********** Variable ");
+ fprintf(ficresphtmfr, "\n
********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++){
+ fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ }
+ fprintf(ficresp, "**********\n#");
+ fprintf(ficresphtm, "**********
\n");
+ fprintf(ficresphtmfr, "**********
\n");
+ fprintf(ficlog, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+ fprintf(ficlog, "**********\n");
}
- for(jk=1; jk <=nlstate ; jk++){
- for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)
- pp[jk] += freq[jk][m][i];
+ fprintf(ficresphtm,"| Age | Prev(%d) | N(%d) | N | ",i,i); } - for(jk=1,pos=0; jk <=nlstate ; jk++) - pos += pp[jk]; + fprintf(ficresp, "\n"); + fprintf(ficresphtm, "\n"); + + /* Header of frequency table by age */ + fprintf(ficresphtmfr,"
|---|
| Age | "); + for(jk=-1; jk <=nlstate+ndeath; jk++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(jk!=0 && m!=0) + fprintf(ficresphtmfr,"%d%d | ",jk,m); + } + } + fprintf(ficresphtmfr, "\n"); + + /* For each age */ + for(iage=iagemin; iage <= iagemax+3; iage++){ + fprintf(ficresphtm,"||||||||
|---|---|---|---|---|---|---|---|---|---|
| 0 | "); + }else if(iage==iagemax+2){ + fprintf(ficlog,"0"); + fprintf(ficresphtmfr,"|||||||||
| Unknown | "); + }else if(iage==iagemax+3){ + fprintf(ficlog,"Total"); + fprintf(ficresphtmfr,"|||||||||
| Total | "); + }else{ + if(first==1){ + first=0; + printf("See log file for details...\n"); + } + fprintf(ficresphtmfr,"|||||||||
| %d | ",iage); + fprintf(ficlog,"Age %d", iage); + } + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) + pp[jk] += freq[jk][m][iage]; + } + for(jk=1; jk <=nlstate ; jk++){ + for(m=-1, pos=0; m <=0 ; m++) + pos += freq[jk][m][iage]; + if(pp[jk]>=1.e-10){ + if(first==1){ + printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + } + fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + }else{ + if(first==1) + printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); + fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); + } + } + + for(jk=1; jk <=nlstate ; jk++){ + /* posprop[jk]=0; */ + for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */ + pp[jk] += freq[jk][m][iage]; + } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */ + + for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){ + pos += pp[jk]; /* pos is the total number of transitions until this age */ + posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state + from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state + from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + } + for(jk=1; jk <=nlstate ; jk++){ + if(pos>=1.e-5){ + if(first==1) + printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + }else{ + if(first==1) + printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + } + if( iage <= iagemax){ + if(pos>=1.e-5){ + fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta); + fprintf(ficresphtm,"%d | %.5f | %.0f | %.0f | ",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta); + /*probs[iage][jk][j1]= pp[jk]/pos;*/ + /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/ + } + else{ + fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta); + fprintf(ficresphtm,"%d | NaNq | %.0f | %.0f | ",iage, prop[jk][iage],pospropta); + } + } + pospropt[jk] +=posprop[jk]; + } /* end loop jk */ + /* pospropt=0.; */ + for(jk=-1; jk <=nlstate+ndeath; jk++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(freq[jk][m][iage] !=0 ) { /* minimizing output */ + if(first==1){ + printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); + } + fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]); + } + if(jk!=0 && m!=0) + fprintf(ficresphtmfr,"%.0f | ",freq[jk][m][iage]); + } + } /* end loop jk */ + posproptt=0.; + for(jk=1; jk <=nlstate; jk++){ + posproptt += pospropt[jk]; + } + fprintf(ficresphtmfr,"
| Tot | "); for(jk=1; jk <=nlstate ; jk++){ - if(pos>=1.e-5) - printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - else - printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - if( i <= (int) agemax){ - if(pos>=1.e-5) - fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); - else - fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); + if(posproptt < 1.e-5){ + fprintf(ficresphtm,"Nanq | %.0f | %.0f | ",pospropt[jk],posproptt); + }else{ + fprintf(ficresphtm,"%.5f | %.0f | %.0f | ",pospropt[jk]/posproptt,pospropt[jk],posproptt); } } - for(jk=-1; jk <=nlstate+ndeath; jk++) - for(m=-1; m <=nlstate+ndeath; m++) - if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); - if(i <= (int) agemax) - fprintf(ficresp,"\n"); - printf("\n"); - } - + 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(ficres,"\n This combination (%d) is not valid and no result will be produced\n\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"); + } /* end selected combination of covariate j1 */ + dateintmean=dateintsum/k2cpt; + fclose(ficresp); - free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); + fclose(ficresphtm); + fclose(ficresphtmfr); + free_vector(meanq,1,nqfveff); + free_matrix(meanqt,1,lastpass,1,nqtveff); + free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE); + free_vector(pospropt,1,nlstate); + free_vector(posprop,1,nlstate); + free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE); free_vector(pp,1,nlstate); + /* End of freqsummary */ +} -} /* End of Freq */ +/************ Prevalence ********************/ +void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) +{ + /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people + in each health status at the date of interview (if between dateprev1 and dateprev2). + We still use firstpass and lastpass as another selection. + */ + + 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+3+AGEMARGE); + /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ + j1=0; + + /*j=cptcoveff;*/ + if (cptcovn<1) {j=1;ncodemax[1]=1;} + + first=1; + for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */ + for (i=1; i<=nlstate; i++) + for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++) + prop[i][iage]=0.0; + 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); + } + + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nresult); + + 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); /* Returns p3mat[i][j][h] for h=1 to nhstepm */ + 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 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 */ + + 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, nresult); + + 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 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]; + } + + } /* End theta */ + + 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]; + + + 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.; + + 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 */ + 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, nresult); + + 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 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) + 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 *ncvyearp, int ij, char strstart[], int nres) { - /* Variance of health expectancies */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - double **newm; + /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ + double **dnewm,**doldm; int i, j, nhstepm, hstepm; - int k; - FILE *ficresvpl; - char fileresvpl[FILENAMELENGTH]; double *xp; double *gp, *gm; double **gradg, **trgradg; + double **mgm, **mgp; double age,agelim; int theta; - - strcpy(fileresvpl,"vpl"); - strcat(fileresvpl,fileres); - if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { - printf("Problem with variance prev lim resultfile: %s\n", fileresvpl); - exit(0); - } - printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl); - - - fprintf(ficresvpl,"# Standard deviation of prevalences limit\n"); + + 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); @@ -1443,6 +5556,8 @@ void varprevlim(char fileres[], double * 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); @@ -1450,18 +5565,27 @@ void varprevlim(char fileres[], double * 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); - for(i=1;i<=nlstate;i++) + if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + for(i=1;i<=nlstate;i++){ gp[i] = prlim[i][i]; - + mgp[theta][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); - for(i=1;i<=nlstate;i++) + if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); + for(i=1;i<=nlstate;i++){ gm[i] = prlim[i][i]; - + mgm[theta][i] = prlim[i][i]; + } for(i=1;i<=nlstate;i++) gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; + /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */ } /* End theta */ trgradg =matrix(1,nlstate,1,npar); @@ -1469,11 +5593,34 @@ void varprevlim(char fileres[], double * for(j=1; j<=nlstate;j++) for(theta=1; theta <=npar; theta++) trgradg[j][theta]=gradg[theta][j]; + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ + /* printf("\nmgm mgp %d ",(int)age); */ + /* for(j=1; j<=nlstate;j++){ */ + /* printf(" %d ",j); */ + /* for(theta=1; theta <=npar; theta++) */ + /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */ + /* printf("\n "); */ + /* } */ + /* } */ + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ + /* printf("\n gradg %d ",(int)age); */ + /* for(j=1; j<=nlstate;j++){ */ + /* printf("%d ",j); */ + /* for(theta=1; theta <=npar; theta++) */ + /* printf("%d %lf ",theta,gradg[theta][j]); */ + /* printf("\n "); */ + /* } */ + /* } */ for(i=1;i<=nlstate;i++) varpl[i][(int)age] =0.; + if((int)age==79 ||(int)age== 80 ||(int)age== 81){ + matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); + }else{ matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); + } for(i=1;i<=nlstate;i++) varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ @@ -1483,733 +5630,5647 @@ void varprevlim(char fileres[], double * fprintf(ficresvpl,"\n"); free_vector(gp,1,nlstate); free_vector(gm,1,nlstate); + free_matrix(mgm,1,npar,1,nlstate); + free_matrix(mgp,1,npar,1,nlstate); free_matrix(gradg,1,npar,1,nlstate); free_matrix(trgradg,1,nlstate,1,npar); } /* End age */ - fclose(ficresvpl); + free_vector(xp,1,npar); free_matrix(doldm,1,nlstate,1,npar); free_matrix(dnewm,1,nlstate,1,nlstate); } +/************ Variance of one-step probabilities ******************/ +void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[]) + { + int i, j=0, k1, l1, tj; + int k2, l2, j1, z1; + int k=0, l; + int first=1, first1, first2; + double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; + double **dnewm,**doldm; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double **mu; + double age, cov[NCOVMAX+1]; + double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ + int theta; + char fileresprob[FILENAMELENGTH]; + char fileresprobcov[FILENAMELENGTH]; + char fileresprobcor[FILENAMELENGTH]; + double ***varpij; + + strcpy(fileresprob,"PROB_"); + strcat(fileresprob,fileres); + if((ficresprob=fopen(fileresprob,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprob); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); + } + strcpy(fileresprobcov,"PROBCOV_"); + strcat(fileresprobcov,fileresu); + if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcov); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); + } + strcpy(fileresprobcor,"PROBCOR_"); + strcat(fileresprobcor,fileresu); + if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobcor); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); + } + printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); + printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); + printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); + pstamp(ficresprob); + fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); + fprintf(ficresprob,"# Age"); + pstamp(ficresprobcov); + fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); + fprintf(ficresprobcov,"# Age"); + pstamp(ficresprobcor); + fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); + fprintf(ficresprobcor,"# Age"); + + + for(i=1; i<=nlstate;i++) + for(j=1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprob," p%1d-%1d (SE)",i,j); + fprintf(ficresprobcov," p%1d-%1d ",i,j); + fprintf(ficresprobcor," p%1d-%1d ",i,j); + } + /* fprintf(ficresprob,"\n"); + fprintf(ficresprobcov,"\n"); + fprintf(ficresprobcor,"\n"); + */ + xp=vector(1,npar); + dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); + varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); + first=1; + fprintf(ficgp,"\n# Routine varprob"); + fprintf(fichtm,"\n
Computing and drawing one step probabilities with their confidence intervals
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.\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*/ + if (cptcovn>0) { + fprintf(ficresprob, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresprob, "**********\n#\n"); + fprintf(ficresprobcov, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresprobcov, "**********\n#\n"); + + fprintf(ficgp, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficgp, "**********\n#\n"); + + + fprintf(fichtmcov, "\n
********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(fichtmcov, "**********\n
"); + + fprintf(ficresprobcor, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresprobcor, "**********\n#"); + if(invalidvarcomb[j1]){ + fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); + fprintf(fichtmcov,"\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)]; + /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4 + * 1 1 1 1 1 + * 2 2 1 1 1 + * 3 1 2 1 1 + */ + /* nbcode[1][1]=0 nbcode[1][2]=1;*/ + } + /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; + + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++) + xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + + k=0; + for(i=1; i<= (nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gp[k]=pmmij[i][j]; + } + } + + for(i=1; i<=npar; i++) + xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gm[k]=pmmij[i][j]; + } + } + + for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) + gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; + } + + for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) + for(theta=1; theta <=npar; theta++) + trgradg[j][theta]=gradg[theta][j]; + + matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); + + pmij(pmmij,cov,ncovmodel,x,nlstate); + + k=0; + for(i=1; i<=(nlstate); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + mu[k][(int) age]=pmmij[i][j]; + } + } + for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) + for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) + varpij[i][j][(int)age] = doldm[i][j]; + + /*printf("\n%d ",(int)age); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + }*/ + + fprintf(ficresprob,"\n%d ",(int)age); + fprintf(ficresprobcov,"\n%d ",(int)age); + fprintf(ficresprobcor,"\n%d ",(int)age); + + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) + fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); + fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); + } + i=0; + for (k=1; k<=(nlstate);k++){ + for (l=1; l<=(nlstate+ndeath);l++){ + i++; + fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); + fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); + for (j=1; j<=i;j++){ + /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ + fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); + fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); + } + } + }/* end of loop for state */ + } /* end of loop for age */ + free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + + /* Confidence intervalle of pij */ + /* + fprintf(ficgp,"\nunset parametric;unset label"); + fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\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 */
+ 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,"\nEllipsoids 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,"\nCorrelation at age %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }else{ + first=0; + fprintf(fichtmcov," %d (%.3f),",(int) age, c12); + fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); + fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); + fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \ + mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \ + mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + }/* if first */ + } /* age mod 5 */ + } /* end loop age */ + fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); + first=1; + } /*l12 */ + } /* k12 */ + } /*l1 */ + }/* k1 */ + } /* loop on combination of covariates j1 */ + free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); + free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); + free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); + free_vector(xp,1,npar); + fclose(ficresprob); + fclose(ficresprobcov); + fclose(ficresprobcor); + fflush(ficgp); + fflush(fichtmcov); + } + + +/******************* Printing html file ***********/ +void printinghtml(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 prevfcast, int backcast, int estepm , \ + double jprev1, double mprev1,double anprev1, double dateprev1, \ + double jprev2, double mprev2,double anprev2, double dateprev2){ + int jj1, k1, i1, cpt; + + fprintf(fichtm,""); + fprintf(fichtm,"
Result files (first order: no variance)
\n"); + fprintf(fichtm,"- - Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file)
\n", + jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm")); + fprintf(fichtm," - - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file) ",
+ jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
+ fprintf(fichtm,", %s (text file)
\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 (stable) prevalence in each health state: %s
\n", + subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); + fprintf(fichtm,"\ + - Period (stable) back 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 ", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
+ }
+ fprintf(fichtm," \n - Graphs
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 ",
+ estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
+ fprintf(fichtm,"\
+ - (a) Health expectancies by health status at initial age (eij) and standard errors (in parentheses) (b) life expectancies and standard errors (ei.=ei1+ei2+...)(estepm=%2d months): \
+ %s - Graphs
- Outputs files
\n - - Observed prevalence in each state: p%s
\n -- Estimated parameters and the covariance matrix: %s
- - Stationary prevalence in each state: pl%s
- - Transition probabilities: pij%s
- - Copy of the parameter file: o%s
- - Life expectancies by age and initial health status: e%s
- - Variances of life expectancies by age and initial health status: v%s
- - Health expectancies with their variances: t%s
- - Standard deviation of stationary prevalences: vpl%s
",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres); - - fprintf(fichtm," - Graphs
"); - -for(cpt=1; cpt![](\"p%s1.gif\")
",strtok(optionfile, "."),strtok(optionfile, "."),cpt); - for(cpt=1; cpt<=nlstate;cpt++) - fprintf(fichtm,"- Observed and stationary prevalence (with confident -interval) in state (%d): v%s%d.gif
-![](\"v%s%d.gif\")
",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt); - - for(cpt=1; cpt<=nlstate;cpt++) - fprintf(fichtm,"- Health life expectancies by age and initial health state (%d): exp%s%d.gif
-![](\"ex%s%d.gif\")
",cpt,strtok(optionfile, "."),cpt,strtok(optionfile, "."),cpt); - - fprintf(fichtm,"- Total life expectancy by age and - health expectancies in states (1) and (2): e%s.gif
-![](\"e%s.gif\")
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,"Life table
\n
"); + + fprintf(fichtm,"\nAge lx qx d(x,x+1) Lx Tx e
"); + + 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]); + + + fflush(fichtm); +} + +/******************* Gnuplot file **************/ +void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ + + char dirfileres[132],optfileres[132]; + + int ng; + + + /*#ifdef windows */ + fprintf(ficgp,"cd \"%s\" \n",pathc); + /*#endif */ + + + 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); + +} + +int readdata(char datafile[], int firstobs, int lastobs, int *imax) +{ + + /*-------- data file ----------*/ + FILE *fic; + char dummy[]=" "; + int i=0, j=0, n=0, iv=0; + int lstra; + int linei, month, year,iout; + char line[MAXLINE], linetmp[MAXLINE]; + char stra[MAXLINE], strb[MAXLINE]; + char *stratrunc; + + + + if((fic=fopen(datafile,"r"))==NULL) { + printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout); + fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1; + } + + i=1; + linei=0; + while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { + linei=linei+1; + for(j=strlen(line); j>=0;j--){ /* Untabifies line */ + if(line[j] == '\t') + line[j] = ' '; + } + for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ + ; + }; + line[j+1]=0; /* Trims blanks at end of line */ + if(line[0]=='#'){ + fprintf(ficlog,"Comment line\n%s\n",line); + printf("Comment line\n%s\n",line); + continue; + } + trimbb(linetmp,line); /* Trims multiple blanks in line */ + strcpy(line, linetmp); + + /* Loops on waves */ + for (j=maxwav;j>=1;j--){ + for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + cotqvar[j][iv][i]=-1; /* 0.0/0.0 */ + cotvar[j][ntv+iv][i]=-1; /* For performance reasons */ + if(isalpha(strb[1])) { /* .m or .d Really Missing value */ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog); + return 1; + } + }else{ + errno=0; + /* what_kind_of_number(strb); */ + dval=strtod(strb,&endptr); + /* if( strb[0]=='\0' || (*endptr != '\0')){ */ + /* if(strb != endptr && *endptr == '\0') */ + /* dval=dlval; */ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog); + return 1; + } + cotqvar[j][iv][i]=dval; + cotvar[j][ntv+iv][i]=dval; + } + strcpy(line,stra); + }/* end loop ntqv */ + + for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + }else{ + errno=0; + lval=strtol(strb,&endptr,10); + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog); + return 1; + } + } + if(lval <-1 || lval >1){ + printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j); + fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j);fflush(ficlog); + return 1; + } + cotvar[j][iv][i]=(double)(lval); + strcpy(line,stra); + }/* end loop ntv */ + + /* Statuses at wave */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + }else{ + errno=0; + lval=strtol(strb,&endptr,10); + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog); + return 1; + } + } + + s[j][i]=lval; + + /* Date of Interview */ + strcpy(line,stra); + cutv(stra, strb,line,' '); + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ + } + else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ + month=99; + year=9999; + }else{ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog); + return 1; + } + anint[j][i]= (double) year; + mint[j][i]= (double)month; + strcpy(line,stra); + } /* End loop on waves */ + + /* Date of death */ + cutv(stra, strb,line,' '); + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ + } + else if( (iout=sscanf(strb,"%s.",dummy)) != 0){ + month=99; + year=9999; + }else{ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); + return 1; + } + andc[i]=(double) year; + moisdc[i]=(double) month; + strcpy(line,stra); + + /* Date of birth */ + cutv(stra, strb,line,' '); + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ + } + else if( (iout=sscanf(strb,"%s.", dummy)) != 0){ + month=99; + year=9999; + }else{ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); + return 1; + } + if (year==9999) { + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog); + return 1; + + } + annais[i]=(double)(year); + moisnais[i]=(double)(month); + strcpy(line,stra); + + /* Sample weight */ + cutv(stra, strb,line,' '); + errno=0; + dval=strtod(strb,&endptr); + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); + fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); + fflush(ficlog); + return 1; + } + weight[i]=dval; + strcpy(line,stra); + + for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + }else{ + errno=0; + /* what_kind_of_number(strb); */ + dval=strtod(strb,&endptr); + /* if(strb != endptr && *endptr == '\0') */ + /* dval=dlval; */ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog); + return 1; + } + coqvar[iv][i]=dval; + covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ + } + strcpy(line,stra); + }/* end loop nqv */ + + /* Covariate values */ + for (j=ncovcol;j>=1;j--){ + cutv(stra, strb,line,' '); + if(strb[0]=='.') { /* Missing covariate value */ + lval=-1; + }else{ + errno=0; + lval=strtol(strb,&endptr,10); + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line); + fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog); + return 1; + } + } + if(lval <-1 || lval >1){ + printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j); + fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j);fflush(ficlog); + return 1; + } + covar[j][i]=(double)(lval); + strcpy(line,stra); + } + lstra=strlen(stra); + + if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ + stratrunc = &(stra[lstra-9]); + num[i]=atol(stratrunc); + } + else + num[i]=atol(stra); + /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ + printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ + + i=i+1; + } /* End loop reading data */ + + *imax=i-1; /* Number of individuals */ + fclose(fic); + + return (0); + /* endread: */ + printf("Exiting readdata: "); + fclose(fic); + return (1); +} + +void removefirstspace(char **stri){/*, char stro[]) {*/ + char *p1 = *stri, *p2 = *stri; + while (*p2 == ' ') + p2++; + /* while ((*p1++ = *p2++) !=0) */ + /* ; */ + /* do */ + /* while (*p2 == ' ') */ + /* p2++; */ + /* while (*p1++ == *p2++); */ + *stri=p2; +} + +int decoderesult ( char resultline[], int nres) +/**< This routine decode one result line and returns the combination # of dummy covariates only **/ +{ + int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0; + char resultsav[MAXLINE]; + int resultmodel[MAXLINE]; + int modelresult[MAXLINE]; + char stra[80], strb[80], strc[80], strd[80],stre[80]; + + removefirstspace(&resultline); + printf("decoderesult:%s\n",resultline); + + if (strstr(resultline,"v") !=0){ + printf("Error. 'v' must be in upper case 'V' result: %s ",resultline); + fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog); + return 1; + } + trimbb(resultsav, resultline); + if (strlen(resultsav) >1){ + j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */ + } + if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */ + printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); + fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); + } + for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */ + if(nbocc(resultsav,'=') >1){ + cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' + resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */ + cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */ + }else + cutl(strc,strd,resultsav,'='); + Tvalsel[k]=atof(strc); /* 1 */ + + cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */; + Tvarsel[k]=atoi(strc); + /* Typevarsel[k]=1; /\* 1 for age product *\/ */ + /* cptcovsel++; */ + if (nbocc(stra,'=') >0) + strcpy(resultsav,stra); /* and analyzes it */ + } + /* Checking for missing or useless values in comparison of current model needs */ + for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + if(Typevar[k1]==0){ /* Single covariate in model */ + match=0; + for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[2]=5 == Tvarsel[1]=4 */ + modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */ + match=1; + break; + } + } + if(match == 0){ + printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + } + } + } + /* Checking for missing or useless values in comparison of current model needs */ + for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + match=0; + for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + if(Typevar[k1]==0){ /* Single */ + if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=5 == Tvarsel[1]=4 */ + resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */ + ++match; + } + } + } + if(match == 0){ + printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + }else if(match > 1){ + printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); + } + } + + /* We need to deduce which combination number is chosen and save quantitative values */ + /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */ + /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/ + /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */ + /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/ + /* 1 0 0 0 */ + /* 2 1 0 0 */ + /* 3 0 1 0 */ + /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */ + /* 5 0 0 1 */ + /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */ + /* 7 0 1 1 */ + /* 8 1 1 1 */ + for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */ + if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */ + k3= resultmodel[k1]; /* resultmodel[2] = 1=k3 */ + k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */ + k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */ + Tresult[nres][k4+1]=Tvalsel[k3]; + Tvresult[nres][k4+1]=(int)Tvarsel[k3]; + printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4); + k4++;; + } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */ + k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */ + k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */ + Tqresult[nres][k4q+1]=Tvalsel[k3q]; + Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; + printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); + k4q++;; + } + } + + TKresult[nres]=++k; /* Combination for the nresult and the model */ + return (0); +} + +int decodemodel( char model[], int lastobs) + /**< This routine decodes the model and returns: + * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age + * - nagesqr = 1 if age*age in the model, otherwise 0. + * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age + * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age + * - cptcovage number of covariates with age*products =2 + * - cptcovs number of simple covariates + * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10 + * which is a new column after the 9 (ncovcol) variables. + * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual + * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage + * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. + * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . + */ +{ + int i, j, k, ks; + int j1, k1, k2, k3, k4; + char modelsav[80]; + char stra[80], strb[80], strc[80], strd[80],stre[80]; + char *strpt; + + /*removespace(model);*/ + if (strlen(model) >1){ /* If there is at least 1 covariate */ + j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; + if (strstr(model,"AGE") !=0){ + printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model); + fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog); + return 1; + } + if (strstr(model,"v") !=0){ + printf("Error. 'v' must be in upper case 'V' model=%s ",model); + fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); + return 1; + } + strcpy(modelsav,model); + if ((strpt=strstr(model,"age*age")) !=0){ + printf(" strpt=%s, model=%s\n",strpt, model); + if(strpt != model){ + printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ + corresponding column of parameters.\n",model); + fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ + corresponding column of parameters.\n",model); fflush(ficlog); + return 1; + } + nagesqr=1; + if (strstr(model,"+age*age") !=0) + substrchaine(modelsav, model, "+age*age"); + else if (strstr(model,"age*age+") !=0) + substrchaine(modelsav, model, "age*age+"); + else + substrchaine(modelsav, model, "age*age"); + }else + nagesqr=0; + if (strlen(modelsav) >1){ + j=nbocc(modelsav,'+'); /**< j=Number of '+' */ + j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ + cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */ + cptcovt= j+1; /* Number of total covariates in the model, not including + * cst, age and age*age + * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/ + /* including age products which are counted in cptcovage. + * but the covariates which are products must be treated + * separately: ncovn=4- 2=2 (V1+V3). */ + cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ + cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ + + + /* Design + * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight + * < ncovcol=8 > + * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + * k= 1 2 3 4 5 6 7 8 + * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 + * covar[k,i], value of kth covariate if not including age for individual i: + * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8) + * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8 + * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and + * Tage[++cptcovage]=k + * if products, new covar are created after ncovcol with k1 + * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 + * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product + * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8 + * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; + * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted + * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 + * < ncovcol=8 > + * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 + * k= 1 2 3 4 5 6 7 8 9 10 11 12 + * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 + * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} + * p Tprod[1]@2={ 6, 5} + *p Tvard[1][1]@4= {7, 8, 5, 6} + * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 + * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + *How to reorganize? + * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age + * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} + * {2, 1, 4, 8, 5, 6, 3, 7} + * Struct [] + */ + + /* This loop fills the array Tvar from the string 'model'.*/ + /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ + /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ + /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ + /* k=3 V4 Tvar[k=3]= 4 (from V4) */ + /* k=2 V1 Tvar[k=2]= 1 (from V1) */ + /* k=1 Tvar[1]=2 (from V2) */ + /* k=5 Tvar[5] */ + /* for (k=1; k<=cptcovn;k++) { */ + /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ + /* } */ + /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */ + /* + * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ + for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/ + Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0; + } + cptcovage=0; + for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ + cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' + modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ + /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ + /*scanf("%d",i);*/ + if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ + cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ + if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ + /* covar is not filled and then is empty */ + cptcovprod--; + cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ + Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ + Typevar[k]=1; /* 1 for age product */ + cptcovage++; /* Sums the number of covariates which include age as a product */ + Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ + /*printf("stre=%s ", stre);*/ + } else if (strcmp(strd,"age")==0) { /* or age*Vn */ + cptcovprod--; + cutl(stre,strb,strc,'V'); + Tvar[k]=atoi(stre); + Typevar[k]=1; /* 1 for age product */ + cptcovage++; + Tage[cptcovage]=k; + } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ + /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ + cptcovn++; + cptcovprodnoage++;k1++; + cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ + Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but + because this model-covariate is a construction we invent a new column + which is after existing variables ncovcol+nqv+ntv+nqtv + k1 + If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 + Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ + Typevar[k]=2; /* 2 for double fixed dummy covariates */ + cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ + Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ + Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */ + Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ + Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ + k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */ + /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */ + /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */ + /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */ + /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */ + for (i=1; i<=lastobs;i++){ + /* Computes the new covariate which is a product of + covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ + covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; + } + } /* End age is not in the model */ + } /* End if model includes a product */ + else { /* no more sum */ + /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ + /* scanf("%d",i);*/ + cutl(strd,strc,strb,'V'); + ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */ + cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */ + Tvar[k]=atoi(strd); + Typevar[k]=0; /* 0 for simple covariates */ + } + strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ + /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); + scanf("%d",i);*/ + } /* end of loop + on total covariates */ + } /* end if strlen(modelsave == 0) age*age might exist */ + } /* end if strlen(model == 0) */ + + /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. + If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ + + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); + printf("cptcovprod=%d ", cptcovprod); + fprintf(ficlog,"cptcovprod=%d ", cptcovprod); + scanf("%d ",i);*/ + + +/* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind + of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */ +/* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying + model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place + k = 1 2 3 4 5 6 7 8 9 + Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5 + Typevar[k]= 0 0 0 2 1 0 2 1 1 + Fixed[k] 1 1 1 1 3 0 0 or 2 2 3 + Dummy[k] 1 0 0 0 3 1 1 2 3 + Tmodelind[combination of covar]=k; +*/ +/* Dispatching between quantitative and time varying covariates */ + /* If Tvar[k] >ncovcol it is a product */ + /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */ + /* Computing effective variables, ie used by the model, that is from the cptcovt variables */ + printf("Model=%s\n\ +Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ +Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ +Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); + fprintf(ficlog,"Model=%s\n\ +Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ +Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ +Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); + + for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */ + if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */ + Fixed[k]= 0; + Dummy[k]= 0; + ncoveff++; + ncovf++; + nsd++; + modell[k].maintype= FTYPE; + TvarsD[nsd]=Tvar[k]; + TvarsDind[nsd]=k; + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */ + Fixed[k]= 0; + Dummy[k]= 0; + ncoveff++; + ncovf++; + modell[k].maintype= FTYPE; + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ + }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ /* Only simple fixed quantitative variable */ + Fixed[k]= 0; + Dummy[k]= 1; + nqfveff++; + modell[k].maintype= FTYPE; + modell[k].subtype= FQ; + nsq++; + TvarsQ[nsq]=Tvar[k]; + TvarsQind[nsq]=k; + ncovf++; + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ + TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ + }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */ + Fixed[k]= 1; + Dummy[k]= 0; + ntveff++; /* Only simple time varying dummy variable */ + modell[k].maintype= VTYPE; + modell[k].subtype= VD; + nsd++; + TvarsD[nsd]=Tvar[k]; + TvarsDind[nsd]=k; + ncovv++; /* Only simple time varying variables */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4 TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */ + TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */ + printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv); + printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv); + }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/ + Fixed[k]= 1; + Dummy[k]= 1; + nqtveff++; + modell[k].maintype= VTYPE; + modell[k].subtype= VQ; + ncovv++; /* Only simple time varying variables */ + nsq++; + TvarsQ[nsq]=Tvar[k]; + TvarsQind[nsq]=k; + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ + TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ + TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */ + /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */ + printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv); + printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv); + }else if (Typevar[k] == 1) { /* product with age */ + ncova++; + TvarA[ncova]=Tvar[k]; + TvarAind[ncova]=k; + if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */ + Fixed[k]= 2; + Dummy[k]= 2; + modell[k].maintype= ATYPE; + modell[k].subtype= APFD; + /* ncoveff++; */ + }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/ + Fixed[k]= 2; + Dummy[k]= 3; + modell[k].maintype= ATYPE; + modell[k].subtype= APFQ; /* Product age * fixed quantitative */ + /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */ + }else if( Tvar[k] <=ncovcol+nqv+ntv ){ + Fixed[k]= 3; + Dummy[k]= 2; + modell[k].maintype= ATYPE; + modell[k].subtype= APVD; /* Product age * varying dummy */ + /* ntveff++; /\* Only simple time varying dummy variable *\/ */ + }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 3; + Dummy[k]= 3; + modell[k].maintype= ATYPE; + modell[k].subtype= APVQ; /* Product age * varying quantitative */ + /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */ + } + }else if (Typevar[k] == 2) { /* product without age */ + k1=Tposprod[k]; + if(Tvard[k1][1] <=ncovcol){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */ + ncovf++; /* Fixed variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 0; /* or 2 ?*/ + Dummy[k]= 1; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */ + ncovf++; /* Varying variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else if(Tvard[k1][1] <=ncovcol+nqv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 0; /* or 2 ?*/ + Dummy[k]= 1; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */ + ncovf++; /* Fixed variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } + }else{ + printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); + fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); + } /* end k1 */ + }else{ + printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]); + fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]); + } + printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); + printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype); + fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); + } + /* Searching for doublons in the model */ + for(k1=1; k1<= cptcovt;k1++){ + for(k2=1; k2+//#include +//#include +typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); + +LPFN_ISWOW64PROCESS fnIsWow64Process; + +BOOL IsWow64() +{ + BOOL bIsWow64 = FALSE; + + //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) + // (HANDLE, PBOOL); + + //LPFN_ISWOW64PROCESS fnIsWow64Process; + + HMODULE module = GetModuleHandle(_T("kernel32")); + const char funcName[] = "IsWow64Process"; + fnIsWow64Process = (LPFN_ISWOW64PROCESS) + GetProcAddress(module, funcName); + + if (NULL != fnIsWow64Process) + { + if (!fnIsWow64Process(GetCurrentProcess(), + &bIsWow64)) + //throw std::exception("Unknown error"); + printf("Unknown error\n"); + } + return bIsWow64 != FALSE; +} +#endif + +void syscompilerinfo(int logged) + { + /* #include "syscompilerinfo.h"*/ + /* command line Intel compiler 32bit windows, XP compatible:*/ + /* /GS /W3 /Gy + /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D + "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D + "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo + /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" + */ + /* 64 bits */ + /* + /GS /W3 /Gy + /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" + /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope + /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir + "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ + /* Optimization are useless and O3 is slower than O2 */ + /* + /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" + /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo + /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel + /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" + */ + /* Link is */ /* /OUT:"visual studio + 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT + /PDB:"visual studio + 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE + "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" + "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" + "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" + /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO + /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' + uiAccess='false'" + /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF + /NOLOGO /TLBID:1 + */ +#if defined __INTEL_COMPILER +#if defined(__GNUC__) + struct utsname sysInfo; /* For Intel on Linux and OS/X */ +#endif +#elif defined(__GNUC__) +#ifndef __APPLE__ +#include /* Only on gnu */ +#endif + struct utsname sysInfo; + int cross = CROSS; + if (cross){ + printf("Cross-"); + if(logged) fprintf(ficlog, "Cross-"); + } +#endif + +#include + + printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); +#if defined(__clang__) + printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ +#endif +#if defined(__ICC) || defined(__INTEL_COMPILER) + printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ +#endif +#if defined(__GNUC__) || defined(__GNUG__) + printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ +#endif +#if defined(__HP_cc) || defined(__HP_aCC) + printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ +#endif +#if defined(__IBMC__) || defined(__IBMCPP__) + printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ +#endif +#if defined(_MSC_VER) + printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ +#endif +#if defined(__PGI) + printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ +#endif +#if defined(__SUNPRO_C) || defined(__SUNPRO_CC) + printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ +#endif + printf(" for "); if (logged) fprintf(ficlog, " for "); + +// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros +#ifdef _WIN32 // note the underscore: without it, it's not msdn official! + // Windows (x64 and x86) + printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) "); +#elif __unix__ // all unices, not all compilers + // Unix + printf("Unix ");if(logged) fprintf(ficlog,"Unix "); +#elif __linux__ + // linux + printf("linux ");if(logged) fprintf(ficlog,"linux "); +#elif __APPLE__ + // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. + printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS "); +#endif + +/* __MINGW32__ */ +/* __CYGWIN__ */ +/* __MINGW64__ */ +// http://msdn.microsoft.com/en-us/library/b0084kay.aspx +/* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ +/* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ +/* _WIN64 // Defined for applications for Win64. */ +/* _M_X64 // Defined for compilations that target x64 processors. */ +/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ + +#if UINTPTR_MAX == 0xffffffff + printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */ +#elif UINTPTR_MAX == 0xffffffffffffffff + printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */ +#else + printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */ +#endif + +#if defined(__GNUC__) +# if defined(__GNUC_PATCHLEVEL__) +# define __GNUC_VERSION__ (__GNUC__ * 10000 \ + + __GNUC_MINOR__ * 100 \ + + __GNUC_PATCHLEVEL__) +# else +# define __GNUC_VERSION__ (__GNUC__ * 10000 \ + + __GNUC_MINOR__ * 100) +# endif + printf(" using GNU C version %d.\n", __GNUC_VERSION__); + if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); + + if (uname(&sysInfo) != -1) { + printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); + if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); + } + else + perror("uname() error"); + //#ifndef __INTEL_COMPILER +#if !defined (__INTEL_COMPILER) && !defined(__APPLE__) + printf("GNU libc version: %s\n", gnu_get_libc_version()); + if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); +#endif +#endif + + // void main() + // { +#if defined(_MSC_VER) + if (IsWow64()){ + printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); + if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); + } + else{ + printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n"); + if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); + } + // printf("\nPress Enter to continue..."); + // getchar(); + // } + +#endif + + +} + +int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){ + /*--------------- Prevalence limit (period or stable prevalence) --------------*/ + int i, j, k, i1, k4=0, nres=0 ; + /* double ftolpl = 1.e-10; */ + double age, agebase, agelim; + double tot; + + strcpy(filerespl,"PL_"); + strcat(filerespl,fileresu); + if((ficrespl=fopen(filerespl,"w"))==NULL) { + printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; + fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; + } + printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); + fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); + pstamp(ficrespl); + fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); + fprintf(ficrespl,"#Age "); + for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); + fprintf(ficrespl,"\n"); + + /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ + + agebase=ageminpar; + agelim=agemaxpar; + + /* i1=pow(2,ncoveff); */ + 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++){ + if(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(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; + } + + 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 */ + return 0; +} + +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 (period or 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 period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; + fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; + } + printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); + fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); + pstamp(ficresplb); + fprintf(ficresplb,"# Period (stable) back 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(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); + }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); + } + 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 */ + } /* cptcov */ + + /* hBijx(p, bage, fage); */ + /* fclose(ficrespijb); */ + + return 0; +} + +int hPijx(double *p, int bage, int fage){ + /*------------- h Pij x at various ages ------------*/ + + int stepsize; + int agelim; + int hstepm; + int nhstepm; + int h, i, i1, j, k, k4, nres=0; + + 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(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]); } - fscanf(ficpar,"\n"); - printf("\n"); - fprintf(ficparo,"\n"); + 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; + + 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=30; + hstepm=stepsize*YEARM; /* Every year of age */ + hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ - npar= (nlstate+ndeath-1)*nlstate*ncov; - p=param[1][1]; + /* hstepm=1; aff par mois*/ + pstamp(ficrespijb); + fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j 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 (k=1; k <= (int) pow(2,cptcoveff); k++){ + fprintf(ficrespijb,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrespijb,"******\n"); + if(invalidvarcomb[k]){ + fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); + continue; + } + + /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */ + for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */ + /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */ + nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */ + + /* nhstepm=nhstepm*YEARM; aff par mois*/ + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + /* 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); + /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */ + fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j="); + 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]); + fprintf(ficrespijb,"\n"); + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + fprintf(ficrespijb,"\n"); + } + /*}*/ + } + return 0; + } /* hBijx */ + + +/***********************************************/ +/**************** Main Program *****************/ +/***********************************************/ + +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=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; + int vpopbased=0; + int nres=0; + + char ca[32], cb[32]; + /* FILE *fichtm; *//* Html File */ + /* FILE *ficgp;*/ /*Gnuplot File */ + struct stat info; + double agedeb=0.; + + double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW; + double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */ + + double fret; + double dum=0.; /* Dummy variable */ + double ***p3mat; + /* double ***mobaverage; */ + + char line[MAXLINE]; + char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE]; + + char modeltemp[MAXLINE]; + char resultline[MAXLINE]; + char pathr[MAXLINE], pathimach[MAXLINE]; + char *tok, *val; /* pathtot */ + int firstobs=1, lastobs=10; + 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 */ + int backcast=0; + int mobilav=0,popforecast=0; + 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=0, fage=110., age, agelim=0., agebase=0.; + double ftolpl=FTOL; + double **prlim; + double **bprlim; + double ***param; /* Matrix of parameters */ + double *p; + 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 dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; + double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000; + + double **ximort; + char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; + int *dcwave; + + char z[1]="c"; + + /*char *strt;*/ + char strtend[80]; + + +/* setlocale (LC_ALL, ""); */ +/* bindtextdomain (PACKAGE, LOCALEDIR); */ +/* textdomain (PACKAGE); */ +/* setlocale (LC_CTYPE, ""); */ +/* setlocale (LC_MESSAGES, ""); */ + + /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ + rstart_time = time(NULL); + /* (void) gettimeofday(&start_time,&tzp);*/ + start_time = *localtime(&rstart_time); + curr_time=start_time; + /*tml = *localtime(&start_time.tm_sec);*/ + /* strcpy(strstart,asctime(&tml)); */ + strcpy(strstart,asctime(&start_time)); + +/* printf("Localtime (at start)=%s",strstart); */ +/* 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.tm_sec = mktime(&tmg); */ +/* strt=asctime(&tmg); */ +/* printf("Time(after) =%s",strstart); */ +/* (void) time (&time_value); +* printf("time=%d,t-=%d\n",time_value,time_value-86400); +* tm = *localtime(&time_value); +* strstart=asctime(&tm); +* printf("tim_value=%d,asctime=%s\n",time_value,strstart); +*/ + + nberr=0; /* Number of errors and warnings */ + nbwarn=0; +#ifdef WIN32 + _getcwd(pathcd, size); +#else + getcwd(pathcd, size); +#endif + syscompilerinfo(0); + printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion); + if(argc <=1){ + printf("\nEnter the parameter file name: "); + if(!fgets(pathr,FILENAMELENGTH,stdin)){ + printf("ERROR Empty parameter file name\n"); + goto end; + } + i=strlen(pathr); + if(pathr[i-1]=='\n') + pathr[i-1]='\0'; + i=strlen(pathr); + if(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); + strcpy (pathtot, val); + if(pathr[0] == '\0') break; /* Dirty */ + } + } + else{ + strcpy(pathtot,argv[1]); + } + /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ + /*cygwin_split_path(pathtot,path,optionfile); + printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ + /* cutv(path,optionfile,pathtot,'\\');*/ + + /* Split argv[0], imach program to get pathimach */ + printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); + split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); + printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); + /* strcpy(pathimach,argv[0]); */ + /* 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 */ +#endif + printf("Current directory %s!\n",pathcd); + strcpy(command,"mkdir "); + strcat(command,optionfilefiname); + if((outcmd=system(command)) != 0){ + 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); */ + } +/* if((imk=mkdir(optionfilefiname))<0){ */ +/* perror("mkdir"); */ +/* } */ + + /*-------- arguments in the command line --------*/ + + /* Main Log file */ + strcat(filelog, optionfilefiname); + strcat(filelog,".log"); /* */ + if((ficlog=fopen(filelog,"w"))==NULL) { + printf("Problem with logfile %s\n",filelog); + goto end; + } + fprintf(ficlog,"Log filename:%s\n",filelog); + 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); + + 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.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 */ + + /* Main ---------arguments file --------*/ + + if((ficpar=fopen(optionfile,"r"))==NULL) { + 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; */ + exit(70); + } + + + + strcpy(filereso,"o"); + 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; + } + /* Reads comments: lines beginning with '#' */ + numlinepar=0; + + /* First parameter line */ + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; + } + 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"); + } + numlinepar++; + printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); + } + /* Second parameter line */ + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; + } + 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); + } + 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); + } + /* 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++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; + } + if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ + if (num_filled == 0) + model[0]='\0'; + else if (num_filled != 1){ + printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); + fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %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); + } + /* 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 with '.' \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 file.\n"); + exit(1); + } + } while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); - puts(line); + numlinepar++; + 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); - delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncov); - delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ - for(i=1; i <=nlstate; i++){ - for(j=1; j <=nlstate+ndeath-1; j++){ - fscanf(ficpar,"%1d%1d",&i1,&j1); - printf("%1d%1d",i,j); - fprintf(ficparo,"%1d%1d",i1,j1); - for(k=1; k<=ncov;k++){ - fscanf(ficpar,"%le",&delti3[i][j][k]); - printf(" %le",delti3[i][j][k]); - fprintf(ficparo," %le",delti3[i][j][k]); + + covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ + coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */ + cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/ + cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */ + 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 */ + prwizard(ncovmodel, nlstate, ndeath, model, ficparo); + printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); + fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); + free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); + fclose (ficparo); + fclose (ficlog); + goto end; + exit(0); + } else if(mle==-5) { /* Main Wizard */ + prwizard(ncovmodel, nlstate, ndeath, model, ficparo); + printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); + fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); + param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); + matcov=matrix(1,npar,1,npar); + hess=matrix(1,npar,1,npar); + } else{ /* Begin of mle != -1 or -5 */ + /* Read guessed parameters */ + /* Reads comments: lines beginning with '#' */ + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + } + ungetc(c,ficpar); + + param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); + for(i=1; i <=nlstate; i++){ + j=0; + for(jj=1; jj <=nlstate+ndeath; jj++){ + if(jj==i) continue; + j++; + fscanf(ficpar,"%1d%1d",&i1,&j1); + if ((i1 != i) || (j1 != jj)){ + printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ +It might be a problem of design; if ncovcol and the model are correct\n \ +run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); + exit(1); + } + fprintf(ficparo,"%1d%1d",i1,j1); + if(mle==1) + printf("%1d%1d",i,jj); + fprintf(ficlog,"%1d%1d",i,jj); + for(k=1; k<=ncovmodel;k++){ + fscanf(ficpar," %lf",¶m[i][j][k]); + if(mle==1){ + printf(" %lf",param[i][j][k]); + fprintf(ficlog," %lf",param[i][j][k]); + } + else + fprintf(ficlog," %lf",param[i][j][k]); + fprintf(ficparo," %lf",param[i][j][k]); + } + fscanf(ficpar,"\n"); + numlinepar++; + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficparo,"\n"); + } + } + fflush(ficlog); + + /* Reads scales values */ + p=param[1][1]; + + /* Reads comments: lines beginning with '#' */ + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + } + ungetc(c,ficpar); + + for(i=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath-1; j++){ + fscanf(ficpar,"%1d%1d",&i1,&j1); + if ( (i1-i) * (j1-j) != 0){ + printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); + exit(1); + } + printf("%1d%1d",i,j); + fprintf(ficparo,"%1d%1d",i1,j1); + fprintf(ficlog,"%1d%1d",i1,j1); + for(k=1; k<=ncovmodel;k++){ + fscanf(ficpar,"%le",&delti3[i][j][k]); + printf(" %le",delti3[i][j][k]); + fprintf(ficparo," %le",delti3[i][j][k]); + fprintf(ficlog," %le",delti3[i][j][k]); + } + fscanf(ficpar,"\n"); + numlinepar++; + printf("\n"); + fprintf(ficparo,"\n"); + fprintf(ficlog,"\n"); + } + } + fflush(ficlog); + + /* Reads covariance matrix */ + delti=delti3[1][1]; + + + /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ + + /* Reads comments: lines beginning with '#' */ + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + } + ungetc(c,ficpar); + + matcov=matrix(1,npar,1,npar); + hess=matrix(1,npar,1,npar); + for(i=1; i <=npar; i++) + for(j=1; j <=npar; j++) matcov[i][j]=0.; + + /* Scans npar lines */ + for(i=1; i <=npar; i++){ + count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk); + if(count != 3){ + printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ +This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ +Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); + fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ +This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ +Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); + exit(1); + }else{ + if(mle==1) + printf("%1d%1d%d",i1,j1,jk); + } + fprintf(ficlog,"%1d%1d%d",i1,j1,jk); + fprintf(ficparo,"%1d%1d%d",i1,j1,jk); + for(j=1; j <=i; j++){ + fscanf(ficpar," %le",&matcov[i][j]); + if(mle==1){ + printf(" %.5le",matcov[i][j]); + } + fprintf(ficlog," %.5le",matcov[i][j]); + fprintf(ficparo," %.5le",matcov[i][j]); } fscanf(ficpar,"\n"); - printf("\n"); + numlinepar++; + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); fprintf(ficparo,"\n"); } - } - delti=delti3[1][1]; + /* End of read covariance matrix npar lines */ + for(i=1; i <=npar; i++) + for(j=i+1;j<=npar;j++) + matcov[i][j]=matcov[j][i]; + + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + + fflush(ficlog); + + /*-------- 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; + } + fprintf(ficres,"#%s\n",version); + } /* End of mle != -3 */ - /* Reads comments: lines beginning with '#' */ - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); + /* Main data + */ + n= lastobs; + num=lvector(1,n); + moisnais=vector(1,n); + annais=vector(1,n); + moisdc=vector(1,n); + andc=vector(1,n); + weight=vector(1,n); + agedc=vector(1,n); + cod=ivector(1,n); + for(i=1;i<=n;i++){ + num[i]=0; + moisnais[i]=0; + annais[i]=0; + moisdc[i]=0; + andc[i]=0; + agedc[i]=0; + cod[i]=0; + weight[i]=1.0; /* Equal weights, 1 by default */ + } + mint=matrix(1,maxwav,1,n); + anint=matrix(1,maxwav,1,n); + s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ + tab=ivector(1,NCOVMAX); + ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ + ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ + + /* Reads data from file datafile */ + if (readdata(datafile, firstobs, lastobs, &imx)==1) + goto end; + + /* Calculation of the number of parameters from char model */ + /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 + k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 + k=3 V4 Tvar[k=3]= 4 (from V4) + k=2 V1 Tvar[k=2]= 1 (from V1) + k=1 Tvar[1]=2 (from V2) + */ - matcov=matrix(1,npar,1,npar); - for(i=1; i <=npar; i++){ - fscanf(ficpar,"%s",&str); - printf("%s",str); - fprintf(ficparo,"%s",str); - for(j=1; j <=i; j++){ - fscanf(ficpar," %le",&matcov[i][j]); - printf(" %.5le",matcov[i][j]); - fprintf(ficparo," %.5le",matcov[i][j]); - } - fscanf(ficpar,"\n"); - printf("\n"); - fprintf(ficparo,"\n"); + Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ + TvarsDind=ivector(1,NCOVMAX); /* */ + TvarsD=ivector(1,NCOVMAX); /* */ + TvarsQind=ivector(1,NCOVMAX); /* */ + TvarsQ=ivector(1,NCOVMAX); /* */ + TvarF=ivector(1,NCOVMAX); /* */ + TvarFind=ivector(1,NCOVMAX); /* */ + TvarV=ivector(1,NCOVMAX); /* */ + TvarVind=ivector(1,NCOVMAX); /* */ + TvarA=ivector(1,NCOVMAX); /* */ + TvarAind=ivector(1,NCOVMAX); /* */ + TvarFD=ivector(1,NCOVMAX); /* */ + TvarFDind=ivector(1,NCOVMAX); /* */ + TvarFQ=ivector(1,NCOVMAX); /* */ + TvarFQind=ivector(1,NCOVMAX); /* */ + TvarVD=ivector(1,NCOVMAX); /* */ + TvarVDind=ivector(1,NCOVMAX); /* */ + TvarVQ=ivector(1,NCOVMAX); /* */ + TvarVQind=ivector(1,NCOVMAX); /* */ + + Tvalsel=vector(1,NCOVMAX); /* */ + Tvarsel=ivector(1,NCOVMAX); /* */ + Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */ + Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */ + Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */ + /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). + For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, + Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. + */ + /* For model-covariate k tells which data-covariate to use but + because this model-covariate is a construction we invent a new column + ncovcol + k1 + If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 + Tvar[3=V1*V4]=4+1 etc */ + Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */ + Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */ + /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 + if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) + Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 + */ + Tvaraff=ivector(1,NCOVMAX); /* Unclear */ + Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm + * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. + * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ + Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age + 4 covariates (3 plus signs) + Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 + */ + Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an + * individual dummy, fixed or varying: + * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4, + * 3, 1, 0, 0, 0, 0, 0, 0}, + * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , + * V1 df, V2 qf, V3 & V4 dv, V5 qv + * Tmodelind[1]@9={9,0,3,2,}*/ + TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/ + TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an + * individual quantitative, fixed or varying: + * Tmodelqind[1]=1,Tvaraff[1]@9={4, + * 3, 1, 0, 0, 0, 0, 0, 0}, + * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ +/* Main decodemodel */ + + + if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/ + goto end; + + if((double)(lastobs-imx)/(double)imx > 1.10){ + nbwarn++; + printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); + fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); + } + /* if(mle==1){*/ + if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ + for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ } - for(i=1; i <=npar; i++) - for(j=i+1;j<=npar;j++) - matcov[i][j]=matcov[j][i]; + + /*-calculation of age at interview from date of interview and age at death -*/ + agev=matrix(1,maxwav,1,imx); + + if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) + goto end; + + + agegomp=(int)agemin; + free_vector(moisnais,1,n); + free_vector(annais,1,n); + /* free_matrix(mint,1,maxwav,1,n); + free_matrix(anint,1,maxwav,1,n);*/ + /* free_vector(moisdc,1,n); */ + /* free_vector(andc,1,n); */ + /* */ + + wav=ivector(1,imx); + /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */ + /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */ + /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */ + dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/ + bh=imatrix(1,lastpass-firstpass+2,1,imx); + mw=imatrix(1,lastpass-firstpass+2,1,imx); - printf("\n"); + /* Concatenates waves */ + /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. + Death is a valid wave (if date is known). + mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i + dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] + and mw[mi+1][i]. dh depends on stepm. + */ + + concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); + /* */ + + free_vector(moisdc,1,n); + free_vector(andc,1,n); + + /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ + nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); + ncodemax[1]=1; + Ndum =ivector(-1,NCOVMAX); + cptcoveff=0; + if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */ + tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ + } + + ncovcombmax=pow(2,cptcoveff); + invalidvarcomb=ivector(1, ncovcombmax); + for(i=1;i IMaCh Cov %s \n %s
%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\n\nIMaCh %s \n IMaCh for Interpolated Markov Chain
\nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-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\ +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\ + - Parameter file: %s.%s
\n\ + - Copy of the parameter file: o%s
\n\ + - Log file of the run: %s
\n\ + - Gnuplot file name: %s
\n\ + - Date and time at start: %s
Total number of 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); + 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 */ + + /* 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); + for(i=1;i<=NDIM;i++) + for(j=1;j<=NDIM;j++) + ximort[i][j]=0.; + /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ + cens=ivector(1,n); + ageexmed=vector(1,n); + agecens=vector(1,n); + dcwave=ivector(1,n); + + for (i=1; i<=imx; i++){ + dcwave[i]=-1; + for (m=firstpass; m<=lastpass; m++) + if (s[m][i]>nlstate) { + dcwave[i]=m; + /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ + 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; + }else if (ageexmed[i]< 1) + cens[i]= -1; + if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) + cens[i]=0 ; + } + else cens[i]=-1; + } + + for (i=1;i<=NDIM;i++) { + for (j=1;j<=NDIM;j++) + ximort[i][j]=(i == j ? 1.0 : 0.0); + } + + /*p[1]=0.0268; p[NDIM]=0.083;*/ + /*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"); +#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); + } - if(mle==1){ - /*-------- data file ----------*/ - if((ficres =fopen(fileres,"w"))==NULL) { - printf("Problem with resultfile: %s\n", fileres);goto end; + /* 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); + + 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); } - fprintf(ficres,"#%s\n",version); - if((fic=fopen(datafile,"r"))==NULL) { - printf("Problem with datafile: %s\n", datafile);goto end; + 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=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 */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm); - fprintf(ficrespij,"# Age"); - 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,"%.0f %.0f",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"); + 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); } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - fprintf(ficrespij,"\n"); - } - fclose(ficrespij); + 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); - /*---------- Health expectancies and variances ------------*/ - - eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm); - - vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl); + /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ + + 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(TKresult[nres]!= k) + continue; + printf("\n#****** Selected:"); + fprintf(ficrest,"\n#****** Selected:"); + fprintf(ficlog,"\n#****** Selected:"); + 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#****** "); + 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); + + + 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 period (stable) prevalences in each health state \n"); + fprintf(ficrest,"# Age popbased mobilav e.. (std) "); + for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); + fprintf(ficrest,"\n"); + /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ + epj=vector(1,nlstate+1); + printf("Computing age specific period (stable) prevalences in each health state \n"); + fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n"); + for(age=bage; age <=fage ;age++){ + prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, 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]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][k]; + } + } + + fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); + /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */ + /* printf(" age %4.0f ",age); */ + for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ + for(i=1, epj[j]=0.;i <=nlstate;i++) { + epj[j] += prlim[i][i]*eij[i][j][(int)age]; + /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ + /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */ + } + epj[nlstate+1] +=epj[j]; + } + /* printf(" age %4.0f \n",age); */ + + for(i=1, vepp=0.;i <=nlstate;i++) + for(j=1;j <=nlstate;j++) + vepp += vareij[i][j][(int)age]; + fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); + for(j=1;j <=nlstate;j++){ + fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); + } + fprintf(ficrest,"\n"); + } + } /* End vpopbased */ + free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_vector(epj,1,nlstate+1); + printf("done selection\n");fflush(stdout); + fprintf(ficlog,"done selection\n");fflush(ficlog); + + /*}*/ + } /* End k selection */ - strcpy(filerest,"t"); - strcat(filerest,fileres); - if((ficrest=fopen(filerest,"w"))==NULL) { - printf("Problem with total LE resultfile: %s\n", filerest);goto end; - } - printf("Computing Total LEs with variances: file '%s' \n", filerest); - fprintf(ficrest,"#Total LEs with variances: e.. (std) "); - for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); - fprintf(ficrest,"\n"); - - hf=1; - if (stepm >= YEARM) hf=stepm/YEARM; - epj=vector(1,nlstate+1); - for(age=bage; age <=fage ;age++){ - prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl); - fprintf(ficrest," %.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]*hf*eij[i][j][(int)age]; - } - epj[nlstate+1] +=epj[j]; - } - for(i=1, vepp=0.;i <=nlstate;i++) - for(j=1;j <=nlstate;j++) - vepp += vareij[i][j][(int)age]; - fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp)); - for(j=1;j <=nlstate;j++){ - fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age])); - } - fprintf(ficrest,"\n"); - } - fclose(ficrest); - fclose(ficpar); - free_vector(epj,1,nlstate+1); + printf("done State-specific expectancies\n");fflush(stdout); + fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog); - /*------- Variance limit prevalence------*/ + /*------- Variance of period (stable) prevalence------*/ + + strcpy(fileresvpl,"VPL_"); + strcat(fileresvpl,fileresu); + 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' ...", fileresvpl);fflush(stdout); + fprintf(ficlog, "Computing Variance-covariance of 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;} - 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); - - - free_matrix(varpl,1,nlstate,(int) bage, (int)fage); - - free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); - free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); - - - free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ + if(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(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres); + free_matrix(varpl,1,nlstate,(int) bage, (int)fage); + /*}*/ + } + + fclose(ficresvpl); + printf("done variance-covariance of period prevalence\n");fflush(stdout); + fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); + + free_vector(weight,1,n); + free_imatrix(Tvard,1,NCOVMAX,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); + free_ivector(tab,1,NCOVMAX); + fclose(ficresstdeij); + fclose(ficrescveij); + fclose(ficresvij); + fclose(ficrest); + fclose(ficpar); + + + /*---------- End : free ----------------*/ + if (mobilav!=0 ||mobilavproj !=0) + free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */ + free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); + free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ + free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); + } /* mle==-3 arrives here for freeing */ + /* endfree:*/ free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); - + free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n); + free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n); + free_matrix(coqvar,1,maxwav,1,n); + free_matrix(covar,0,NCOVMAX,1,n); free_matrix(matcov,1,npar,1,npar); - free_vector(delti,1,npar); - - free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncov); - - printf("End of Imach\n"); + 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(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(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. 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 */ - - /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/ - /*printf("Total time was %d uSec.\n", total_usecs);*/ + /*(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(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,"
Local time at start %s
Local time at end %s
\n",strstart, strtend); + fclose(fichtm); + fprintf(fichtmcov,"
Local time at start %s
Local time at end %s
\n",strstart, strtend); + fclose(fichtmcov); + fclose(ficgp); + fclose(ficlog); /*------ End -----------*/ - - end: -#ifdef windows - chdir(pathcd); + + + 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) +#else + if(chdir(pathcd) != 0) + printf("Can't move to directory %s!\n", path); + if (getcwd(pathcd, MAXLINE) > 0) #endif - system("gnuplot graph.gp"); - -#ifdef windows + printf("Current directory %s!\n",pathcd); + /*strcat(plotcmd,CHARSEPARATOR);*/ + sprintf(plotcmd,"gnuplot"); +#ifdef _WIN32 + sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); +#endif + if(!stat(plotcmd,&info)){ + printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); + if(!stat(getenv("GNUPLOTBIN"),&info)){ + printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); + }else + strcpy(pplotcmd,plotcmd); +#ifdef __unix + strcpy(plotcmd,GNUPLOTPROGRAM); + if(!stat(plotcmd,&info)){ + printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); + }else + strcpy(pplotcmd,plotcmd); +#endif + }else + strcpy(pplotcmd,plotcmd); + + sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); + printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); + + if((outcmd=system(plotcmd)) != 0){ + printf("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); + } + printf(" Successful, please wait..."); while (z[0] != 'q') { - chdir(pathcd); - printf("\nType e to edit output files, c to start again, and q for exiting: "); + /* chdir(path); */ + 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"); - else if (z[0] == 'e') { - chdir(path); - system("index.htm"); +/* if (z[0] == 'c') system("./imach"); */ + if (z[0] == 'e') { +#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); } -#endif +end: + while (z[0] != 'q') { + printf("\nType q for exiting: "); fflush(stdout); + scanf("%s",z); + } } -
");
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
-
-/*int main(int argc, char *argv[])*/
-int main()
-{
-
- int i,j, k, n=MAXN,iter,m,size;
- double agedeb, agefin,hf;
- double agemin=1.e20, agemax=-1.e20;
-
- double fret;
- double **xi,tmp,delta;
-
- double dum; /* Dummy variable */
- double ***p3mat;
- int *indx;
- char line[MAXLINE], linepar[MAXLINE];
- char title[MAXLINE];
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
- char filerest[FILENAMELENGTH];
- char fileregp[FILENAMELENGTH];
- char path[80],pathc[80],pathcd[80],pathtot[80];
- 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,jk,aa,bb, stepsize;
- int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
-
- int hstepm, nhstepm;
- double bage, fage, age, agelim, agebase;
- double ftolpl=FTOL;
- double **prlim;
- double *severity;
- double ***param; /* Matrix of parameters */
- double *p;
- double **matcov; /* Matrix of covariance */
- double ***delti3; /* Scale */
- double *delti; /* Scale */
- double ***eij, ***vareij;
- double **varpl; /* Variances of prevalence limits by age */
- double *epj, vepp;
- char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";
- char *alph[]={"a","a","b","c","d","e"}, str[4];
- char z[1]="c";
-#include
************ Results for covariates");
+ for (cpt=1; cpt<=cptcoveff;cpt++){
+ 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);
+ }
+ /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+ fprintf(fichtm," ************\n
");
+ if(invalidvarcomb[k1]){
+ fprintf(fichtm,"\nCombination (%d) ignored because no cases
\n",k1);
+ printf("\nCombination (%d) ignored because no cases \n",k1);
+ continue;
+ }
+ }
+ /* aij, bij */
+ fprintf(fichtm,"
- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: %s_%d-1.svg
\
+![](\"%s_%d-1.svg\")
",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ /* 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.svg
\
+![](\"%s_%d-2.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ /* Quasi-incidences */
+ fprintf(fichtm,"
\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
+ incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
+divided by h: hPij/h : %s_%d-3.svg
\
+![](\"%s_%d-3.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ /* Survival functions (period) in state j */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
\
+![](\"%s_%d-%d.svg\")
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
+ }
+ /* State specific survival functions (period) */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Survival functions from state %d in each live state and total.\
+ Or probability to survive in various states (1 to %d) being in state %d at different ages. \
+ %s%d_%d.svg
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
+ }
+ /* Period (stable) prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d.svg
\
+", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+ }
+ if(backcast==1){
+ /* Period (stable) back prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d.svg
\
+", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
+ }
+ }
+ if(prevfcast==1){
+ /* Projection of prevalence up to period (stable) prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
\
+", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
+ }
+ }
+
+ for(cpt=1; cpt<=nlstate;cpt++) {
+ fprintf(fichtm,"\n
- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d%d.svg
\
+![](\"%s_%d%d.svg\")
",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
+ }
+ /* } /\* end i1 *\/ */
+ }/* End k1 */
+ fprintf(fichtm,"
![%s%d_%d.svg](\"%s%d_%d.svg\"){kind=link}
\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 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 period (stable) prevalences: %s
\n",\ + subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); + +/* 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); + fprintf(fichtm,"
"); + + m=pow(2,cptcoveff); + if (cptcovn < 1) {m=1;ncodemax[1]=1;} + + jj1=0; + for(k1=1; k1<=m;k1++){ + /* for(i1=1; i1<=ncodemax[k1];i1++){ */ + jj1++; + if (cptcovn > 0) { + fprintf(fichtm,"
************ Results for covariates"); + for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */ + fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); + fprintf(fichtm," ************\n
"); + + if(invalidvarcomb[k1]){ + fprintf(fichtm,"\n
Combination (%d) ignored because no cases
\n",k1); + continue; + } + } + for(cpt=1; cpt<=nlstate;cpt++) { + fprintf(fichtm,"\n- Observed (cross-sectional) and period (incidence based) \ +prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d.svg\n
\ +
",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,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). If popbased=1 the smooth (due to the model) \ +true period expectancies (those weighted with period prevalences are also\ + drawn in addition to the population based expectancies computed using\ + observed and cahotic prevalences: %s_%d.svg\n
\ +
![](\"%s_%d.svg\")
",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
+ /* } /\* end i1 *\/ */
+ }/* End k1 */
+ fprintf(fichtm,"