
+ fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
+ fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
+ fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
+ for (i=1; i<= nlstate ; i ++) {
+ fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
+ fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
+ fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
+ for (j=2; j<= nlstate+ndeath ; j ++) {
+ fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
+ }
+ fprintf(ficgp,";\nset out; unset ylabel;\n");
+ }
+ /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
+ /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
+ /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
+ fprintf(ficgp,"\nset out;unset log\n");
+ /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
- for (age=bage; age<=fage; age ++){
- nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
- /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- /* if (stepm >= YEARM) hstepm=1;*/
- nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
+ strcpy(dirfileres,optionfilefiname);
+ strcpy(optfileres,"vpl");
+ /* 1eme*/
+ for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
+ for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ /* We are interested in selected combination by the resultline */
+ /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
+ fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
+ strcpy(gplotlabel,"(");
+ for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
+ lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
+ /* 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 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 */
+ /* printf(" V%d=%d ",Tvaraff[k],vlv); */
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ /* printf("\n#\n"); */
+ fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ /*k1=k1-1;*/ /* To be checked */
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
+
+ fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
+ fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
+ /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
+ fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+ /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
+ /* k1-1 error should be nres-1*/
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
+
+ fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
+ if(cptcoveff ==0){
+ fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
+ }else{
+ kl=0;
+ for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
+ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+ /* 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];
+ 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):($5==2000? 3:2) t 'p.1' with line lc variable*/
+ if(k==cptcoveff){
+ fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+ 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
+ }else{
+ fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+ kl++;
+ }
+ } /* end covariate */
+ } /* end if no covariate */
- /* If stepm=6 months */
- /* Computed by stepm unit matrices, product of hstepma matrices, stored
- in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
+ if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+ /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+ fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
+ if(cptcoveff ==0){
+ fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
+ }else{
+ kl=0;
+ for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
+ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+ /* 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];
+ 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):($5==2000? 3:2) t 'p.1' with line lc variable*/
+ if(k==cptcoveff){
+ fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+ 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
+ }else{
+ fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+ kl++;
+ }
+ } /* end covariate */
+ } /* end if no covariate */
+ if(prevbcast == 1){
+ fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+ /* k1-1 error should be nres-1*/
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"\" w l lt 4");
+ } /* end if backprojcast */
+ } /* end if prevbcast */
+ /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+ fprintf(ficgp,"\nset out ;unset title;\n");
+ } /* nres */
+ } /* k1 */
+ } /* cpt */
- /* Computing Variances of health expectancies */
- /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
- 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);
- }
- 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.;
+ /*2 eme*/
+ for (k1=1; k1<= m ; k1 ++){
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
+ strcpy(gplotlabel,"(");
+ 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);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ /* for(k=1; k <= ncovds; k++){ */
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ 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,"E_"),k1,nres);
+ for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+ fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
+ if(vpopbased==0){
+ fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
+ }else
+ fprintf(ficgp,"\nreplot ");
+ for (i=1; i<= nlstate+1 ; i ++) {
+ k=2*i;
+ fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
+ for (j=1; j<= nlstate+1 ; j ++) {
+ if (j==i) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
+ else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+ fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+ for (j=1; j<= nlstate+1 ; j ++) {
+ if (j==i) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"\" w l lt 0,");
+ fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+ for (j=1; j<= nlstate+1 ; j ++) {
+ if (j==i) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+ else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+ } /* state */
+ } /* vpopbased */
+ fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
+ } /* end nres */
+ } /* k1 end 2 eme*/
+
+
+ /*3eme*/
+ for (k1=1; k1<= m ; k1 ++){
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+
+ for (cpt=1; cpt<= nlstate ; cpt ++) {
+ fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
+ strcpy(gplotlabel,"(");
+ 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);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ 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);
+ fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+ fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+ fprintf(ficgp,"set ter svg size 640, 480\n\
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
+ /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+
+ */
+ for (i=1; i< nlstate ; i ++) {
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
+ /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+
+ }
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
+ }
+ fprintf(ficgp,"\nunset label;\n");
+ } /* end nres */
+ } /* end kl 3eme */
+
+ /* 4eme */
+ /* Survival functions (period) from state i in state j by initial state i */
+ for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
+ strcpy(gplotlabel,"(");
+ 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 ",Tvaraff[k],vlv);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ 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-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+ fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+set ter svg size 640, 480\nunset log y\nplot [%.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);
+ } /* nlstate */
+ fprintf(ficgp,"\nset out; unset label;\n");
+ } /* end cpt state*/
+ } /* end nres */
+ } /* end covariate k1 */
+
+/* 5eme */
+ /* Survival functions (period) from state i in state j by final state j */
+ for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
+ strcpy(gplotlabel,"(");
+ 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 ",Tvaraff[k],vlv);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ 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-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+ fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+set ter svg size 640, 480\nunset log y\nplot [%.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);
+ } /* 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);
}
+ fprintf(ficgp,"\nset out; unset label;\n");
+ } /* end cpt state*/
+ } /* end covariate */
+ } /* end nres */
+
+/* 6eme */
+ /* CV preval stable (period) for each covariate */
+ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
+ strcpy(gplotlabel,"(");
+ fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): '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);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
}
-
- 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];
+
+ fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+ fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
+ k=3; /* Offset */
+ for (i=1; i<= nlstate ; i ++){ /* State of origin */
+ if(i==1)
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+ else
+ fprintf(ficgp,", '' ");
+ l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
+ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+ for (j=2; j<= nlstate ; j ++)
+ fprintf(ficgp,"+$%d",k+l+j-1);
+ fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+ } /* nlstate */
+ fprintf(ficgp,"\nset out; unset label;\n");
+ } /* end cpt state*/
+ } /* end covariate */
+
+
+/* 7eme */
+ if(prevbcast == 1){
+ /* CV backward prevalence for each covariate */
+ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
+ strcpy(gplotlabel,"(");
+ fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' 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);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
}
- }/* 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(ij=1;ij<=nlstate*nlstate;ij++)
- for(ji=1;ji<=nlstate*nlstate;ji++)
- 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++){
- 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;
+
+ fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
+ fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
+ k=3; /* Offset */
+ for (i=1; i<= nlstate ; i ++){ /* State of arrival */
+ if(i==1)
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+ else
+ fprintf(ficgp,", '' ");
+ /* l=(nlstate+ndeath)*(i-1)+1; */
+ l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
+ /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a veÌrifier *\/ */
+ /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a veÌrifier *\/ */
+ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
+ /* 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",cpt,i);
+ } /* nlstate */
+ fprintf(ficgp,"\nset out; unset label;\n");
+ } /* end cpt state*/
+ } /* end covariate */
+ } /* End if prevbcast */
+
+ /* 8eme */
+ if(prevfcast==1){
+ /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
+
+ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+ strcpy(gplotlabel,"(");
+ fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
+ for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
+ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+ /* 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);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ 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-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
+
+ /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
+ istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+ /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+ for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
+ /*# 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 */
+ /*# 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 */
+ if(i==istart){
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
+ }else{
+ fprintf(ficgp,",\\\n '' ");
+ }
+ if(cptcoveff ==0){ /* No covariate */
+ ioffset=2; /* Age is in 2 */
+ /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
+ /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
+ fprintf(ficgp," u %d:(", ioffset);
+ if(i==nlstate+1){
+ fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+ fprintf(ficgp,",\\\n '' ");
+ fprintf(ficgp," u %d:(",ioffset);
+ fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
+ offyear, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
+ }else
+ fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+ }else{ /* more than 2 covariates */
+ ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
+ /*# 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 */
+ iyearc=ioffset-1;
+ iagec=ioffset;
+ fprintf(ficgp," u %d:(",ioffset);
+ kl=0;
+ 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]; /* Value of the modality of Tvaraff[k] */
+ kl++;
+ sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+ kl++;
+ if(k ");
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ jj1++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"\n
");
- }
+ jj1=0;
- fprintf(ficreseij,"%3.0f",age );
- for(i=1; i<=nlstate;i++){
- eip=0;
- for(j=1; j<=nlstate;j++){
- eip +=eij[i][j][(int)age];
- fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ for(k1=1; k1<=m;k1++){
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+ jj1++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"\n
************ Results for covariates");
+ for (cpt=1; cpt<=cptcoveff;cpt++){ /**< cptcoveff number of variables */
+ fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
+ printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+ /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}
- fprintf(ficreseij,"%9.4f", eip );
- }
- fprintf(ficreseij,"\n");
-
- }
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- printf("\n");
- fprintf(ficlog,"\n");
-
-}
-void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+ fprintf(fichtm," (model=%s) ************\n
",model);
-{
- /* Covariances of health expectancies eij and of total life expectancies according
- 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 */
- double age, agelim, hf;
- double ***p3matp, ***p3matm, ***varhe;
- double **dnewm,**doldm;
- double *xp, *xm;
- double **gp, **gm;
- double ***gradg, ***trgradg;
- int theta;
+ 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 with mov_average=%d) and period (incidence based) \
+prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d-%d.svg",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s)\n
",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+ fprintf(fichtm,"",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
+ }
+ fprintf(fichtm,"\n
- Total life expectancy by age and \
+health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
+true period expectancies (those weighted with period prevalences are also\
+ drawn in addition to the population based expectancies computed using\
+ observed and cahotic prevalences: %s_%d-%d.svg",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
+ fprintf(fichtm," (data from text file %s.txt) \n
",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
+ fprintf(fichtm,"![](\"%s_%d-%d.svg\")
",subdirf2(optionfilefiname,"E_"),k1,nres);
+ /* } /\* end i1 *\/ */
+ }/* End k1 */
+ }/* End nres */
+ fprintf(fichtm," Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)
%s
\n",digitp);
-/* } */
- varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- pstamp(ficresvij);
- fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
- if(popbased==1)
- fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
- else
- fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
- fprintf(ficresvij,"# Age");
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate;j++)
- fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
- fprintf(ficresvij,"\n");
+ strcpy(fileresf,"F_");
+ strcat(fileresf,fileresu);
+ if((ficresf=fopen(fileresf,"w"))==NULL) {
+ printf("Problem with forecast resultfile: %s\n", fileresf);
+ fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+ }
+ printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
+ fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
- xp=vector(1,npar);
- dnewm=matrix(1,nlstate,1,npar);
- doldm=matrix(1,nlstate,1,nlstate);
- dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
- doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ if (cptcoveff==0) ncodemax[cptcoveff]=1;
- gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
- gpp=vector(nlstate+1,nlstate+ndeath);
- gmp=vector(nlstate+1,nlstate+ndeath);
- trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-
+
+ stepsize=(int) (stepm+YEARM-1)/YEARM;
+ if (stepm<=12) stepsize=1;
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
- else hstepm=estepm;
- /* For example we decided to compute the life expectancy with the smallest unit */
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- nhstepm is the number of hstepm from age to agelim
- nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
- and note for a fixed period like k years */
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- survival function given by stepm (the optimization length). Unfortunately it
- means that if the survival funtion is printed every two years of age and if
- you sum them up and add 1 year (area under the trapezoids) you won't get the same
- results. So we changed our mind and took the option of the best precision.
- */
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
- agelim = AGESUP;
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
- nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
- gp=matrix(0,nhstepm,1,nlstate);
- gm=matrix(0,nhstepm,1,nlstate);
+ else{
+ hstepm=estepm;
+ }
+ if(estepm > stepm){ /* Yes every two year */
+ stepsize=2;
+ }
+ hstepm=hstepm/stepm;
+
+ /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
+ /* fractional in yp1 *\/ */
+ /* aintmean=yp; */
+ /* yp2=modf((yp1*12),&yp); */
+ /* mintmean=yp; */
+ /* yp1=modf((yp2*30.5),&yp); */
+ /* jintmean=yp; */
+ /* if(jintmean==0) jintmean=1; */
+ /* if(mintmean==0) mintmean=1; */
- for(theta=1; theta <=npar; theta++){
- for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
- xp[i] = x[i] + (i==theta ?delti[theta]:0);
- }
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- if (popbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][ij];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][ij];
- }
- }
+ /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
+ /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
+ /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
+ i1=pow(2,cptcoveff);
+ if (cptcovn < 1){i1=1;}
- for(j=1; j<= nlstate; j++){
- for(h=0; h<=nhstepm; h++){
- for(i=1, gp[h][j]=0.;i<=nlstate;i++)
- gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+ fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
+
+ fprintf(ficresf,"#****** Routine prevforecast **\n");
+
+/* if (h==(int)(YEARM*yearp)){ */
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ if(invalidvarcomb[k]){
+ printf("\nCombination (%d) projection ignored because no cases \n",k);
+ continue;
+ }
+ fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ fprintf(ficresf," yearproj age");
+ for(j=1; j<=nlstate+ndeath;j++){
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresf," p%d%d",i,j);
+ fprintf(ficresf," wp.%d",j);
+ }
+ for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
+ fprintf(ficresf,"\n");
+ fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
+ /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
+ for (agec=fage; agec>=(bage); agec--){
+ nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+ nhstepm = nhstepm/hstepm;
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ oldm=oldms;savm=savms;
+ /* We compute pii at age agec over nhstepm);*/
+ hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
+ /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+ for (h=0; h<=nhstepm; h++){
+ if (h*hstepm/YEARM*stepm ==yearp) {
+ break;
+ }
}
- }
- /* This for computing probability of death (h=1 means
- computed over hstepm matrices product = hstepm*stepm months)
- as a weighted average of prlim.
- */
- for(j=nlstate+1;j<=nlstate+ndeath;j++){
- for(i=1,gpp[j]=0.; i<= nlstate; i++)
- gpp[j] += prlim[i][i]*p3mat[i][j][1];
- }
- /* end probability of death */
+ fprintf(ficresf,"\n");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
+
+ for(j=1; j<=nlstate+ndeath;j++) {
+ ppij=0.;
+ for(i=1; i<=nlstate;i++) {
+ if (mobilav>=1)
+ ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
+ else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
+ ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+ }
+ fprintf(ficresf," %.3f", p3mat[i][j][h]);
+ } /* end i */
+ fprintf(ficresf," %.3f", ppij);
+ }/* end j */
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ } /* end agec */
+ /* diffyear=(int) anproj1+yearp-ageminpar-1; */
+ /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
+ } /* end yearp */
+ } /* end k */
+
+ fclose(ficresf);
+ printf("End of Computing forecasting \n");
+ fprintf(ficlog,"End of Computing forecasting\n");
+
+}
+
+/************** Back Forecasting ******************/
+ /* void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
+ void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
+ /* back1, year, month, day of starting backprojection
+ agemin, agemax range of age
+ dateprev1 dateprev2 range of dates during which prevalence is computed
+ anback2 year of end of backprojection (same day and month as back1).
+ prevacurrent and prev are prevalences.
+ */
+ int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
+ double agec; /* generic age */
+ double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
+ double *popeffectif,*popcount;
+ double ***p3mat;
+ /* double ***mobaverage; */
+ char fileresfb[FILENAMELENGTH];
+
+ agelim=AGEINF;
+ /* 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.
+ */
+ /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+ /* firstpass, lastpass, stepm, weightopt, model); */
+
+ /*Do we need to compute prevalence again?*/
+
+ /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+
+ strcpy(fileresfb,"FB_");
+ strcat(fileresfb,fileresu);
+ if((ficresfb=fopen(fileresfb,"w"))==NULL) {
+ printf("Problem with back forecast resultfile: %s\n", fileresfb);
+ fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
+ }
+ printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+ fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+
+ if (cptcoveff==0) ncodemax[cptcoveff]=1;
+
+
+ stepsize=(int) (stepm+YEARM-1)/YEARM;
+ if (stepm<=12) stepsize=1;
+ if(estepm < stepm){
+ printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
+ else{
+ hstepm=estepm;
+ }
+ if(estepm >= stepm){ /* Yes every two year */
+ stepsize=2;
+ }
+
+ hstepm=hstepm/stepm;
+ /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
+ /* fractional in yp1 *\/ */
+ /* aintmean=yp; */
+ /* yp2=modf((yp1*12),&yp); */
+ /* mintmean=yp; */
+ /* yp1=modf((yp2*30.5),&yp); */
+ /* jintmean=yp; */
+ /* if(jintmean==0) jintmean=1; */
+ /* if(mintmean==0) jintmean=1; */
+
+ i1=pow(2,cptcoveff);
+ if (cptcovn < 1){i1=1;}
+
+ fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
+ printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
+
+ fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
+
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ if(invalidvarcomb[k]){
+ printf("\nCombination (%d) projection ignored because no cases \n",k);
+ continue;
+ }
+ fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ fprintf(ficresfb," yearbproj age");
+ for(j=1; j<=nlstate+ndeath;j++){
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresfb," b%d%d",i,j);
+ fprintf(ficresfb," b.%d",j);
+ }
+ for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
+ /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
+ fprintf(ficresfb,"\n");
+ fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
+ /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
+ /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
+ for (agec=bage; agec<=fage; agec++){ /* testing */
+ /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
+ nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
+ nhstepm = nhstepm/hstepm;
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ oldm=oldms;savm=savms;
+ /* computes hbxij at age agec over 1 to nhstepm */
+ /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
+ hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
+ /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
+ /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+ /* printf(" agec=%.2f\n",agec);fflush(stdout); */
+ for (h=0; h<=nhstepm; h++){
+ if (h*hstepm/YEARM*stepm ==-yearp) {
+ break;
+ }
+ }
+ fprintf(ficresfb,"\n");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
+ for(i=1; i<=nlstate+ndeath;i++) {
+ ppij=0.;ppi=0.;
+ for(j=1; j<=nlstate;j++) {
+ /* if (mobilav==1) */
+ ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
+ ppi=ppi+prevacurrent[(int)agec][j][k];
+ /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
+ /* ppi=ppi+mobaverage[(int)agec][j][k]; */
+ /* else { */
+ /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
+ /* } */
+ fprintf(ficresfb," %.3f", p3mat[i][j][h]);
+ } /* end j */
+ if(ppi <0.99){
+ printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+ fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+ }
+ fprintf(ficresfb," %.3f", ppij);
+ }/* end j */
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ } /* end agec */
+ } /* end yearp */
+ } /* end k */
+
+ /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+
+ fclose(ficresfb);
+ printf("End of Computing Back forecasting \n");
+ fprintf(ficlog,"End of Computing Back forecasting\n");
+
+}
- for(i=1; i<=npar; i++) /* Computes gradient x - delta */
- xp[i] = x[i] - (i==theta ?delti[theta]:0);
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+/* Variance of prevalence limit: varprlim */
+ void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
+ /*------- Variance of forward period (stable) prevalence------*/
- if (popbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][ij];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][ij];
- }
- }
-
- for(j=1; j<= nlstate; j++){
- for(h=0; h<=nhstepm; h++){
- for(i=1, gm[h][j]=0.;i<=nlstate;i++)
- gm[h][j] += prlim[i][i]*p3mat[i][j][h];
- }
- }
- /* This for computing probability of death (h=1 means
- computed over hstepm matrices product = hstepm*stepm months)
- as a weighted average of prlim.
- */
- for(j=nlstate+1;j<=nlstate+ndeath;j++){
- for(i=1,gmp[j]=0.; i<= nlstate; i++)
- gmp[j] += prlim[i][i]*p3mat[i][j][1];
- }
- /* end probability of death */
-
- for(j=1; j<= nlstate; j++) /* vareij */
- for(h=0; h<=nhstepm; h++){
- gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
- }
-
- for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
- gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
- }
+ char fileresvpl[FILENAMELENGTH];
+ FILE *ficresvpl;
+ double **oldm, **savm;
+ double **varpl; /* Variances of prevalence limits by age */
+ int i1, k, nres, j ;
+
+ strcpy(fileresvpl,"VPL_");
+ strcat(fileresvpl,fileresu);
+ if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+ printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
+ exit(0);
+ }
+ printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+ fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+
+ /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+
+ i1=pow(2,cptcoveff);
+ if (cptcovn < 1){i1=1;}
- } /* End theta */
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ fprintf(ficresvpl,"\n#****** ");
+ printf("\n#****** ");
+ fprintf(ficlog,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficresvpl,"******\n");
+ printf("******\n");
+ fprintf(ficlog,"******\n");
+
+ varpl=matrix(1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
+ free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+ /*}*/
+ }
+
+ fclose(ficresvpl);
+ printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
+ fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
- trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+ }
+/* Variance of back prevalence: varbprlim */
+ void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
+ /*------- Variance of back (stable) prevalence------*/
+
+ char fileresvbl[FILENAMELENGTH];
+ FILE *ficresvbl;
+
+ double **oldm, **savm;
+ double **varbpl; /* Variances of back prevalence limits by age */
+ int i1, k, nres, j ;
+
+ strcpy(fileresvbl,"VBL_");
+ strcat(fileresvbl,fileresu);
+ if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
+ printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
+ exit(0);
+ }
+ printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
+ fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
+
+
+ i1=pow(2,cptcoveff);
+ if (cptcovn < 1){i1=1;}
+
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ fprintf(ficresvbl,"\n#****** ");
+ printf("\n#****** ");
+ fprintf(ficlog,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficresvbl,"******\n");
+ printf("******\n");
+ fprintf(ficlog,"******\n");
+
+ varbpl=matrix(1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+
+ varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
+ free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
+ /*}*/
+ }
+
+ fclose(ficresvbl);
+ printf("done variance-covariance of back prevalence\n");fflush(stdout);
+ fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
- for(h=0; h<=nhstepm; h++) /* veij */
- for(j=1; j<=nlstate;j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[h][j][theta]=gradg[h][theta][j];
+ } /* End of varbprlim */
- for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
- for(theta=1; theta <=npar; theta++)
- trgradgp[j][theta]=gradgp[theta][j];
+/************** Forecasting *****not tested NB*************/
+/* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
+/* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
+/* int *popage; */
+/* double calagedatem, agelim, kk1, kk2; */
+/* double *popeffectif,*popcount; */
+/* double ***p3mat,***tabpop,***tabpopprev; */
+/* /\* double ***mobaverage; *\/ */
+/* char filerespop[FILENAMELENGTH]; */
+
+/* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+/* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+/* agelim=AGESUP; */
+/* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
+
+/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+
+
+/* strcpy(filerespop,"POP_"); */
+/* strcat(filerespop,fileresu); */
+/* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
+/* printf("Problem with forecast resultfile: %s\n", filerespop); */
+/* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
+/* } */
+/* printf("Computing forecasting: result on file '%s' \n", filerespop); */
+/* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
- for(i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate;j++)
- vareij[i][j][(int)age] =0.;
+/* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
- for(h=0;h<=nhstepm;h++){
- for(k=0;k<=nhstepm;k++){
- matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
- for(i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate;j++)
- vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
- }
- }
+/* /\* if (mobilav!=0) { *\/ */
+/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+/* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
+/* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
+/* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
+/* /\* } *\/ */
+/* /\* } *\/ */
+
+/* stepsize=(int) (stepm+YEARM-1)/YEARM; */
+/* if (stepm<=12) stepsize=1; */
+
+/* agelim=AGESUP; */
+
+/* hstepm=1; */
+/* hstepm=hstepm/stepm; */
+
+/* if (popforecast==1) { */
+/* if((ficpop=fopen(popfile,"r"))==NULL) { */
+/* printf("Problem with population file : %s\n",popfile);exit(0); */
+/* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
+/* } */
+/* popage=ivector(0,AGESUP); */
+/* popeffectif=vector(0,AGESUP); */
+/* popcount=vector(0,AGESUP); */
+
+/* i=1; */
+/* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
+
+/* imx=i; */
+/* for (i=1; i
File (multiple files are possible if covariates are present): %s\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
- fprintf(fichtm,"\n
Probability is computed over estepm=%d months.
![](\"%s%s.png\")
\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
- /* fprintf(fichtm,"\n
Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year
![](\"varmuptjgr%s%s.png\")
\n", stepm,YEARM,digitp,digit);
-*/
-/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
- fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-
- free_vector(xp,1,npar);
- free_matrix(doldm,1,nlstate,1,nlstate);
- free_matrix(dnewm,1,nlstate,1,npar);
- free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
- free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- fclose(ficresprobmorprev);
- fflush(ficgp);
- fflush(fichtm);
-} /* end varevsij */
-
-/************ Variance of prevlim ******************/
-void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+int fileappend(FILE *fichier, char *optionfich)
{
- /* Variance of prevalence limit */
- /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- double **newm;
- double **dnewm,**doldm;
- int i, j, nhstepm, hstepm;
- int k, cptcode;
- double *xp;
- double *gp, *gm;
- double **gradg, **trgradg;
- double age,agelim;
- int theta;
-
- pstamp(ficresvpl);
- fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
- fprintf(ficresvpl,"# Age");
- for(i=1; i<=nlstate;i++)
- fprintf(ficresvpl," %1d-%1d",i,i);
- fprintf(ficresvpl,"\n");
+ if((fichier=fopen(optionfich,"a"))==NULL) {
+ printf("Problem with file: %s\n", optionfich);
+ fprintf(ficlog,"Problem with file: %s\n", optionfich);
+ return (0);
+ }
+ fflush(fichier);
+ return (1);
+}
- xp=vector(1,npar);
- dnewm=matrix(1,nlstate,1,npar);
- doldm=matrix(1,nlstate,1,nlstate);
-
- hstepm=1*YEARM; /* Every year of age */
- hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
- agelim = AGESUP;
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
- nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- if (stepm >= YEARM) hstepm=1;
- nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
- gradg=matrix(1,npar,1,nlstate);
- gp=vector(1,nlstate);
- gm=vector(1,nlstate);
- for(theta=1; theta <=npar; theta++){
- for(i=1; i<=npar; i++){ /* Computes gradient */
- xp[i] = x[i] + (i==theta ?delti[theta]:0);
- }
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- for(i=1;i<=nlstate;i++)
- gp[i] = prlim[i][i];
-
- for(i=1; i<=npar; i++) /* Computes gradient */
- xp[i] = x[i] - (i==theta ?delti[theta]:0);
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- for(i=1;i<=nlstate;i++)
- gm[i] = prlim[i][i];
+/**************** function prwizard **********************/
+void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
+{
- for(i=1;i<=nlstate;i++)
- gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
- } /* End theta */
+ /* Wizard to print covariance matrix template */
- trgradg =matrix(1,nlstate,1,npar);
+ char ca[32], cb[32];
+ int i,j, k, li, lj, lk, ll, jj, npar, itimes;
+ int numlinepar;
- for(j=1; j<=nlstate;j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[j][theta]=gradg[theta][j];
+ printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ for(i=1; i <=nlstate; i++){
+ jj=0;
+ for(j=1; j <=nlstate+ndeath; j++){
+ if(j==i) continue;
+ jj++;
+ /*ca[0]= k+'a'-1;ca[1]='\0';*/
+ printf("%1d%1d",i,j);
+ fprintf(ficparo,"%1d%1d",i,j);
+ for(k=1; k<=ncovmodel;k++){
+ /* printf(" %lf",param[i][j][k]); */
+ /* fprintf(ficparo," %lf",param[i][j][k]); */
+ printf(" 0.");
+ fprintf(ficparo," 0.");
+ }
+ printf("\n");
+ fprintf(ficparo,"\n");
+ }
+ }
+ printf("# Scales (for hessian or gradient estimation)\n");
+ fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+ npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+ for(i=1; i <=nlstate; i++){
+ jj=0;
+ for(j=1; j <=nlstate+ndeath; j++){
+ if(j==i) continue;
+ jj++;
+ fprintf(ficparo,"%1d%1d",i,j);
+ printf("%1d%1d",i,j);
+ fflush(stdout);
+ for(k=1; k<=ncovmodel;k++){
+ /* printf(" %le",delti3[i][j][k]); */
+ /* fprintf(ficparo," %le",delti3[i][j][k]); */
+ printf(" 0.");
+ fprintf(ficparo," 0.");
+ }
+ numlinepar++;
+ printf("\n");
+ fprintf(ficparo,"\n");
+ }
+ }
+ printf("# Covariance matrix\n");
+/* # 121 Var(a12)\n\ */
+/* # 122 Cov(b12,a12) Var(b12)\n\ */
+/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+ fflush(stdout);
+ fprintf(ficparo,"# Covariance matrix\n");
+ /* # 121 Var(a12)\n\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ /* # ...\n\ */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+
+ 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){
+ printf("#%1d%1d%d",i,j,k);
+ fprintf(ficparo,"#%1d%1d%d",i,j,k);
+ }else{
+ printf("%1d%1d%d",i,j,k);
+ fprintf(ficparo,"%1d%1d%d",i,j,k);
+ /* printf(" %.5le",matcov[i][j]); */
+ }
+ 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 Computing and drawing one step probabilities with their confidence intervals
Matrix of variance-covariance of pairs of step probabilities (drawings)
Matrix of variance-covariance of pairs of step probabilities
\n\
- file %s
\n",optionfilehtmcov);
- fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p
\n");
- 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.
\
- Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
- 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");
+#ifdef GSL
+/******************* Gompertz_f Likelihood ******************************/
+double gompertz_f(const gsl_vector *v, void *params)
+{
+ double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
+ double *x= (double *) v->data;
+ int i,n=0; /* n is the size of the sample */
- cov[1]=1;
- tj=cptcoveff;
- if (cptcovn<1) {tj=1;ncodemax[1]=1;}
- j1=0;
- for(t=1; t<=tj;t++){
- 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]][codtab[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]][codtab[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]][codtab[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]][codtab[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]][codtab[j1][z1]]);
- fprintf(ficresprobcor, "**********\n#");
- }
+ for (i=0;i<=imx-1 ; i++) {
+ sump=sump+weight[i];
+ /* sump=sump+1;*/
+ num=num+1;
+ }
+
+
+ /* for (i=0; i<=imx; i++)
+ if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+ printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+ for (i=1;i<=imx ; i++)
+ {
+ if (cens[i] == 1 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
- for (age=bage; age<=fage; age ++){
- cov[2]=age;
- for (k=1; k<=cptcovn;k++) {
- cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
- }
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
- for (k=1; k<=cptcovprod;k++)
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-
- 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(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);
- 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);
-
- 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=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++){
- 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 */
-
- /* Confidence intervalle of pij */
- /*
- fprintf(ficgp,"\nset noparametric;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);
- */
+ if (cens[i] == 0 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+ +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+ if (wav[i] > 1 ) { /* ??? */
+ LL=LL+A*weight[i];
+ /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+ }
+ }
- /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
- first1=1;
- 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.;
- /* 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,"\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 png small\nset size 0.65,0.65");
- fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\
- :\
-%s%d%1d%1d-%1d%1d.png, ",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.png\")
",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.png\"",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 \"%s%d%1d%1d-%1d%1d.png\";replot;",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);
+ /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+ printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+
+ return -2*LL*num/sump;
}
-
+#endif
/******************* Printing html file ***********/
-void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\
- int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
- int popforecast, int estepm ,\
- double jprev1, double mprev1,double anprev1, \
- double jprev2, double mprev2,double anprev2){
- int jj1, k1, i1, cpt;
-
- fprintf(fichtm,"");
- fprintf(fichtm,"Result files (first order: no variance)
\n \
- - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s
\n ",
- jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
- fprintf(fichtm,"\
- - Estimated transition probabilities over %d (stepm) months: %s
\n ",
- stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
- fprintf(fichtm,"\
- - Period (stable) prevalence in each health state: %s
\n",
- subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
- fprintf(fichtm,"\
- - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
- %s
\n",
- estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
- fprintf(fichtm,"\
- - Population projections by age and states: \
- %s
\n
");
-
-
- fprintf(fichtm,"\
-\n
************ Results for covariates");
- for (cpt=1; cpt<=cptcoveff;cpt++)
- fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
- fprintf(fichtm," ************\n
");
- }
- /* Pij */
- fprintf(fichtm,"
- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png
\
-![](\"%s%d1.png\")
",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
- /* Quasi-incidences */
- fprintf(fichtm,"
- Pij 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: %s%d2.png
\
-![](\"%s%d2.png\")
",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
- /* Period (stable) prevalence in each health state */
- for(cpt=1; cpt
\
-![](\"%s%d%d.png\")
",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),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 : %s%d%d.png
\
-",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
- }
- } /* end i1 */
- }/* End k1 */
- fprintf(fichtm," Result files (second order: variances)
\n\
- - Parameter file with estimated parameters and covariance matrix: %s
\n", rfileres,rfileres);
+ int imx, double p[],double **matcov,double agemortsup){
+ int i,k;
- fprintf(fichtm," - Variance of one-step probabilities: %s
\n",
- subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
- fprintf(fichtm,"\
- - Variance-covariance of one-step probabilities: %s
\n",
- subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+ fprintf(fichtm,"
");
- fprintf(fichtm,"\
- - Correlation matrix of one-step probabilities: %s Result files
\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):
");
+ fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year
",p[1],p[2],agegomp);
+ for (i=1;i<=2;i++)
+ fprintf(fichtm," p[%d] = %lf [%f ; %f]
\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+ fprintf(fichtm,"![](\"graphmort.svg\")
");
+ fprintf(fichtm,"
\n",
- subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
- fprintf(fichtm,"\
- - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \
- %s
\n
\n",
- estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
- 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(fileres,"v"),subdirf2(fileres,"v"));
- fprintf(fichtm,"\
- - Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors: %s
\n",
- subdirf2(fileres,"t"),subdirf2(fileres,"t"));
- fprintf(fichtm,"\
- - Standard deviation of period (stable) prevalences: %s
\n",\
- subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+fprintf(fichtm,"Life table
\n
");
-/* if(popforecast==1) fprintf(fichtm,"\n */
-/* - Prevalences forecasting: f%s
\n */
-/* - Population forecasting (if popforecast=1): pop%s
\n */
-/*
",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 .)
");
- fflush(fichtm);
+
+ fflush(fichtm);
}
/******************* Gnuplot file **************/
-void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
char dirfileres[132],optfileres[132];
- int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
- int ng;
-/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-/* printf("Problem with file %s",optionfilegnuplot); */
-/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-/* } */
-
- /*#ifdef windows */
- fprintf(ficgp,"cd \"%s\" \n",pathc);
- /*#endif */
- m=pow(2,cptcoveff);
-
- strcpy(dirfileres,optionfilefiname);
- strcpy(optfileres,"vpl");
- /* 1eme*/
- for (cpt=1; cpt<= nlstate ; cpt ++) {
- for (k1=1; k1<= m ; k1 ++) {
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
- fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
- fprintf(ficgp,"set xlabel \"Age\" \n\
-set ylabel \"Probability\" \n\
-set ter png small\n\
-set size 0.65,0.65\n\
-plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-
- for (i=1; i<= nlstate ; i ++) {
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
- for (i=1; i<= nlstate ; i ++) {
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
- for (i=1; i<= nlstate ; i ++) {
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
- }
- }
- /*2 eme*/
-
- for (k1=1; k1<= m ; k1 ++) {
- fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
- fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
-
- for (i=1; i<= nlstate+1 ; i ++) {
- k=2*i;
- fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
- for (j=1; j<= nlstate+1 ; j ++) {
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
- else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
- fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
- for (j=1; j<= nlstate+1 ; j ++) {
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"\" w l 0,");
- fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
- for (j=1; j<= nlstate+1 ; j ++) {
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
- else fprintf(ficgp,"\" t\"\" w l 0,");
- }
- }
-
- /*3eme*/
-
- for (k1=1; k1<= m ; k1 ++) {
- for (cpt=1; cpt<= nlstate ; cpt ++) {
- /* k=2+nlstate*(2*cpt-2); */
- k=2+(nlstate+1)*(cpt-1);
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
- fprintf(ficgp,"set ter png small\n\
-set size 0.65,0.65\n\
-plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
- /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
- for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
- for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-
- */
- for (i=1; i< nlstate ; i ++) {
- fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
- /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-
- }
- fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
- }
- }
-
- /* CV preval stable (period) */
- for (k1=1; k1<= m ; k1 ++) {
- for (cpt=1; cpt<=nlstate ; cpt ++) {
- k=3;
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-set ter png small\nset size 0.65,0.65\n\
-unset log y\n\
-plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-
- for (i=1; i< nlstate ; i ++)
- fprintf(ficgp,"+$%d",k+i+1);
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-
- l=3+(nlstate+ndeath)*cpt;
- fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
- for (i=1; i< nlstate ; i ++) {
- l=3+(nlstate+ndeath)*cpt;
- fprintf(ficgp,"+$%d",l+i+1);
- }
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
- }
- }
-
- /* proba elementaires */
- for(i=1,jk=1; i <=nlstate; i++){
- for(k=1; k <=(nlstate+ndeath); k++){
- if (k != i) {
- for(j=1; j <=ncovmodel; j++){
- fprintf(ficgp,"p%d=%f ",jk,p[jk]);
- jk++;
- fprintf(ficgp,"\n");
- }
- }
- }
- }
-
- for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
- for(jk=1; jk <=m; jk++) {
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
- if (ng==2)
- fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
- else
- fprintf(ficgp,"\nset title \"Probability\"\n");
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
- i=1;
- for(k2=1; k2<=nlstate; k2++) {
- k3=i;
- for(k=1; k<=(nlstate+ndeath); k++) {
- if (k != k2){
- if(ng==2)
- fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
- else
- fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
- ij=1;
- for(j=3; j <=ncovmodel; j++) {
- if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
- fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
- ij++;
- }
- else
- fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
- }
- fprintf(ficgp,")/(1");
-
- for(k1=1; k1 <=nlstate; k1++){
- fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
- ij=1;
- for(j=3; j <=ncovmodel; j++){
- if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
- fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
- ij++;
- }
- else
- fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
- }
- fprintf(ficgp,")");
- }
- fprintf(ficgp,") t \"p%d%d\" ", k2,k);
- if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
- i=i+ncovmodel;
- }
- } /* end k */
- } /* end k2 */
- } /* end jk */
- } /* end ng */
- fflush(ficgp);
-} /* end gnuplot */
-
-
-/*************** Moving average **************/
-int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-
- int i, cpt, cptcod;
- int modcovmax =1;
- int mobilavrange, mob;
- double age;
-
- modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
- a covariate has 2 modalities */
- if (cptcovn<1) modcovmax=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;
- return 0;
-}/* End movingaverage */
-
-
-/************** Forecasting ******************/
-prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
- /* proj1, year, month, day of starting projection
- agemin, agemax range of age
- dateprev1 dateprev2 range of dates during which prevalence is computed
- anproj2 year of en of projection (same day and month as proj1).
- */
- int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
- int *popage;
- double agec; /* generic age */
- double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
- double *popeffectif,*popcount;
- double ***p3mat;
- double ***mobaverage;
- char fileresf[FILENAMELENGTH];
-
- agelim=AGESUP;
- prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-
- strcpy(fileresf,"f");
- strcat(fileresf,fileres);
- if((ficresf=fopen(fileresf,"w"))==NULL) {
- printf("Problem with forecast resultfile: %s\n", fileresf);
- fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
- }
- printf("Computing forecasting: result on file '%s' \n", fileresf);
- fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
- if (cptcoveff==0) ncodemax[cptcoveff]=1;
-
- if (mobilav!=0) {
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
- fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- printf(" Error in movingaverage mobilav=%d\n",mobilav);
- }
- }
+ int ng;
- stepsize=(int) (stepm+YEARM-1)/YEARM;
- if (stepm<=12) stepsize=1;
- if(estepm < stepm){
- printf ("Problem %d lower than %d\n",estepm, stepm);
- }
- else hstepm=estepm;
- hstepm=hstepm/stepm;
- yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
- fractional in yp1 */
- anprojmean=yp;
- yp2=modf((yp1*12),&yp);
- mprojmean=yp;
- yp1=modf((yp2*30.5),&yp);
- jprojmean=yp;
- if(jprojmean==0) jprojmean=1;
- if(mprojmean==0) jprojmean=1;
+ /*#ifdef windows */
+ fprintf(ficgp,"cd \"%s\" \n",pathc);
+ /*#endif */
- i1=cptcoveff;
- if (cptcovn < 1){i1=1;}
-
- fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-
- fprintf(ficresf,"#****** Routine prevforecast **\n");
-/* if (h==(int)(YEARM*yearp)){ */
- for(cptcov=1, k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- k=k+1;
- fprintf(ficresf,"\n#******");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
- fprintf(ficresf,"******\n");
- fprintf(ficresf,"# Covariate valuofcovar yearproj age");
- for(j=1; j<=nlstate+ndeath;j++){
- for(i=1; i<=nlstate;i++)
- fprintf(ficresf," p%d%d",i,j);
- fprintf(ficresf," p.%d",j);
- }
- for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
- fprintf(ficresf,"\n");
- fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+ strcpy(dirfileres,optionfilefiname);
+ strcpy(optfileres,"vpl");
+ fprintf(ficgp,"set out \"graphmort.svg\"\n ");
+ fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+ fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
+ /* fprintf(ficgp, "set size 0.65,0.65\n"); */
+ fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
- for (agec=fage; agec>=(ageminpar-1); agec--){
- nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
- nhstepm = nhstepm/hstepm;
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- oldm=oldms;savm=savms;
- hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-
- for (h=0; h<=nhstepm; h++){
- if (h*hstepm/YEARM*stepm ==yearp) {
- fprintf(ficresf,"\n");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
- }
- for(j=1; j<=nlstate+ndeath;j++) {
- ppij=0.;
- for(i=1; i<=nlstate;i++) {
- if (mobilav==1)
- ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
- else {
- ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
- }
- if (h*hstepm/YEARM*stepm== yearp) {
- fprintf(ficresf," %.3f", p3mat[i][j][h]);
- }
- } /* end i */
- if (h*hstepm/YEARM*stepm==yearp) {
- fprintf(ficresf," %.3f", ppij);
- }
- }/* end j */
- } /* end h */
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- } /* end agec */
- } /* end yearp */
- } /* end cptcod */
- } /* end cptcov */
-
- if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+}
- fclose(ficresf);
-}
+int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+{
-/************** Forecasting *****not tested NB*************/
-populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
-
- int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
- int *popage;
- double calagedatem, agelim, kk1, kk2;
- double *popeffectif,*popcount;
- double ***p3mat,***tabpop,***tabpopprev;
- double ***mobaverage;
- char filerespop[FILENAMELENGTH];
+ /*-------- data file ----------*/
+ FILE *fic;
+ char dummy[]=" ";
+ int i=0, j=0, n=0, iv=0, v;
+ int lstra;
+ int linei, month, year,iout;
+ int noffset=0; /* This is the offset if BOM data file */
+ char line[MAXLINE], linetmp[MAXLINE];
+ char stra[MAXLINE], strb[MAXLINE];
+ char *stratrunc;
- tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- agelim=AGESUP;
- calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-
- prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-
-
- strcpy(filerespop,"pop");
- strcat(filerespop,fileres);
- if((ficrespop=fopen(filerespop,"w"))==NULL) {
- printf("Problem with forecast resultfile: %s\n", filerespop);
- fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
+ FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
+ for(v=1;v
");
- m=cptcoveff;
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+ for (k=agegomp;k<(agemortsup-2);k++)
+ fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf
\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
- 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]][codtab[jj1][cpt]]);
- fprintf(fichtm," ************\n
");
- }
- for(cpt=1; cpt<=nlstate;cpt++) {
- fprintf(fichtm,"
- Observed (cross-sectional) and period (incidence based) \
-prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png
\
-",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
- }
- fprintf(fichtm,"\n
- Total life expectancy by age and \
-health expectancies in states (1) and (2): %s%d.png
\
-![](\"%s%d.png\")
",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
- } /* end i1 */
- }/* End k1 */
- fprintf(fichtm,"
");
+ agebase=ageminpar;
+ agelim=agemaxpar;
-fprintf(fichtm,"Result files
\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):
");
- fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year
",p[1],p[2],agegomp);
- for (i=1;i<=2;i++)
- fprintf(fichtm," p[%d] = %lf [%f ; %f]
\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
- fprintf(fichtm,"![](\"graphmort.png\")
");
- fprintf(fichtm,"Life table
\n
");
+ /* i1=pow(2,ncoveff); */
+ i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+ if (cptcovn < 1){i1=1;}
- fprintf(fichtm,"\nAge l
");
+ for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+
+ /* 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; */
+ /* to clean */
+ //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+ fprintf(ficrespl,"#******");
+ printf("#******");
+ fprintf(ficlog,"#******");
+ for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+ fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
+ printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ fprintf(ficrespl,"******\n");
+ printf("******\n");
+ fprintf(ficlog,"******\n");
+ if(invalidvarcomb[k]){
+ printf("\nCombination (%d) ignored because no case \n",k);
+ fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
+ fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
+ continue;
+ }
- for (k=agegomp;k<(agemortsup-2);k++)
- fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf
\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+ fprintf(ficrespl,"#Age ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
+ fprintf(ficrespl,"Total Years_to_converge\n");
+
+ for (age=agebase; age<=agelim; age++){
+ /* for (age=agebase; age<=agebase; age++){ */
+ prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
+ fprintf(ficrespl,"%.0f ",age );
+ for(j=1;j<=cptcoveff;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]);
+ }
+ fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+ } /* Age */
+ /* was end of cptcod */
+ } /* cptcov */
+ } /* nres */
+ return 0;
+}
-
- fflush(fichtm);
+int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
+ /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
+
+ /* Computes the back prevalence limit for any combination of covariate values
+ * at any age between ageminpar and agemaxpar
+ */
+ int i, j, k, i1, nres=0 ;
+ /* double ftolpl = 1.e-10; */
+ double age, agebase, agelim;
+ double tot;
+ /* double ***mobaverage; */
+ /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
+
+ strcpy(fileresplb,"PLB_");
+ strcat(fileresplb,fileresu);
+ if((ficresplb=fopen(fileresplb,"w"))==NULL) {
+ printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
+ fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
+ }
+ printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
+ fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
+ pstamp(ficresplb);
+ fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
+ fprintf(ficresplb,"#Age ");
+ for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
+ fprintf(ficresplb,"\n");
+
+
+ /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+
+ agebase=ageminpar;
+ agelim=agemaxpar;
+
+
+ i1=pow(2,cptcoveff);
+ if (cptcovn < 1){i1=1;}
+
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+ fprintf(ficresplb,"#******");
+ printf("#******");
+ fprintf(ficlog,"#******");
+ for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+ fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ 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++) {
+ fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
+ fprintf(ficresplb,"Total Years_to_converge\n");
+
+
+ for (age=agebase; age<=agelim; age++){
+ /* for (age=agebase; age<=agebase; age++){ */
+ if(mobilavproj > 0){
+ /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
+ /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+ bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
+ }else if (mobilavproj == 0){
+ printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+ fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+ exit(1);
+ }else{
+ /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+ bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
+ /* printf("TOTOT\n"); */
+ /* exit(1); */
+ }
+ fprintf(ficresplb,"%.0f ",age );
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ tot=0.;
+ for(i=1; i<=nlstate;i++){
+ tot += bprlim[i][i];
+ fprintf(ficresplb," %.5f", bprlim[i][i]);
+ }
+ fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+ } /* Age */
+ /* was end of cptcod */
+ /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
+ } /* end of any combination */
+ } /* end of nres */
+ /* hBijx(p, bage, fage); */
+ /* fclose(ficrespijb); */
+
+ return 0;
}
+
+int hPijx(double *p, int bage, int fage){
+ /*------------- h Pij x at various ages ------------*/
-/******************* Gnuplot file **************/
-void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-
- char dirfileres[132],optfileres[132];
- int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
- int ng;
-
-
- /*#ifdef windows */
- fprintf(ficgp,"cd \"%s\" \n",pathc);
- /*#endif */
-
+ int stepsize;
+ int agelim;
+ int hstepm;
+ int nhstepm;
+ int h, i, i1, j, k, k4, nres=0;
- strcpy(dirfileres,optionfilefiname);
- strcpy(optfileres,"vpl");
- fprintf(ficgp,"set out \"graphmort.png\"\n ");
- fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
- fprintf(ficgp, "set ter png small\n set log y\n");
- fprintf(ficgp, "set size 0.65,0.65\n");
- fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+ double agedeb;
+ double ***p3mat;
-}
+ strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
+ if((ficrespij=fopen(filerespij,"w"))==NULL) {
+ printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+ fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
+ }
+ printf("Computing pij: result on file '%s' \n", filerespij);
+ fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+
+ stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*if (stepm<=24) stepsize=2;*/
+ agelim=AGESUP;
+ hstepm=stepsize*YEARM; /* Every year of age */
+ hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+
+ /* hstepm=1; aff par mois*/
+ pstamp(ficrespij);
+ fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+ i1= pow(2,cptcoveff);
+ /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+ /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+ /* k=k+1; */
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ fprintf(ficrespij,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ fprintf(ficrespij,"******\n");
+
+ for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+ nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+
+ /* nhstepm=nhstepm*YEARM; aff par mois*/
+
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ oldm=oldms;savm=savms;
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
+ fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate+ndeath;j++)
+ fprintf(ficrespij," %1d-%1d",i,j);
+ fprintf(ficrespij,"\n");
+ for (h=0; h<=nhstepm; h++){
+ /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+ fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate+ndeath;j++)
+ fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+ fprintf(ficrespij,"\n");
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ fprintf(ficrespij,"\n");
+ }
+ /*}*/
+ }
+ return 0;
+}
+
+ int hBijx(double *p, int bage, int fage, double ***prevacurrent){
+ /*------------- h Bij x at various ages ------------*/
+ int stepsize;
+ /* int agelim; */
+ int ageminl;
+ int hstepm;
+ int nhstepm;
+ int h, i, i1, j, k, nres;
+
+ double agedeb;
+ double ***p3mat;
+
+ strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
+ if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
+ printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+ fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+ }
+ printf("Computing pij back: result on file '%s' \n", filerespijb);
+ fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
+
+ stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*if (stepm<=24) stepsize=2;*/
+
+ /* agelim=AGESUP; */
+ ageminl=AGEINF; /* was 30 */
+ hstepm=stepsize*YEARM; /* Every year of age */
+ hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+
+ /* hstepm=1; aff par mois*/
+ pstamp(ficrespijb);
+ fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
+ i1= pow(2,cptcoveff);
+ /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+ /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+ /* k=k+1; */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ fprintf(ficrespijb,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficrespijb,"******\n");
+ if(invalidvarcomb[k]){ /* Is it necessary here? */
+ 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) */
+ /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+ nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
+ nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
+
+ /* nhstepm=nhstepm*YEARM; aff par mois*/
+
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
+ /* and memory limitations if stepm is small */
+ /* oldm=oldms;savm=savms; */
+ /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
+ hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
+ /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+ fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate+ndeath;j++)
+ fprintf(ficrespijb," %1d-%1d",i,j);
+ fprintf(ficrespijb,"\n");
+ for (h=0; h<=nhstepm; h++){
+ /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+ fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+ /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate+ndeath;j++)
+ fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
+ fprintf(ficrespijb,"\n");
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ fprintf(ficrespijb,"\n");
+ } /* end age deb */
+ } /* end combination */
+ } /* end nres */
+ return 0;
+ } /* hBijx */
/***********************************************/
@@ -4381,74 +11277,106 @@ void printinggnuplotmort(char fileres[],
int main(int argc, char *argv[])
{
+#ifdef GSL
+ const gsl_multimin_fminimizer_type *T;
+ size_t iteri = 0, it;
+ int rval = GSL_CONTINUE;
+ int status = GSL_SUCCESS;
+ double ssval;
+#endif
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
- int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
- int linei, month, year,iout;
- int jj, ll, li, lj, lk, imk;
+ int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
+ /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
+ int ncvyear=0; /* Number of years needed for the period prevalence to converge */
+ int jj, ll, li, lj, lk;
int numlinepar=0; /* Current linenumber of parameter file */
+ int num_filled;
int itimes;
int NDIM=2;
-
- char ca[32], cb[32], cc[32];
- char dummy[]=" ";
+ int vpopbased=0;
+ int nres=0;
+ int endishere=0;
+ int noffset=0;
+ int ncurrv=0; /* Temporary variable */
+
+ char ca[32], cb[32];
/* FILE *fichtm; *//* Html File */
/* FILE *ficgp;*/ /*Gnuplot File */
struct stat info;
- double agedeb, agefin,hf;
- double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+ double agedeb=0.;
- double fret;
- double **xi,tmp,delta;
+ double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
+ double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
- double dum; /* Dummy variable */
+ double fret;
+ double dum=0.; /* Dummy variable */
double ***p3mat;
- double ***mobaverage;
- int *indx;
- char line[MAXLINE], linepar[MAXLINE];
- char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+ /* double ***mobaverage; */
+ double wald;
+
+ char line[MAXLINE];
+ char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
+
+ char modeltemp[MAXLINE];
+ char resultline[MAXLINE];
+
char pathr[MAXLINE], pathimach[MAXLINE];
- char **bp, *tok, *val; /* pathtot */
- int firstobs=1, lastobs=10;
- int sdeb, sfin; /* Status at beginning and end */
- int c, h , cpt,l;
- int ju,jl, mi;
- int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
- int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+ char *tok, *val; /* pathtot */
+ int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
+ int c, h , cpt, c2;
+ int jl=0;
+ int i1, j1, jk, stepsize=0;
+ int count=0;
+
+ int *tab;
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+ /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
+ /* double anprojf, mprojf, jprojf; */
+ /* double jintmean,mintmean,aintmean; */
+ int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
+ int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
+ double yrfproj= 10.0; /* Number of years of forward projections */
+ double yrbproj= 10.0; /* Number of years of backward projections */
+ int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
int mobilav=0,popforecast=0;
- int hstepm, nhstepm;
+ int hstepm=0, nhstepm=0;
int agemortsup;
float sumlpop=0.;
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
- double bage, fage, age, agelim, agebase;
+ double bage=0, fage=110., age, agelim=0., agebase=0.;
double ftolpl=FTOL;
double **prlim;
- double *severity;
- double ***param; /* Matrix of parameters */
- double *p;
+ double **bprlim;
+ double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel)
+ state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
+ double ***paramstart; /* Matrix of starting parameter values */
+ double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
double **matcov; /* Matrix of covariance */
+ double **hess; /* Hessian matrix */
double ***delti3; /* Scale */
double *delti; /* Scale */
double ***eij, ***vareij;
double **varpl; /* Variances of prevalence limits by age */
+
double *epj, vepp;
- double kk1, kk2;
- double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+
+ double dateprev1, dateprev2;
+ double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
+ double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
+
+
double **ximort;
- char *alph[]={"a","a","b","c","d","e"}, str[4];
+ char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
int *dcwave;
- char z[1]="c", occ;
+ char z[1]="c";
+
+ /*char *strt;*/
+ char strtend[80];
- char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
- char *strt, strtend[80];
- char *stratrunc;
- int lstra;
- long total_usecs;
-
/* setlocale (LC_ALL, ""); */
/* bindtextdomain (PACKAGE, LOCALEDIR); */
/* textdomain (PACKAGE); */
@@ -4456,19 +11384,21 @@ int main(int argc, char *argv[])
/* setlocale (LC_MESSAGES, ""); */
/* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
- (void) gettimeofday(&start_time,&tzp);
+ rstart_time = time(NULL);
+ /* (void) gettimeofday(&start_time,&tzp);*/
+ start_time = *localtime(&rstart_time);
curr_time=start_time;
- tm = *localtime(&start_time.tv_sec);
- tmg = *gmtime(&start_time.tv_sec);
- strcpy(strstart,asctime(&tm));
+ /*tml = *localtime(&start_time.tm_sec);*/
+ /* strcpy(strstart,asctime(&tml)); */
+ strcpy(strstart,asctime(&start_time));
/* printf("Localtime (at start)=%s",strstart); */
-/* tp.tv_sec = tp.tv_sec +86400; */
-/* tm = *localtime(&start_time.tv_sec); */
+/* tp.tm_sec = tp.tm_sec +86400; */
+/* tm = *localtime(&start_time.tm_sec); */
/* tmg.tm_year=tmg.tm_year +dsign*dyear; */
/* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
/* tmg.tm_hour=tmg.tm_hour + 1; */
-/* tp.tv_sec = mktime(&tmg); */
+/* tp.tm_sec = mktime(&tmg); */
/* strt=asctime(&tmg); */
/* printf("Time(after) =%s",strstart); */
/* (void) time (&time_value);
@@ -4480,16 +11410,32 @@ int main(int argc, char *argv[])
nberr=0; /* Number of errors and warnings */
nbwarn=0;
+#ifdef WIN32
+ _getcwd(pathcd, size);
+#else
getcwd(pathcd, size);
-
- printf("\n%s\n%s",version,fullversion);
+#endif
+ syscompilerinfo(0);
+ printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
if(argc <=1){
printf("\nEnter the parameter file name: ");
- fgets(pathr,FILENAMELENGTH,stdin);
+ if(!fgets(pathr,FILENAMELENGTH,stdin)){
+ printf("ERROR Empty parameter file name\n");
+ goto end;
+ }
i=strlen(pathr);
if(pathr[i-1]=='\n')
pathr[i-1]='\0';
- for (tok = pathr; tok != NULL; ){
+ i=strlen(pathr);
+ if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
+ pathr[i-1]='\0';
+ }
+ i=strlen(pathr);
+ if( i==0 ){
+ printf("ERROR Empty parameter file name\n");
+ goto end;
+ }
+ for (tok = pathr; tok != NULL; ){
printf("Pathr |%s|\n",pathr);
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
printf("val= |%s| pathr=%s\n",val,pathr);
@@ -4497,8 +11443,13 @@ int main(int argc, char *argv[])
if(pathr[0] == '\0') break; /* Dirty */
}
}
+ else if (argc<=2){
+ strcpy(pathtot,argv[1]);
+ }
else{
strcpy(pathtot,argv[1]);
+ strcpy(z,argv[2]);
+ printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
}
/*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
/*cygwin_split_path(pathtot,path,optionfile);
@@ -4513,13 +11464,18 @@ int main(int argc, char *argv[])
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+#ifdef WIN32
+ _chdir(path); /* Can be a relative path */
+ if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+#else
chdir(path); /* Can be a relative path */
- if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
- printf("Current directory %s!\n",pathcd);
+ if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
+#endif
+ printf("Current directory %s!\n",pathcd);
strcpy(command,"mkdir ");
strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){
- printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+ printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
/* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
/* fclose(ficlog); */
/* exit(1); */
@@ -4530,7 +11486,7 @@ int main(int argc, char *argv[])
/*-------- arguments in the command line --------*/
- /* Log file */
+ /* Main Log file */
strcat(filelog, optionfilefiname);
strcat(filelog,".log"); /* */
if((ficlog=fopen(filelog,"w"))==NULL) {
@@ -4538,123 +11494,288 @@ int main(int argc, char *argv[])
goto end;
}
fprintf(ficlog,"Log filename:%s\n",filelog);
- fprintf(ficlog,"\n%s\n%s",version,fullversion);
+ fprintf(ficlog,"Version %s %s",version,fullversion);
fprintf(ficlog,"\nEnter the parameter file name: \n");
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
path=%s \n\
optionfile=%s\n\
optionfilext=%s\n\
- optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+ optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+
+ syscompilerinfo(1);
printf("Local time (at start):%s",strstart);
fprintf(ficlog,"Local time (at start): %s",strstart);
fflush(ficlog);
/* (void) gettimeofday(&curr_time,&tzp); */
-/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
/* */
strcpy(fileres,"r");
strcat(fileres, optionfilefiname);
+ strcat(fileresu, optionfilefiname); /* Without r in front */
strcat(fileres,".txt"); /* Other files have txt extension */
+ strcat(fileresu,".txt"); /* Other files have txt extension */
- /*---------arguments file --------*/
+ /* Main ---------arguments file --------*/
if((ficpar=fopen(optionfile,"r"))==NULL) {
- printf("Problem with optionfile %s\n",optionfile);
- fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+ printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+ fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
fflush(ficlog);
- goto end;
+ /* goto end; */
+ exit(70);
}
-
-
strcpy(filereso,"o");
- strcat(filereso,fileres);
+ strcat(filereso,fileresu);
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
printf("Problem with Output resultfile: %s\n", filereso);
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
fflush(ficlog);
goto end;
}
+ /*-------- Rewriting parameter file ----------*/
+ strcpy(rfileres,"r"); /* "Rparameterfile */
+ strcat(rfileres,optionfilefiname); /* Parameter file first name */
+ strcat(rfileres,"."); /* */
+ strcat(rfileres,optionfilext); /* Other files have txt extension */
+ if((ficres =fopen(rfileres,"w"))==NULL) {
+ printf("Problem writing new parameter file: %s\n", rfileres);goto end;
+ fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
+ fflush(ficlog);
+ goto end;
+ }
+ fprintf(ficres,"#IMaCh %s\n",version);
+
/* Reads comments: lines beginning with '#' */
numlinepar=0;
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
+ /* Is it a BOM UTF-8 Windows file? */
+ /* First parameter line */
+ while(fgets(line, MAXLINE, ficpar)) {
+ noffset=0;
+ if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
+ {
+ noffset=noffset+3;
+ printf("# File is an UTF8 Bom.\n"); // 0xBF
+ }
+/* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
+ else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
+ {
+ noffset=noffset+2;
+ printf("# File is an UTF16BE BOM file\n");
+ }
+ else if( line[0] == 0 && line[1] == 0)
+ {
+ if( line[2] == (char)0xFE && line[3] == (char)0xFF){
+ noffset=noffset+4;
+ printf("# File is an UTF16BE BOM file\n");
+ }
+ } else{
+ ;/*printf(" Not a BOM file\n");*/
+ }
+
+ /* If line starts with a # it is a comment */
+ if (line[noffset] == '#') {
+ numlinepar++;
+ fputs(line,stdout);
+ fputs(line,ficparo);
+ fputs(line,ficres);
+ fputs(line,ficlog);
+ continue;
+ }else
+ break;
+ }
+ if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
+ title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
+ if (num_filled != 5) {
+ printf("Should be 5 parameters\n");
+ fprintf(ficlog,"Should be 5 parameters\n");
+ }
numlinepar++;
- puts(line);
- fputs(line,ficparo);
- fputs(line,ficlog);
+ printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+ fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+ fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+ fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+ }
+ /* Second parameter line */
+ while(fgets(line, MAXLINE, ficpar)) {
+ /* while(fscanf(ficpar,"%[^\n]", line)) { */
+ /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
+ if (line[0] == '#') {
+ numlinepar++;
+ printf("%s",line);
+ fprintf(ficres,"%s",line);
+ fprintf(ficparo,"%s",line);
+ fprintf(ficlog,"%s",line);
+ continue;
+ }else
+ break;
}
- ungetc(c,ficpar);
-
- fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
- numlinepar++;
- printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
- fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
- fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+ if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+ &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+ if (num_filled != 11) {
+ printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+ printf("but line=%s\n",line);
+ fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+ fprintf(ficlog,"but line=%s\n",line);
+ }
+ if( lastpass > maxwav){
+ printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+ fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+ fflush(ficlog);
+ goto end;
+ }
+ printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+ fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+ fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
+ fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+ }
+ /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+ /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+ /* Third parameter line */
+ while(fgets(line, MAXLINE, ficpar)) {
+ /* If line starts with a # it is a comment */
+ if (line[0] == '#') {
+ numlinepar++;
+ printf("%s",line);
+ fprintf(ficres,"%s",line);
+ fprintf(ficparo,"%s",line);
+ fprintf(ficlog,"%s",line);
+ continue;
+ }else
+ break;
+ }
+ if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+ if (num_filled != 1){
+ printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
+ fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
+ model[0]='\0';
+ goto end;
+ }
+ else{
+ if (model[0]=='+'){
+ for(i=1; i<=strlen(model);i++)
+ modeltemp[i-1]=model[i];
+ strcpy(model,modeltemp);
+ }
+ }
+ /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+ printf("model=1+age+%s\n",model);fflush(stdout);
+ fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
+ fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
+ fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
+ }
+ /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
+ /* numlinepar=numlinepar+3; /\* In general *\/ */
+ /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
+ /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
+ /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fflush(ficlog);
+ /* if(model[0]=='#'|| model[0]== '\0'){ */
+ if(model[0]=='#'){
+ printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
+ 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
+ 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
+ if(mle != -1){
+ printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
+ exit(1);
+ }
+ }
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
numlinepar++;
- puts(line);
+ if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+ z[0]=line[1];
+ }
+ /* printf("****line [1] = %c \n",line[1]); */
+ fputs(line, stdout);
+ //puts(line);
fputs(line,ficparo);
fputs(line,ficlog);
}
ungetc(c,ficpar);
- covar=matrix(0,NCOVMAX,1,n);
- cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
- if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
-
- ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
- nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
- npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-
+ covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
+ if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
+ if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
+ if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
+ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+ v1+v2*age+v2*v3 makes cptcovn = 3
+ */
+ if (strlen(model)>1)
+ ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
+ else
+ ncovmodel=2; /* Constant and age */
+ nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
+ npar= nforce*ncovmodel; /* Number of parameters like aij*/
+ if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+ printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+ fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+ fflush(stdout);
+ fclose (ficlog);
+ goto end;
+ }
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
delti=delti3[1][1];
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+/* We could also provide initial parameters values giving by simple logistic regression
+ * only one way, that is without matrix product. We will have nlstate maximizations */
+ /* for(i=1;i
%s \
\n\
-Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n",\
+Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}
- fprintf(fichtm,"\n
%s \
+ fprintf(fichtm,"\n\n\n
\nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longeÌviteÌ-2013-2016-Japan Society for the Promotion of Sciences 日本å¦è¡“振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
\
\n\
-Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n\
+IMaCh-%s
%s \
+
\n\
+Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n\
\n\
\
Parameter files
\n\
@@ -5227,37 +12245,68 @@ Title=%s
Datafile=%s Firstpass=%d La
strcpy(pathr,path);
strcat(pathr,optionfilefiname);
+#ifdef WIN32
+ _chdir(optionfilefiname); /* Move to directory named optionfile */
+#else
chdir(optionfilefiname); /* Move to directory named optionfile */
+#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, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
+ firstpass, lastpass, stepm, weightopt, model);
fprintf(fichtm,"\n");
- fprintf(fichtm,"
Total number of observations=%d
\n\
+ fprintf(fichtm,"Parameter line 2
\n", \
+ nlstate, ndeath, maxwav, mle, weightopt);
+
+ fprintf(fichtm,"
Number of alive states: nlstate=%d
Number of death states (not really implemented): ndeath=%d \n Diagram of states %s_.svg
\n\
+![](\"%s_.svg\")
", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
+
+
+ fprintf(fichtm,"\nSome descriptive statistics
\n
Number of (used) observations=%d
\n\
Youngest age at first (selected) pass %.2f, oldest age %.2f
\n\
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
\n",\
- imx,agemin,agemax,jmin,jmax,jmean);
+ 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] */
p=param[1][1]; /* *(*(*(param +1)+1)+0) */
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-
+ /* For mortality only */
if (mle==-3){
- ximort=matrix(1,NDIM,1,NDIM);
- cens=ivector(1,n);
- ageexmed=vector(1,n);
- agecens=vector(1,n);
- dcwave=ivector(1,n);
-
+ 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(firstobs,lastobs);
+ ageexmed=vector(firstobs,lastobs);
+ agecens=vector(firstobs,lastobs);
+ dcwave=ivector(firstobs,lastobs);
+
for (i=1; i<=imx; i++){
dcwave[i]=-1;
for (m=firstpass; m<=lastpass; m++)
@@ -5267,13 +12316,13 @@ Interval (in months) between two waves:
break;
}
}
-
+
for (i=1; i<=imx; i++) {
if (wav[i]>0){
ageexmed[i]=agev[mw[1][i]][i];
j=wav[i];
agecens[i]=1.;
-
+
if (ageexmed[i]> 1 && wav[i] > 0){
agecens[i]=agev[mw[j][i]][i];
cens[i]= 1;
@@ -5291,47 +12340,135 @@ Interval (in months) between two waves:
}
p[1]=0.0268; p[NDIM]=0.083;
- /*printf("%lf %lf", p[1], p[2]);*/
+ /* printf("%lf %lf", p[1], p[2]); */
+#ifdef GSL
+ printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
+#else
printf("Powell\n"); fprintf(ficlog,"Powell\n");
- strcpy(filerespow,"pow-mort");
- strcat(filerespow,fileres);
+#endif
+ strcpy(filerespow,"POW-MORT_");
+ strcat(filerespow,fileresu);
if((ficrespow=fopen(filerespow,"w"))==NULL) {
printf("Problem with resultfile: %s\n", filerespow);
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
}
+#ifdef GSL
+ fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+#else
fprintf(ficrespow,"# Powell\n# iter -2*LL");
+#endif
/* for (i=1;i<=nlstate;i++)
for(j=1;j<=nlstate+ndeath;j++)
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
*/
fprintf(ficrespow,"\n");
+#ifdef GSL
+ /* gsl starts here */
+ T = gsl_multimin_fminimizer_nmsimplex;
+ gsl_multimin_fminimizer *sfm = NULL;
+ gsl_vector *ss, *x;
+ gsl_multimin_function minex_func;
+
+ /* Initial vertex size vector */
+ ss = gsl_vector_alloc (NDIM);
+
+ if (ss == NULL){
+ GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+ }
+ /* Set all step sizes to 1 */
+ gsl_vector_set_all (ss, 0.001);
+
+ /* Starting point */
+
+ x = gsl_vector_alloc (NDIM);
+
+ if (x == NULL){
+ gsl_vector_free(ss);
+ GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+ }
+
+ /* Initialize method and iterate */
+ /* p[1]=0.0268; p[NDIM]=0.083; */
+ /* gsl_vector_set(x, 0, 0.0268); */
+ /* gsl_vector_set(x, 1, 0.083); */
+ gsl_vector_set(x, 0, p[1]);
+ gsl_vector_set(x, 1, p[2]);
+
+ minex_func.f = &gompertz_f;
+ minex_func.n = NDIM;
+ minex_func.params = (void *)&p; /* ??? */
+
+ sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+ gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
- powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ printf("Iterations beginning .....\n\n");
+ printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
+
+ iteri=0;
+ while (rval == GSL_CONTINUE){
+ iteri++;
+ status = gsl_multimin_fminimizer_iterate(sfm);
+
+ if (status) printf("error: %s\n", gsl_strerror (status));
+ fflush(0);
+
+ if (status)
+ break;
+
+ rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+ ssval = gsl_multimin_fminimizer_size (sfm);
+
+ if (rval == GSL_SUCCESS)
+ printf ("converged to a local maximum at\n");
+
+ printf("%5d ", iteri);
+ for (it = 0; it < NDIM; it++){
+ printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+ }
+ printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+ }
+
+ printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+
+ gsl_vector_free(x); /* initial values */
+ gsl_vector_free(ss); /* inital step size */
+ for (it=0; it
", model);
+
+ fprintf(fichtm,"\n\n");
+ fprintf(fichtm, "
\n");
+ fprintf(fichtm, "\n");
+
+ if(mle != 0){
+ /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
ftolhess=ftol; /* Usually correct */
- hesscov(matcov, p, npar, delti, ftolhess, func);
- }
+ hesscov(matcov, hess, p, npar, delti, ftolhess, func);
+ 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");
+ fprintf(fichtm, "\nModel= 1 + age ");
+ if(nagesqr==1){
+ printf(" + age*age ");
+ fprintf(ficres," + age*age ");
+ fprintf(ficlog," + age*age ");
+ fprintf(fichtm, "+ age*age ");
+ }
+ for(j=1;j <=ncovmodel-2;j++){
+ if(Typevar[j]==0) {
+ printf(" + V%d ",Tvar[j]);
+ fprintf(ficres," + V%d ",Tvar[j]);
+ fprintf(ficlog," + V%d ",Tvar[j]);
+ fprintf(fichtm, "+ V%d ",Tvar[j]);
+ }else if(Typevar[j]==1) {
+ printf(" + V%d*age ",Tvar[j]);
+ fprintf(ficres," + V%d*age ",Tvar[j]);
+ fprintf(ficlog," + V%d*age ",Tvar[j]);
+ fprintf(fichtm, "+ V%d*age ",Tvar[j]);
+ }else if(Typevar[j]==2) {
+ printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+ fprintf(ficres," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+ fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+ fprintf(fichtm, "+ V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+ }
+ }
+ printf("\n");
+ fprintf(ficres,"\n");
+ fprintf(ficlog,"\n");
+ fprintf(fichtm, "");
printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);
+ fprintf(fichtm, " \n");
}
}
}
- if(mle!=0){
- /* Computing hessian and covariance matrix */
+ /* fprintf(fichtm,"\n"); */
+ fprintf(fichtm,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){
- printf("%lf ",p[jk]);
- fprintf(ficlog,"%lf ",p[jk]);
- fprintf(ficres,"%lf ",p[jk]);
+ printf("%12.7f ",p[jk]);
+ fprintf(ficlog,"%12.7f ",p[jk]);
+ fprintf(ficres,"%12.7f ",p[jk]);
+ fprintf(fichtm, "%12.7f ",p[jk]);
jk++;
}
printf("\n");
fprintf(ficlog,"\n");
fprintf(ficres,"\n");
+ fprintf(fichtm, "");
+ fprintf(fichtm, "\n
\n");
+
+ /* */
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");
@@ -5441,7 +12709,7 @@ Interval (in months) between two waves:
}
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
- if(mle>=1)
+ if(mle >= 1) /* To big for the screen */
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
/* # 121 Var(a12)\n\ */
@@ -5504,9 +12772,9 @@ Interval (in months) between two waves:
fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
}else{
if(mle>=1)
- printf(" %.5e",matcov[jj][ll]);
- fprintf(ficlog," %.5e",matcov[jj][ll]);
- fprintf(ficres," %.5e",matcov[jj][ll]);
+ printf(" %.7e",matcov[jj][ll]);
+ fprintf(ficlog," %.7e",matcov[jj][ll]);
+ fprintf(ficres," %.7e",matcov[jj][ll]);
}
}
}
@@ -5525,17 +12793,41 @@ Interval (in months) between two waves:
fflush(ficlog);
fflush(ficres);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
+ 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);
+ fputs(line,ficres);
+ continue;
+ }else
+ break;
}
- ungetc(c,ficpar);
+
+ /* while((c=getc(ficpar))=='#' && c!= EOF){ */
+ /* ungetc(c,ficpar); */
+ /* fgets(line, MAXLINE, ficpar); */
+ /* fputs(line,stdout); */
+ /* fputs(line,ficparo); */
+ /* } */
+ /* ungetc(c,ficpar); */
estepm=0;
- fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+ if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
+
+ if (num_filled != 6) {
+ printf("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) {
bage = ageminpar;
@@ -5543,341 +12835,520 @@ Interval (in months) between two waves:
}
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\n",ageminpar,agemaxpar,bage,fage, estepm);
- fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
+ 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(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);
+ fputs(line,ficres);
+ continue;
+ }else
+ break;
}
- ungetc(c,ficpar);
-
- fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
- fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
- fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
- printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
- fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
+
+ if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
+
+ if (num_filled != 7) {
+ printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+ fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+ goto end;
+ }
+ printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+ fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+ fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+ fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+ }
+
+ while(fgets(line, MAXLINE, ficpar)) {
+ /* If line starts with a # it is a comment */
+ if (line[0] == '#') {
+ numlinepar++;
+ fputs(line,stdout);
+ fputs(line,ficparo);
+ fputs(line,ficlog);
+ fputs(line,ficres);
+ continue;
+ }else
+ break;
}
- ungetc(c,ficpar);
dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
- fscanf(ficpar,"pop_based=%d\n",&popbased);
- fprintf(ficparo,"pop_based=%d\n",popbased);
- fprintf(ficres,"pop_based=%d\n",popbased);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
+ if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
+ if (num_filled != 1) {
+ printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+ fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+ goto end;
+ }
+ printf("pop_based=%d\n",popbased);
+ fprintf(ficlog,"pop_based=%d\n",popbased);
+ fprintf(ficparo,"pop_based=%d\n",popbased);
+ fprintf(ficres,"pop_based=%d\n",popbased);
}
- ungetc(c,ficpar);
-
- fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
- fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
- printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
- fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
- fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
- /* day and month of proj2 are not used but only year anproj2.*/
-
-
+
+ /* Results */
+ endishere=0;
+ nresult=0;
+ parameterline=0;
+ do{
+ if(!fgets(line, MAXLINE, ficpar)){
+ endishere=1;
+ parameterline=15;
+ }else if (line[0] == '#') {
+ /* If line starts with a # it is a comment */
+ numlinepar++;
+ fputs(line,stdout);
+ fputs(line,ficparo);
+ fputs(line,ficlog);
+ fputs(line,ficres);
+ continue;
+ }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
+ parameterline=11;
+ else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
+ parameterline=12;
+ else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
+ parameterline=13;
+ }
+ else{
+ parameterline=14;
+ }
+ switch (parameterline){ /* =0 only if only comments */
+ case 11:
+ if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
+ fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+ printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+ fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+ fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+ /* day and month of proj2 are not used but only year anproj2.*/
+ dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
+ dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
+ prvforecast = 1;
+ }
+ else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
+ printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+ fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+ fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+ prvforecast = 2;
+ }
+ else {
+ printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+ fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+ goto end;
+ }
+ break;
+ case 12:
+ if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
+ fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+ printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+ fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+ fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+ /* day and month of back2 are not used but only year anback2.*/
+ dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
+ dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
+ prvbackcast = 1;
+ }
+ else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
+ printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+ fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+ fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+ prvbackcast = 2;
+ }
+ else {
+ printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+ fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+ goto end;
+ }
+ break;
+ case 13:
+ num_filled=sscanf(line,"result:%[^\n]\n",resultline);
+ nresult++; /* Sum of resultlines */
+ printf("Result %d: result:%s\n",nresult, resultline);
+ if(nresult > MAXRESULTLINESPONE-1){
+ printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
+ fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
+ goto end;
+ }
+ if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+ fprintf(ficparo,"result: %s\n",resultline);
+ fprintf(ficres,"result: %s\n",resultline);
+ fprintf(ficlog,"result: %s\n",resultline);
+ } else
+ goto end;
+ break;
+ case 14:
+ printf("Error: Unknown command '%s'\n",line);
+ fprintf(ficlog,"Error: Unknown command '%s'\n",line);
+ if(line[0] == ' ' || line[0] == '\n'){
+ printf("It should not be an empty line '%s'\n",line);
+ fprintf(ficlog,"It should not be an empty line '%s'\n",line);
+ }
+ if(ncovmodel >=2 && nresult==0 ){
+ printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+ fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+ }
+ /* goto end; */
+ break;
+ case 15:
+ printf("End of resultlines.\n");
+ fprintf(ficlog,"End of resultlines.\n");
+ break;
+ default: /* parameterline =0 */
+ nresult=1;
+ decoderesult(".",nresult ); /* No covariate */
+ } /* End switch parameterline */
+ }while(endishere==0); /* End do */
- /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
- /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+ /* 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 / */
- printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-
- printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
- model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
- jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+ 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\
+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\
+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{
+ /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
+ /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
+ /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
+ if(prvforecast==1){
+ dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
+ jprojd=jproj1;
+ mprojd=mproj1;
+ anprojd=anproj1;
+ dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
+ jprojf=jproj2;
+ mprojf=mproj2;
+ anprojf=anproj2;
+ } else if(prvforecast == 2){
+ dateprojd=dateintmean;
+ date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
+ dateprojf=dateintmean+yrfproj;
+ date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
+ }
+ if(prvbackcast==1){
+ datebackd=(jback1+12*mback1+365*anback1)/365;
+ jbackd=jback1;
+ mbackd=mback1;
+ anbackd=anback1;
+ datebackf=(jback2+12*mback2+365*anback2)/365;
+ jbackf=jback2;
+ mbackf=mback2;
+ anbackf=anback2;
+ } else if(prvbackcast == 2){
+ datebackd=dateintmean;
+ date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
+ datebackf=dateintmean-yrbproj;
+ date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
+ }
- /*------------ free_vector -------------*/
- /* chdir(path); */
-
- free_ivector(wav,1,imx);
- free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
- free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
- free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
- free_lvector(num,1,n);
- free_vector(agedc,1,n);
+ printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
+ }
+ printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
+ model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
+ jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
+
+ /*------------ 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); */
+ /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
+ free_lvector(num,firstobs,lastobs);
+ free_vector(agedc,firstobs,lastobs);
/*free_matrix(covar,0,NCOVMAX,1,n);*/
/*free_matrix(covar,1,NCOVMAX,1,n);*/
fclose(ficparo);
fclose(ficres);
-
-
+
+
+ /* Other results (useful)*/
+
+
/*--------------- Prevalence limit (period or stable prevalence) --------------*/
-
- strcpy(filerespl,"pl");
- strcat(filerespl,fileres);
- if((ficrespl=fopen(filerespl,"w"))==NULL) {
- printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
- fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
- }
- printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
- fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
- pstamp(ficrespl);
- fprintf(ficrespl,"# Period (stable) prevalence \n");
- fprintf(ficrespl,"#Age ");
- for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
- fprintf(ficrespl,"\n");
-
+ /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
prlim=matrix(1,nlstate,1,nlstate);
-
- agebase=ageminpar;
- agelim=agemaxpar;
- ftolpl=1.e-10;
- i1=cptcoveff;
- if (cptcovn < 1){i1=1;}
-
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
- fprintf(ficrespl,"\n#******");
- printf("\n#******");
- fprintf(ficlog,"\n#******");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
- fprintf(ficrespl,"******\n");
- printf("******\n");
- fprintf(ficlog,"******\n");
-
- for (age=agebase; age<=agelim; age++){
- prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
- fprintf(ficrespl,"%.0f ",age );
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- for(i=1; i<=nlstate;i++)
- fprintf(ficrespl," %.5f", prlim[i][i]);
- fprintf(ficrespl,"\n");
- }
- }
- }
+ prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
fclose(ficrespl);
/*------------- h Pij x at various ages ------------*/
-
- strcpy(filerespij,"pij"); strcat(filerespij,fileres);
- if((ficrespij=fopen(filerespij,"w"))==NULL) {
- printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
- fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
- }
- printf("Computing pij: result on file '%s' \n", filerespij);
- fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-
- stepsize=(int) (stepm+YEARM-1)/YEARM;
- /*if (stepm<=24) stepsize=2;*/
-
- agelim=AGESUP;
- hstepm=stepsize*YEARM; /* Every year of age */
- hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-
- /* hstepm=1; aff par mois*/
- pstamp(ficrespij);
- fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- fprintf(ficrespij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficrespij,"******\n");
-
- for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-
- /* nhstepm=nhstepm*YEARM; aff par mois*/
-
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- oldm=oldms;savm=savms;
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate+ndeath;j++)
- fprintf(ficrespij," %1d-%1d",i,j);
- fprintf(ficrespij,"\n");
- for (h=0; h<=nhstepm; h++){
- fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate+ndeath;j++)
- fprintf(ficrespij," %.5f", p3mat[i][j][h]);
- fprintf(ficrespij,"\n");
- }
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- fprintf(ficrespij,"\n");
- }
- }
- }
-
- varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-
+ /*#include "hpijx.h"*/
+ hPijx(p, bage, fage);
fclose(ficrespij);
-
- probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
- for(i=1;i<=AGESUP;i++)
- for(j=1;j<=NCOVMAX;j++)
- for(k=1;k<=NCOVMAX;k++)
+
+ /* ncovcombmax= pow(2,cptcoveff); */
+ /*-------------- Variance of one-step probabilities---*/
+ k=1;
+ varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+
+ /* Prevalence for each covariate combination in probs[age][status][cov] */
+ probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+ for(i=AGEINF;i<=AGESUP;i++)
+ for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
+ for(k=1;k<=ncovcombmax;k++)
probs[i][j][k]=0.;
-
+ prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
+ ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ if (mobilav!=0 ||mobilavproj !=0 ) {
+ mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+ for(i=AGEINF;i<=AGESUP;i++)
+ for(j=1;j<=nlstate+ndeath;j++)
+ for(k=1;k<=ncovcombmax;k++)
+ mobaverages[i][j][k]=0.;
+ mobaverage=mobaverages;
+ if (mobilav!=0) {
+ printf("Movingaveraging observed prevalence\n");
+ fprintf(ficlog,"Movingaveraging observed prevalence\n");
+ if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
+ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ }
+ } else if (mobilavproj !=0) {
+ printf("Movingaveraging projected observed prevalence\n");
+ fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
+ if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
+ fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
+ printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
+ }
+ }else{
+ printf("Internal error moving average\n");
+ fflush(stdout);
+ exit(1);
+ }
+ }/* end if moving average */
+
/*---------- Forecasting ------------------*/
- /*if((stepm == 1) && (strcmp(model,".")==0)){*/
- if(prevfcast==1){
- /* if(stepm ==1){*/
- prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
- /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
- /* } */
- /* else{ */
- /* erreur=108; */
- /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
- /* } */
- }
-
-
- /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
-
- prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
- /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
- ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
- */
+ if(prevfcast==1){
+ /* /\* if(stepm ==1){*\/ */
+ /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
+ /*This done previously after freqsummary.*/
+ /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
+ /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
+
+ /* } else if (prvforecast==2){ */
+ /* /\* if(stepm ==1){*\/ */
+ /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
+ /* } */
+ /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
+ prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
+ }
+
+ /* Prevbcasting */
+ if(prevbcast==1){
+ ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
+ ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
+ ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
+
+ /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
+
+ bprlim=matrix(1,nlstate,1,nlstate);
+
+ back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
+ fclose(ficresplb);
+
+ hBijx(p, bage, fage, mobaverage);
+ fclose(ficrespijb);
+
+ /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
+ /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
+ /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
+ /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+ prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
+ mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
- if (mobilav!=0) {
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
- fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- printf(" Error in movingaverage mobilav=%d\n",mobilav);
- }
- }
+
+ varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
+
+ free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
+ free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+ free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+ free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+ } /* end Prevbcasting */
+
+
+ /* ------ Other prevalence ratios------------ */
+ free_ivector(wav,1,imx);
+ free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
+ free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
+ free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
+
+
/*---------- Health expectancies, no variances ------------*/
-
- strcpy(filerese,"e");
- strcat(filerese,fileres);
+
+ strcpy(filerese,"E_");
+ strcat(filerese,fileresu);
if((ficreseij=fopen(filerese,"w"))==NULL) {
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
}
- printf("Computing Health Expectancies: result on file '%s' \n", filerese);
- fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- fprintf(ficreseij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
- fprintf(ficreseij,"******\n");
+ printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
+ fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
- eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
-
- free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+ pstamp(ficreseij);
+
+ i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+ if (cptcovn < 1){i1=1;}
+
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ fprintf(ficreseij,"\n#****** ");
+ printf("\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
}
+ fprintf(ficreseij,"******\n");
+ printf("******\n");
+
+ eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
+
+ free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
}
fclose(ficreseij);
+ printf("done evsij\n");fflush(stdout);
+ fprintf(ficlog,"done evsij\n");fflush(ficlog);
-
- /*---------- Health expectancies and variances ------------*/
-
-
- strcpy(filerest,"t");
- strcat(filerest,fileres);
+
+ /*---------- State-specific expectancies and variances ------------*/
+
+ strcpy(filerest,"T_");
+ strcat(filerest,fileresu);
if((ficrest=fopen(filerest,"w"))==NULL) {
printf("Problem with total LE resultfile: %s\n", filerest);goto end;
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
}
- printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
- fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
-
-
- strcpy(fileresstde,"stde");
- strcat(fileresstde,fileres);
+ printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
+ fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
+ strcpy(fileresstde,"STDE_");
+ strcat(fileresstde,fileresu);
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
- printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
- fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
}
- printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
- fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+ printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
+ fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
- strcpy(filerescve,"cve");
- strcat(filerescve,fileres);
+ strcpy(filerescve,"CVE_");
+ strcat(filerescve,fileresu);
if((ficrescveij=fopen(filerescve,"w"))==NULL) {
- printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
- fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+ printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
+ fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
}
- printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
- fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+ printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
+ fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
- strcpy(fileresv,"v");
- strcat(fileresv,fileres);
+ strcpy(fileresv,"V_");
+ strcat(fileresv,fileresu);
if((ficresvij=fopen(fileresv,"w"))==NULL) {
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
}
- printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
- fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- fprintf(ficrest,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficrest,"******\n");
-
- fprintf(ficresstdeij,"\n#****** ");
- fprintf(ficrescveij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
- fprintf(ficresstdeij,"******\n");
- fprintf(ficrescveij,"******\n");
-
- fprintf(ficresvij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficresvij,"******\n");
-
- eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
-
- vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
- if(popbased==1){
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
- }
+ printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
+ fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
- pstamp(ficrest);
- fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+ i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+ if (cptcovn < 1){i1=1;}
+
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ printf("\n# model %s \n#****** Result for:", model);
+ fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
+ fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
+ for(j=1;j<=cptcoveff;j++){
+ printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficrest,"******\n");
+ fprintf(ficlog,"******\n");
+ printf("******\n");
+
+ fprintf(ficresstdeij,"\n#****** ");
+ fprintf(ficrescveij,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficresstdeij,"******\n");
+ fprintf(ficrescveij,"******\n");
+
+ fprintf(ficresvij,"\n#****** ");
+ /* pstamp(ficresvij); */
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficresvij,"******\n");
+
+ eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ printf(" cvevsij ");
+ fprintf(ficlog, " cvevsij ");
+ cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
+ printf(" end cvevsij \n ");
+ fprintf(ficlog, " end cvevsij \n ");
+
+ /*
+ */
+ /* goto endfree; */
+
+ vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ pstamp(ficrest);
+
+ epj=vector(1,nlstate+1);
+ 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 vpopbased=%d \n",vpopbased);
+ fprintf(ficlog, "varevsij vpopbased=%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, nres); /* 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 forward 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");
-
- epj=vector(1,nlstate+1);
+ /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+ printf("Computing age specific forward period (stable) prevalences in each health state \n");
+ fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
for(age=bage; age <=fage ;age++){
- prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
- if (popbased==1) {
+ prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*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];
@@ -5886,16 +13357,20 @@ Interval (in months) between two waves:
prlim[i][i]=mobaverage[(int)age][i][k];
}
}
-
- fprintf(ficrest," %4.0f",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];
- /* printf("%lf %lf ", 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];
@@ -5905,101 +13380,123 @@ Interval (in months) between two waves:
}
fprintf(ficrest,"\n");
}
- free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
- free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
- free_vector(epj,1,nlstate+1);
- }
- }
- free_vector(weight,1,n);
- free_imatrix(Tvard,1,15,1,2);
- free_imatrix(s,1,maxwav+1,1,n);
- free_matrix(anint,1,maxwav,1,n);
- free_matrix(mint,1,maxwav,1,n);
- free_ivector(cod,1,n);
+ } /* End vpopbased */
+ free_vector(epj,1,nlstate+1);
+ free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+ free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+ printf("done selection\n");fflush(stdout);
+ fprintf(ficlog,"done selection\n");fflush(ficlog);
+
+ } /* End k selection */
+
+ printf("done State-specific expectancies\n");fflush(stdout);
+ fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
+
+ /* variance-covariance of forward period prevalence*/
+ varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
+
+
+ free_vector(weight,firstobs,lastobs);
+ free_imatrix(Tvard,1,NCOVMAX,1,2);
+ free_imatrix(s,1,maxwav+1,firstobs,lastobs);
+ free_matrix(anint,1,maxwav,firstobs,lastobs);
+ free_matrix(mint,1,maxwav,firstobs,lastobs);
+ free_ivector(cod,firstobs,lastobs);
free_ivector(tab,1,NCOVMAX);
fclose(ficresstdeij);
fclose(ficrescveij);
fclose(ficresvij);
fclose(ficrest);
fclose(ficpar);
-
- /*------- Variance of period (stable) prevalence------*/
-
- strcpy(fileresvpl,"vpl");
- strcat(fileresvpl,fileres);
- if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
- printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
- exit(0);
- }
- printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- fprintf(ficresvpl,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficresvpl,"******\n");
-
- varpl=matrix(1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
- free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
- }
- }
-
- fclose(ficresvpl);
-
+
+
/*---------- End : free ----------------*/
- if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-
- } /* mle==-3 arrives here for freeing */
- free_matrix(prlim,1,nlstate,1,nlstate);
+ if (mobilav!=0 ||mobilavproj !=0)
+ free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
+ free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+ free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
- 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);
- free_matrix(covar,0,NCOVMAX,1,n);
- free_matrix(matcov,1,npar,1,npar);
- /*free_vector(delti,1,npar);*/
- free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
- free_matrix(agev,1,maxwav,1,imx);
- free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-
- free_ivector(ncodemax,1,8);
- free_ivector(Tvar,1,15);
- free_ivector(Tprod,1,15);
- free_ivector(Tvaraff,1,15);
- free_ivector(Tage,1,15);
- free_ivector(Tcode,1,100);
-
- free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
- free_imatrix(codtab,1,100,1,10);
+ } /* 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);
+ if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
+ if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
+ if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
+ free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
+ free_matrix(matcov,1,npar,1,npar);
+ free_matrix(hess,1,npar,1,npar);
+ /*free_vector(delti,1,npar);*/
+ free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+ free_matrix(agev,1,maxwav,1,imx);
+ free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+ free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+
+ free_ivector(ncodemax,1,NCOVMAX);
+ free_ivector(ncodemaxwundef,1,NCOVMAX);
+ free_ivector(Dummy,-1,NCOVMAX);
+ free_ivector(Fixed,-1,NCOVMAX);
+ free_ivector(DummyV,1,NCOVMAX);
+ free_ivector(FixedV,1,NCOVMAX);
+ free_ivector(Typevar,-1,NCOVMAX);
+ free_ivector(Tvar,1,NCOVMAX);
+ free_ivector(TvarsQ,1,NCOVMAX);
+ free_ivector(TvarsQind,1,NCOVMAX);
+ free_ivector(TvarsD,1,NCOVMAX);
+ free_ivector(TvarsDind,1,NCOVMAX);
+ free_ivector(TvarFD,1,NCOVMAX);
+ free_ivector(TvarFDind,1,NCOVMAX);
+ free_ivector(TvarF,1,NCOVMAX);
+ free_ivector(TvarFind,1,NCOVMAX);
+ free_ivector(TvarV,1,NCOVMAX);
+ free_ivector(TvarVind,1,NCOVMAX);
+ free_ivector(TvarA,1,NCOVMAX);
+ free_ivector(TvarAind,1,NCOVMAX);
+ free_ivector(TvarFQ,1,NCOVMAX);
+ free_ivector(TvarFQind,1,NCOVMAX);
+ free_ivector(TvarVD,1,NCOVMAX);
+ free_ivector(TvarVDind,1,NCOVMAX);
+ free_ivector(TvarVQ,1,NCOVMAX);
+ free_ivector(TvarVQind,1,NCOVMAX);
+ free_ivector(Tvarsel,1,NCOVMAX);
+ free_vector(Tvalsel,1,NCOVMAX);
+ free_ivector(Tposprod,1,NCOVMAX);
+ free_ivector(Tprod,1,NCOVMAX);
+ free_ivector(Tvaraff,1,NCOVMAX);
+ free_ivector(invalidvarcomb,1,ncovcombmax);
+ free_ivector(Tage,1,NCOVMAX);
+ free_ivector(Tmodelind,1,NCOVMAX);
+ free_ivector(TmodelInvind,1,NCOVMAX);
+ free_ivector(TmodelInvQind,1,NCOVMAX);
+
+ free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+ /* free_imatrix(codtab,1,100,1,10); */
fflush(fichtm);
fflush(ficgp);
-
+
if((nberr >0) || (nbwarn>0)){
- printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
- fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+ printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
+ fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
}else{
printf("End of Imach\n");
fprintf(ficlog,"End of Imach\n");
}
printf("See log file on %s\n",filelog);
/* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
- (void) gettimeofday(&end_time,&tzp);
- tm = *localtime(&end_time.tv_sec);
- tmg = *gmtime(&end_time.tv_sec);
- strcpy(strtend,asctime(&tm));
+ /*(void) gettimeofday(&end_time,&tzp);*/
+ rend_time = time(NULL);
+ end_time = *localtime(&rend_time);
+ /* tml = *localtime(&end_time.tm_sec); */
+ strcpy(strtend,asctime(&end_time));
printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
- printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-
- printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
- fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
- fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+ printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+
+ printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+ fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+ fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */
fprintf(fichtm,"Model= 1 + age ");
+ if(nagesqr==1){
+ printf(" + age*age ");
+ fprintf(ficres," + age*age ");
+ fprintf(ficlog," + age*age ");
+ fprintf(fichtm, "+ age*age ");
+ }
+ for(j=1;j <=ncovmodel-2;j++){
+ if(Typevar[j]==0) {
+ printf(" + V%d ",Tvar[j]);
+ fprintf(fichtm, "+ V%d ",Tvar[j]);
+ }else if(Typevar[j]==1) {
+ printf(" + V%d*age ",Tvar[j]);
+ fprintf(fichtm, "+ V%d*age ",Tvar[j]);
+ }else if(Typevar[j]==2) {
+ fprintf(fichtm, "+ V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+ }
+ }
+ fprintf(fichtm, "");
+ printf("%d%d ",i,k);
+ fprintf(ficlog,"%d%d ",i,k);
+ fprintf(fichtm, " \n");
+ }
+ }
+ }
+ } /* end of hesscov and Wald tests */
+ fprintf(fichtm,"%1d%1d ",i,k);
+ for(j=1; j <=ncovmodel; j++){
+ wald=p[jk]/sqrt(matcov[jk][jk]);
+ printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][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(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+ if(fabs(wald) > 1.96){
+ fprintf(fichtm, "%12.7f (%12.7f)",p[jk],sqrt(matcov[jk][jk]));
+ }else{
+ fprintf(fichtm, " %12.7f (%12.7f)",p[jk],sqrt(matcov[jk][jk]));
+ }
+ fprintf(fichtm,"W=%8.3f",wald);
+ fprintf(fichtm,"[%12.7f;%12.7f] ", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(fichtm, "
Local time at start %s
Local time at end %s
\n",strstart, strtend);
@@ -6009,28 +13506,36 @@ Interval (in months) between two waves:
fclose(ficgp);
fclose(ficlog);
/*------ End -----------*/
+
-
- printf("Before Current directory %s!\n",pathcd);
- if(chdir(pathcd) != 0)
+/* Executes gnuplot */
+
+ printf("Before Current directory %s!\n",pathcd);
+#ifdef WIN32
+ if (_chdir(pathcd) != 0)
printf("Can't move to directory %s!\n",path);
- if(getcwd(pathcd,MAXLINE) > 0)
+ if(_getcwd(pathcd,MAXLINE) > 0)
+#else
+ if(chdir(pathcd) != 0)
+ printf("Can't move to directory %s!\n", path);
+ if (getcwd(pathcd, MAXLINE) > 0)
+#endif
printf("Current directory %s!\n",pathcd);
/*strcat(plotcmd,CHARSEPARATOR);*/
sprintf(plotcmd,"gnuplot");
-#ifndef UNIX
+#ifdef _WIN32
sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
#endif
if(!stat(plotcmd,&info)){
- printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
if(!stat(getenv("GNUPLOTBIN"),&info)){
- printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+ printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
}else
strcpy(pplotcmd,plotcmd);
-#ifdef UNIX
+#ifdef __unix
strcpy(plotcmd,GNUPLOTPROGRAM);
if(!stat(plotcmd,&info)){
- printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
}else
strcpy(pplotcmd,plotcmd);
#endif
@@ -6038,30 +13543,43 @@ Interval (in months) between two waves:
strcpy(pplotcmd,plotcmd);
sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
- printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
-
+ printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+ strcpy(pplotcmd,plotcmd);
+
if((outcmd=system(plotcmd)) != 0){
- printf("\n Problem with gnuplot\n");
+ printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+ printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+ sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+ if((outcmd=system(plotcmd)) != 0){
+ printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+ strcpy(plotcmd,pplotcmd);
+ }
}
- printf(" Wait...");
+ printf(" Successful, please wait...");
while (z[0] != 'q') {
/* chdir(path); */
- printf("\nType e to edit output files, g to graph again and q for exiting: ");
+ printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
scanf("%s",z);
/* if (z[0] == 'c') system("./imach"); */
if (z[0] == 'e') {
- printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
- system(optionfilehtm);
+#ifdef __APPLE__
+ sprintf(pplotcmd, "open %s", optionfilehtm);
+#elif __linux
+ sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+#else
+ sprintf(pplotcmd, "%s", optionfilehtm);
+#endif
+ printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+ system(pplotcmd);
}
else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);
}
- end:
+end:
while (z[0] != 'q') {
- printf("\nType q for exiting: ");
+ printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);
}
+ printf("End\n");
+ exit(0);
}
-
-
-