********** 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(i=1; i<=nlstate;i++)
+ fprintf(ficresphtm,"| Age | Prev(%d) | N(%d) | N | ",i,i); + } fprintf(ficresp, "\n"); + fprintf(ficresphtm, "\n"); + + /* Header of frequency table by age */ + fprintf(ficresphtmfr,"
|---|
| 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(i=(int)agemin; i <= (int)agemax+3; i++){ - if(i==(int)agemax+3){ + /* For each age */ + for(i=iagemin; i <= iagemax+3; i++){ + fprintf(ficresphtm,"||||||||
|---|---|---|---|---|---|---|---|---|---|
| 0 | "); + }else if(i==iagemax+2){ + fprintf(ficlog,"0"); + fprintf(ficresphtmfr,"|||||||||
| Unknown | "); + }else if(i==iagemax+3){ fprintf(ficlog,"Total"); + fprintf(ficresphtmfr,"|||||||||
| Total | "); }else{ if(first==1){ first=0; printf("See log file for details...\n"); } + fprintf(ficresphtmfr,"|||||||||
| %d | ",i); fprintf(ficlog,"Age %d", i); } for(jk=1; jk <=nlstate ; jk++){ @@ -1334,7 +3861,7 @@ void freqsummary(char fileres[], int ag pos += freq[jk][m][i]; if(pp[jk]>=1.e-10){ if(first==1){ - printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + 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{ @@ -1347,10 +3874,11 @@ void freqsummary(char fileres[], int ag for(jk=1; jk <=nlstate ; jk++){ for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) pp[jk] += freq[jk][m][i]; - } - - for(jk=1,pos=0; jk <=nlstate ; jk++) + } + for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ pos += pp[jk]; + posprop += prop[jk][i]; + } for(jk=1; jk <=nlstate ; jk++){ if(pos>=1.e-5){ if(first==1) @@ -1361,303 +3889,490 @@ void freqsummary(char fileres[], int ag printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); } - if( i <= (int) agemax){ + if( i <= iagemax){ if(pos>=1.e-5){ - fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); - probs[i][jk][j1]= pp[jk]/pos; + fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); + fprintf(ficresphtm,"%d | %.5f | %.0f | %.0f | ",i,prop[jk][i]/posprop, prop[jk][i],posprop); + /*probs[i][jk][j1]= pp[jk]/pos;*/ /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ } - else - fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); + else{ + fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); + fprintf(ficresphtm,"%d | NaNq | %.0f | %.0f | ",i, prop[jk][i],posprop); + } } } - for(jk=-1; jk <=nlstate+ndeath; jk++) - for(m=-1; m <=nlstate+ndeath; m++) - if(freq[jk][m][i] !=0 ) { - if(first==1) - printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); + for(jk=-1; jk <=nlstate+ndeath; jk++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(freq[jk][m][i] !=0 ) { /* minimizing output */ + if(first==1){ + printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); + } fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); } - if(i <= (int) agemax) + if(jk!=0 && m!=0) + fprintf(ficresphtmfr,"%.0f | ",freq[jk][m][i]); + } + } + fprintf(ficresphtmfr,"
Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)
%s (à revoir)
\n",digitp); + varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); + xp=vector(1,npar); + xm=vector(1,npar); + dnewm=matrix(1,nlstate*nlstate,1,npar); + doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); + + pstamp(ficresstdeij); + fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); + fprintf(ficresstdeij,"# Age"); + for(i=1; i<=nlstate;i++){ + for(j=1; j<=nlstate;j++) + fprintf(ficresstdeij," e%1d%1d (SE)",i,j); + fprintf(ficresstdeij," e%1d. ",i); } - varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + fprintf(ficresstdeij,"\n"); - fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n"); - fprintf(ficresvij,"# Age"); + pstamp(ficrescveij); + fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); + fprintf(ficrescveij,"# Age"); for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate;j++) - 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*/ + for(j=1; j<=nlstate;j++){ + cptj= (j-1)*nlstate+i; + for(i2=1; i2<=nlstate;i2++) + for(j2=1; j2<=nlstate;j2++){ + cptj2= (j2-1)*nlstate+i2; + if(cptj2 <= cptj) + fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); + } + } + fprintf(ficrescveij,"\n"); if(estepm < stepm){ printf ("Problem %d lower than %d\n",estepm, stepm); } else hstepm=estepm; + /* We compute the life expectancy from trapezoids spaced every estepm months + * This is mainly to measure the difference between two models: for example + * if stepm=24 months pijx are given only every 2 years and by summing them + * we are calculating an estimate of the Life Expectancy assuming a linear + * progression in between and thus overestimating or underestimating according + * to the curvature of the survival function. If, for the same date, we + * estimate the model with stepm=1 month, we can keep estepm to 24 months + * to compare the new estimate of Life expectancy with the same linear + * hypothesis. A more precise result, taking into account a more precise + * curvature will be obtained if estepm is as small as stepm. */ + /* For example we decided to compute the life expectancy with the smallest unit */ /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. nhstepm is the number of hstepm from age to agelim nstepm is the number of stepm from age to agelin. Look at hpijx to understand the reason of that which relies in memory size - and note for a fixed period like k years */ + and note for a fixed period like estepm months */ /* We decided (b) to get a life expectancy respecting the most precise curvature of the survival function given by stepm (the optimization length). Unfortunately it means that if the survival funtion is printed only each two years of age and if @@ -1918,238 +4536,516 @@ void varevsij(char optionfilefiname[], d 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); + /* If stepm=6 months */ + /* nhstepm age range expressed in number of stepm */ + agelim=AGESUP; + nstepm=(int) rint((agelim-bage)*YEARM/stepm); + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ + + p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); + trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); + gp=matrix(0,nhstepm,1,nlstate*nlstate); + gm=matrix(0,nhstepm,1,nlstate*nlstate); + for (age=bage; age<=fage; age ++){ + nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ + + /* If stepm=6 months */ + /* Computed by stepm unit matrices, product of hstepma matrices, stored + in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ + + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ + + /* Computing Variances of health expectancies */ + /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to + decrease memory allocation */ for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++){ /* Computes gradient */ - xp[i] = x[i] + (i==theta ?delti[theta]:0); - } - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][ij]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][ij]; - } - } - - 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]; - } - } - /* This for computing forces of mortality (h=1)as a weighted average */ - for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) - gpp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end force of mortality */ - - for(i=1; i<=npar; i++) /* Computes gradient */ - xp[i] = x[i] - (i==theta ?delti[theta]:0); - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][ij]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][ij]; - } + for(i=1; i<=npar; i++){ + xp[i] = x[i] + (i==theta ?delti[theta]:0); + xm[i] = x[i] - (i==theta ?delti[theta]:0); } - + hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); + hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); + for(j=1; j<= nlstate; j++){ - for(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 force of mortality (h=1)as a weighted average */ - for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) - gmp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end force of mortality */ - - 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; + for(i=1; i<=nlstate; i++){ + for(h=0; h<=nhstepm-1; h++){ + gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; + gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; + } + } + } + + for(ij=1; ij<= nlstate*nlstate; ij++) + for(h=0; h<=nhstepm-1; h++){ + gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; + } + }/* End theta */ + + + for(h=0; h<=nhstepm-1; h++) + for(j=1; j<=nlstate*nlstate;j++) + for(theta=1; theta <=npar; theta++) + trgradg[h][j][theta]=gradg[h][theta][j]; + + + for(ij=1;ij<=nlstate*nlstate;ij++) + for(ji=1;ji<=nlstate*nlstate;ji++) + varhe[ij][ji][(int)age] =0.; + + printf("%d|",(int)age);fflush(stdout); + fprintf(ficlog,"%d|",(int)age);fflush(ficlog); + for(h=0;h<=nhstepm-1;h++){ + for(k=0;k<=nhstepm-1;k++){ + matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); + for(ij=1;ij<=nlstate*nlstate;ij++) + for(ji=1;ji<=nlstate*nlstate;ji++) + varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; } } - - /* 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 */ - hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); - - if (popbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][ij]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][ij]; + + /* Computing expectancies */ + hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++) + for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ + eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; + + /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ + + } + + fprintf(ficresstdeij,"%3.0f",age ); + for(i=1; i<=nlstate;i++){ + eip=0.; + vip=0.; + for(j=1; j<=nlstate;j++){ + eip += eij[i][j][(int)age]; + for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ + vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; + fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); } + fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); } - - /* This for computing force of mortality (h=1)as a weighted average */ - for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) - gmp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end force of mortality */ - - 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 ); + fprintf(ficresstdeij,"\n"); + + fprintf(ficrescveij,"%3.0f",age ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ - fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); + cptj= (j-1)*nlstate+i; + for(i2=1; i2<=nlstate;i2++) + for(j2=1; j2<=nlstate;j2++){ + cptj2= (j2-1)*nlstate+i2; + if(cptj2 <= cptj) + fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); + } } - fprintf(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,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); - /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ - fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); - 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(fichtm,"\n
File (multiple files are possible if covariates are present): %s\n",fileresprobmorprev,fileresprobmorprev); - fprintf(fichtm,"\n
Probability is computed over estepm=%d months.
![](\"varmuptjgr%s%s.png\")
\n", stepm,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
\n", stepm,YEARM,digitp,digit); -*/ - fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit); - + fprintf(ficrescveij,"\n"); + + } + free_matrix(gm,0,nhstepm,1,nlstate*nlstate); + free_matrix(gp,0,nhstepm,1,nlstate*nlstate); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); + free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); + free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + printf("\n"); + fprintf(ficlog,"\n"); + + free_vector(xm,1,npar); 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); - fclose(ficgp); - fclose(fichtm); + free_matrix(dnewm,1,nlstate*nlstate,1,npar); + free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); + free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); } + +/************ Variance ******************/ + void varevsij(char optionfilefiname[], double ***vareij, 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, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) + { + /* Variance of health expectancies */ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ + /* double **newm;*/ + /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ + + /* int movingaverage(); */ + double **dnewm,**doldm; + double **dnewmp,**doldmp; + int i, j, nhstepm, hstepm, h, nstepm ; + int k; + double *xp; + double **gp, **gm; /* for var eij */ + double ***gradg, ***trgradg; /*for var eij */ + double **gradgp, **trgradgp; /* for var p point j */ + double *gpp, *gmp; /* for var p point j */ + double **varppt; /* for var p point j nlstate to nlstate+ndeath */ + double ***p3mat; + double age,agelim, hf; + /* double ***mobaverage; */ + int theta; + char digit[4]; + char digitp[25]; + + char fileresprobmorprev[FILENAMELENGTH]; + + if(popbased==1){ + if(mobilav!=0) + strcpy(digitp,"-POPULBASED-MOBILAV_"); + else strcpy(digitp,"-POPULBASED-NOMOBIL_"); + } + else + strcpy(digitp,"-STABLBASED_"); -/************ Variance of prevlim ******************/ -void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) -{ - /* Variance of prevalence limit */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - double **newm; - double **dnewm,**doldm; - int i, j, nhstepm, hstepm; - int k, cptcode; - double *xp; - double *gp, *gm; - double **gradg, **trgradg; - double age,agelim; - int theta; - - fprintf(ficresvpl,"# Standard deviation of stable prevalences \n"); - fprintf(ficresvpl,"# Age"); - for(i=1; i<=nlstate;i++) - fprintf(ficresvpl," %1d-%1d",i,i); - fprintf(ficresvpl,"\n"); - - xp=vector(1,npar); - dnewm=matrix(1,nlstate,1,npar); - doldm=matrix(1,nlstate,1,nlstate); + /* if (mobilav!=0) { */ + /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ + /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */ + /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */ + /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */ + /* } */ + /* } */ + + strcpy(fileresprobmorprev,"PRMORPREV-"); + sprintf(digit,"%-d",ij); + /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/ + strcat(fileresprobmorprev,digit); /* Tvar to be done */ + strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */ + strcat(fileresprobmorprev,fileresu); + if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresprobmorprev); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); + } + printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + pstamp(ficresprobmorprev); + fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); + fprintf(ficresprobmorprev,"# Age cov=%-d",ij); + for(j=nlstate+1; j<=(nlstate+ndeath);j++){ + fprintf(ficresprobmorprev," p.%-d SE",j); + for(i=1; i<=nlstate;i++) + fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); + } + fprintf(ficresprobmorprev,"\n"); + + fprintf(ficgp,"\n# Routine varevsij"); + fprintf(ficgp,"\nunset title \n"); + /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ + fprintf(fichtm,"\n
Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)
%s
\n",digitp); + /* } */ + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); + pstamp(ficresvij); + fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); + if(popbased==1) + fprintf(ficresvij,"the age specific prevalence observed (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*/ - hstepm=1*YEARM; /* Every year of age */ - hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ - agelim = AGESUP; - for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ - nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ - if (stepm >= YEARM) hstepm=1; - nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ - gradg=matrix(1,npar,1,nlstate); - gp=vector(1,nlstate); - gm=vector(1,nlstate); - - for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++){ /* Computes gradient */ - xp[i] = x[i] + (i==theta ?delti[theta]:0); + 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); + + 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); /* 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); + + 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); + + 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); + + 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); + 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, int *ncvyearp, int ij, char strstart[]) +{ + /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ + + double **dnewm,**doldm; + int i, j, nhstepm, hstepm; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double **mgm, **mgp; + double age,agelim; + int theta; + + pstamp(ficresvpl); + fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); + fprintf(ficresvpl,"# Age"); + for(i=1; i<=nlstate;i++) + fprintf(ficresvpl," %1d-%1d",i,i); + fprintf(ficresvpl,"\n"); + + xp=vector(1,npar); + dnewm=matrix(1,nlstate,1,npar); + doldm=matrix(1,nlstate,1,nlstate); + + hstepm=1*YEARM; /* Every year of age */ + hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ + agelim = AGESUP; + for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ + nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + if (stepm >= YEARM) hstepm=1; + nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ + gradg=matrix(1,npar,1,nlstate); + mgp=matrix(1,npar,1,nlstate); + mgm=matrix(1,npar,1,nlstate); + gp=vector(1,nlstate); + gm=vector(1,nlstate); + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++){ /* Computes gradient */ + xp[i] = x[i] + (i==theta ?delti[theta]:0); } - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); - for(i=1;i<=nlstate;i++) + if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); + 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,ij); - 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); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); + 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); @@ -2157,11 +5053,34 @@ 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 */ @@ -2171,6 +5090,8 @@ 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 */ @@ -2182,41 +5103,40 @@ void varprevlim(char fileres[], double * } /************ 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) +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, i1, k1, l1, t, tj; + int i, j=0, k1, l1, tj; int k2, l2, j1, z1; - int k=0,l, cptcode; - int first=1, first1; + 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,agelim, cov[NCOVMAX]; + 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"); + 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,fileres); + 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,fileres); + 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); @@ -2227,13 +5147,15 @@ void varprob(char optionfilefiname[], do 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(ficresprobcov,"# Age"); + fprintf(ficresprobcor,"# Age"); for(i=1; i<=nlstate;i++) @@ -2242,86 +5164,89 @@ void varprob(char optionfilefiname[], do fprintf(ficresprobcov," p%1d-%1d ",i,j); fprintf(ficresprobcor," p%1d-%1d ",i,j); } - fprintf(ficresprob,"\n"); + /* 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; - if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { - printf("Problem with gnuplot file: %s\n", optionfilegnuplot); - fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot); - exit(0); - } - else{ - fprintf(ficgp,"\n# Routine varprob"); - } - if((fichtm=fopen(optionfilehtm,"a"))==NULL) { - printf("Problem with html file: %s\n", optionfilehtm); - fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); - exit(0); - } - else{ - fprintf(fichtm,"\n
Computing and drawing one step probabilities with their confidence intervals
Computing matrix of variance-covariance of step probabilities
\n"); - fprintf(fichtm,"\n
We have drawn x'cov-1x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis.
When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.
\n"); + 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=cptcoveff; */ + tj = (int) pow(2,cptcoveff); if (cptcovn<1) {tj=1;ncodemax[1]=1;} j1=0; - for(t=1; t<=tj;t++){ - for(i1=1; i1<=ncodemax[t];i1++){ - j1++; - + for(j1=1; j1<=tj;j1++){ + /*for(i1=1; i1<=ncodemax[t];i1++){ */ + /*j1++;*/ if (cptcovn>0) { fprintf(ficresprob, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresprob, "**********\n#"); + 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]][codtab[j1][z1]]); - fprintf(ficresprobcov, "**********\n#"); + 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]][codtab[j1][z1]]); - fprintf(ficgp, "**********\n#"); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficgp, "**********\n#\n"); - fprintf(fichtm, "\n
********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(fichtm, "**********\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]][codtab[j1][z1]]); - fprintf(ficgp, "**********\n#"); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresprobcor, "**********\n#"); } + gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); + trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + gp=vector(1,(nlstate)*(nlstate+ndeath)); + gm=vector(1,(nlstate)*(nlstate+ndeath)); for (age=bage; age<=fage; age ++){ cov[2]=age; + if(nagesqr==1) + cov[3]= age*age; for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[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]]=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+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; - gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); - trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); - gp=vector(1,(nlstate)*(nlstate+ndeath)); - gm=vector(1,(nlstate)*(nlstate+ndeath)); for(theta=1; theta <=npar; theta++){ for(i=1; i<=npar; i++) - xp[i] = x[i] + (i==theta ?delti[theta]:0); + xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); pmij(pmmij,cov,ncovmodel,xp,nlstate); @@ -2334,7 +5259,7 @@ void varprob(char optionfilefiname[], do } for(i=1; i<=npar; i++) - xp[i] = x[i] - (i==theta ?delti[theta]:0); + xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); pmij(pmmij,cov,ncovmodel,xp,nlstate); k=0; @@ -2346,7 +5271,7 @@ void varprob(char optionfilefiname[], do } for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) - gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; + gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; } for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) @@ -2355,7 +5280,7 @@ void varprob(char optionfilefiname[], do 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; @@ -2370,10 +5295,10 @@ void varprob(char optionfilefiname[], do 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])); - }*/ + 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); @@ -2388,30 +5313,35 @@ void varprob(char optionfilefiname[], do i=0; for (k=1; k<=(nlstate);k++){ for (l=1; l<=(nlstate+ndeath);l++){ - i=i++; + i++; fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); for (j=1; j<=i;j++){ + /* 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,"\nset noparametric;unset label"); - fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); - fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); - fprintf(fichtm,"\n
Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); - fprintf(fichtm,"\n
![](\"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);
+ 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
",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;
+ first1=1;first2=2;
for (k2=1; k2<=(nlstate);k2++){
for (l2=1; l2<=(nlstate+ndeath);l2++){
if(l2==k2) continue;
@@ -2432,6 +5362,16 @@ void varprob(char optionfilefiname[], do
/* 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 */
@@ -2449,13 +5389,18 @@ void varprob(char optionfilefiname[], do
/* 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 png small\nset size 0.65,0.65");
- fprintf(fichtm,"\nEllipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1 :varpijgr%s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2); - fprintf(fichtm,"\n
![](\"varpijgr%s%d%1d%1d-%1d%1d.png\")
",optionfilefiname, j1,k1,l1,k2,l2);
- fprintf(fichtm,"\nCorrelation at age %d (%.3f),",(int) age, c12); - fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2); + fprintf(ficgp,"\nset ter svg size 640, 480"); + fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ + :\ +%s_%d%1d%1d-%1d%1d.svg, ",k1,l1,k2,l2,\ + subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\ + subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); + fprintf(fichtmcov,"\n
![](\"%s_%d%1d%1d-%1d%1d.svg\")
",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+ fprintf(fichtmcov,"\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",\ @@ -2463,7 +5408,7 @@ void varprob(char optionfilefiname[], do mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); }else{ first=0; - fprintf(fichtm," %d (%.3f),",(int) age, c12); + 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",\ @@ -2472,206 +5417,371 @@ void varprob(char optionfilefiname[], do }/* if first */ } /* age mod 5 */ } /* end loop age */ - fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2); + fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); first=1; } /*l12 */ } /* k12 */ } /*l1 */ }/* k1 */ - } /* loop covariates */ - free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); - free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); - free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); - free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + /* } */ /* loop covariates */ } + free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); + free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); + free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); free_vector(xp,1,npar); fclose(ficresprob); fclose(ficresprobcov); fclose(ficresprobcor); - fclose(ficgp); - fclose(fichtm); + fflush(ficgp); + fflush(fichtmcov); } /******************* Printing html file ***********/ -void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ +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 estepm ,\ - double jprev1, double mprev1,double anprev1, \ - double jprev2, double mprev2,double anprev2){ + 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; - /*char optionfilehtm[FILENAMELENGTH];*/ - if((fichtm=fopen(optionfilehtm,"a"))==NULL) { - printf("Problem with %s \n",optionfilehtm), exit(0); - fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); - } - fprintf(fichtm,"
Result files (first order: no variance)
\n - - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): p%s
\n - - Estimated transition probabilities over %d (stepm) months: pij%s
\n - - Stable prevalence in each health state: pl%s
\n - - Life expectancies by age and initial health status (estepm=%2d months): - e%s
\n ", \
- jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+ 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
Result files (second order: variances)
\n - - Parameter file with estimated parameters and covariance matrix: %s
\n - - Variance of one-step probabilities: prob%s
\n - - Variance-covariance of one-step probabilities: probcov%s
\n - - Correlation matrix of one-step probabilities: probcor%s
\n - - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): v%s
\n - - Health expectancies with their variances (no covariance): t%s
\n - - Standard deviation of stable prevalences: vpl%s
\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); - - 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);
-fprintf(fichtm," - Graphs
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
"); - /*---------arguments file --------*/ + fprintf(fichtm,"\nAge lx qx d(x,x+1) Lx Tx e
"); - if((ficpar=fopen(optionfile,"r"))==NULL) { - printf("Problem with optionfile %s\n",optionfile); - fprintf(ficlog,"Problem with optionfile %s\n",optionfile); - goto end; - } + 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]); - strcpy(filereso,"o"); - strcat(filereso,fileres); - if((ficparo=fopen(filereso,"w"))==NULL) { - printf("Problem with Output resultfile: %s\n", filereso); - fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); - goto end; - } + + fflush(fichtm); +} - /* 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); +/******************* Gnuplot file **************/ +void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ - fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); - printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); -while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - - covar=matrix(0,NCOVMAX,1,n); - cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ - if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; + char dirfileres[132],optfileres[132]; - ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */ - nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ - - /* Read guess parameters */ - /* 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); - - param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); - for(i=1; i <=nlstate; i++) - for(j=1; j <=nlstate+ndeath-1; j++){ - fscanf(ficpar,"%1d%1d",&i1,&j1); - fprintf(ficparo,"%1d%1d",i1,j1); - if(mle==1) - printf("%1d%1d",i,j); - fprintf(ficlog,"%1d%1d",i,j); - 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"); - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficparo,"\n"); - } - - npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ + int ng; - p=param[1][1]; - - /* 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); - delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); - 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<=ncovmodel;k++){ - fscanf(ficpar,"%le",&delti3[i][j][k]); - printf(" %le",delti3[i][j][k]); - fprintf(ficparo," %le",delti3[i][j][k]); + /*#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; + int linei, month, year,iout; + char line[MAXLINE], linetmp[MAXLINE]; + char stra[MAXLINE], strb[MAXLINE]; + char *stratrunc; + int lstra; + + + 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); + + + for (j=maxwav;j>=1;j--){ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing status */ + 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; + } } - fscanf(ficpar,"\n"); - printf("\n"); - fprintf(ficparo,"\n"); + s[j][i]=lval; + + 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 Waves */ + + cutv(stra, strb,line,' '); + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - } - delti=delti3[1][1]; - - /* 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); - - matcov=matrix(1,npar,1,npar); - for(i=1; i <=npar; i++){ - fscanf(ficpar,"%s",&str); - if(mle==1) - printf("%s",str); - fprintf(ficlog,"%s",str); - fprintf(ficparo,"%s",str); - 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]); - } - else - fprintf(ficlog," %.5le",matcov[i][j]); - fprintf(ficparo," %.5le",matcov[i][j]); + 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); + + cutv(stra, strb,line,' '); + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - fscanf(ficpar,"\n"); - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficparo,"\n"); - } - 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"); - - - /*-------- Rewriting paramater 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", fileres);goto end; - fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; + 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); + + 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; } - fprintf(ficres,"#%s\n",version); + weight[i]=dval; + strcpy(line,stra); - /*-------- data file ----------*/ - if((fic=fopen(datafile,"r"))==NULL) { - printf("Problem with datafile: %s\n", datafile);goto end; - fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; - } - - n= lastobs; - severity = vector(1,maxwav); - outcome=imatrix(1,maxwav+1,1,n); - num=ivector(1,n); - moisnais=vector(1,n); - annais=vector(1,n); - moisdc=vector(1,n); - andc=vector(1,n); - agedc=vector(1,n); - cod=ivector(1,n); - weight=vector(1,n); - for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ - mint=matrix(1,maxwav,1,n); - anint=matrix(1,maxwav,1,n); - s=imatrix(1,maxwav+1,1,n); - adl=imatrix(1,maxwav+1,1,n); - tab=ivector(1,NCOVMAX); - ncodemax=ivector(1,8); - - i=1; - while (fgets(line, MAXLINE, fic) != NULL) { - if ((i >= firstobs) && (i <=lastobs)) { - - for (j=maxwav;j>=1;j--){ - cutv(stra, strb,line,' '); s[j][i]=atoi(strb); - strcpy(line,stra); - cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra); - } - - cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); + for (j=ncovcol;j>=1;j--){ + cutv(stra, strb,line,' '); + if(strb[0]=='.') { /* Missing status */ + 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 */ - cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); + *imax=i-1; /* Number of individuals */ + fclose(fic); + + return (0); + /* endread: */ + printf("Exiting readdata: "); + fclose(fic); + return (1); - cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); - for (j=ncovcol;j>=1;j--){ - cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); - } - num[i]=atol(stra); - - /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ - printf("%d %.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; - } - } - /* printf("ii=%d", ij); - scanf("%d",i);*/ - imx=i-1; /* Number of individuals */ - - /* for (i=1; i<=imx; i++){ - if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3; - if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3; - if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3; - }*/ - /* for (i=1; i<=imx; i++){ - if (s[4][i]==9) s[4][i]=-1; - printf("%d %.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]));}*/ - - - /* Calculation of the number of parameter from char model*/ - Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ - Tprod=ivector(1,15); - Tvaraff=ivector(1,15); - Tvard=imatrix(1,15,1,2); - Tage=ivector(1,15); - + +} +void removespace(char *str) { + char *p1 = str, *p2 = str; + do + while (*p2 == ' ') + p2++; + while (*p1++ == *p2++); +} + +int decodemodel ( char model[], int lastobs) /**< This routine decode 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; + 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=1, k2=1; - j=nbocc(model,'+'); /* j=Number of '+' */ - j1=nbocc(model,'*'); /* j1=Number of '*' */ - cptcovn=j+1; - cptcovprod=j1; /*Number of products */ - - strcpy(modelsav,model); - if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){ - printf("Error. Non available option model=%s ",model); - fprintf(ficlog,"Error. Non available option model=%s ",model); - goto end; + 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; } - - /* This loop fill the array Tvar from the string 'model'.*/ + 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 =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=> 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 */ - for(i=(j+1); i>=1;i--){ - cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ - if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze 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 */ - cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/ - if (strcmp(strc,"age")==0) { /* Vn*age */ - cptcovprod--; - cutv(strb,stre,strd,'V'); - Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/ - cptcovage++; - Tage[cptcovage]=i; + + /* 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]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) + * Tvar[k] # of the kth covariate: Tvar[1]=2 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 */ + Tvar[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 */ + 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--; - cutv(strb,stre,strc,'V'); - Tvar[i]=atoi(stre); - cptcovage++; - Tage[cptcovage]=i; - } - else { /* Age is not in the model */ - cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/ - Tvar[i]=ncovcol+k1; - cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ - Tprod[k1]=i; - Tvard[k1][1]=atoi(strc); /* m*/ - Tvard[k1][2]=atoi(stre); /* n */ - Tvar[cptcovn+k2]=Tvard[k1][1]; - Tvar[cptcovn+k2+1]=Tvard[k1][2]; - for (k=1; k<=lastobs;k++) - covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; - k1++; - k2=k2+2; - } - } - else { /* no more sum */ - /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ - /* scanf("%d",i);*/ - cutv(strd,strc,strb,'V'); - Tvar[i]=atoi(strc); - } - strcpy(modelsav,stra); - /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); - scanf("%d",i);*/ - } /* end of loop + */ - } /* end model */ + } else if (strcmp(strd,"age")==0) { /* or age*Vn */ + cptcovprod--; + cutl(stre,strb,strc,'V'); + Tvar[k]=atoi(stre); + 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+k1; /* 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+V3*V2 + Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ + 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 */ + Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ + Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ + k2=k2+2; + 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) */ + 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 */ + cptcovn++; + Tvar[k]=atoi(strd); + } + 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*/ @@ -3492,690 +7343,2512 @@ while((c=getc(ficpar))=='#' && c!= EOF){ printf("cptcovprod=%d ", cptcovprod); fprintf(ficlog,"cptcovprod=%d ", cptcovprod); - scanf("%d ",i); - fclose(fic);*/ + scanf("%d ",i);*/ - /* if(mle==1){*/ - if (weightopt != 1) { /* Maximisation without weights*/ - for(i=1;i<=n;i++) weight[i]=1.0; - } - /*-calculation of age at interview from date of interview and age at death -*/ - agev=matrix(1,maxwav,1,imx); - for (i=1; i<=imx; i++) { - for(m=2; (m<= maxwav); m++) { - if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ - anint[m][i]=9999; - s[m][i]=-1; - } - if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; + return (0); /* with covar[new additional covariate if product] and Tage if age */ + /*endread:*/ + printf("Exiting decodemodel: "); + return (1); +} + +int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) +{ + int i, m; + int firstone=0; + + for (i=1; i<=imx; i++) { + for(m=2; (m<= maxwav); m++) { + if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ + anint[m][i]=9999; + if (s[m][i] != -2) /* Keeping initial status of unknown vital status */ + s[m][i]=-1; + } + if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ + *nberr = *nberr + 1; + if(firstone == 0){ + firstone=1; + printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m); + } + fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m); + s[m][i]=-1; + } + if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ + (*nberr)++; + printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); + fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); + s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ } } + } - for (i=1; i<=imx; i++) { - agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); - for(m=1; (m<= maxwav); m++){ - if(s[m][i] >0){ - if (s[m][i] >= nlstate+1) { - if(agedc[i]>0) - if(moisdc[i]!=99 && andc[i]!=9999) - agev[m][i]=agedc[i]; - /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ - else { - if (andc[i]!=9999){ - printf("Warning negative age at death: %d line:%d\n",num[i],i); - fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); - agev[m][i]=-1; + for (i=1; i<=imx; i++) { + agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); + for(m=firstpass; (m<= lastpass); m++){ + if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */ + if (s[m][i] >= nlstate+1) { + if(agedc[i]>0){ + if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ + agev[m][i]=agedc[i]; + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + }else { + if ((int)andc[i]!=9999){ + nbwarn++; + printf("Warning negative age at death: %ld line:%d\n",num[i],i); + fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); + agev[m][i]=-1; } } - } - else if(s[m][i] !=9){ /* Should no more exist */ - agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); - if(mint[m][i]==99 || anint[m][i]==9999) - agev[m][i]=1; - else if(agev[m][i]+//#include +//#include +//#include +typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); - jk=1; - fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(k=1; k <=(nlstate+ndeath); k++){ - if (k != i) - { - printf("%d%d ",i,k); - fprintf(ficlog,"%d%d ",i,k); - fprintf(ficres,"%1d%1d ",i,k); - for(j=1; j <=ncovmodel; j++){ - printf("%f ",p[jk]); - fprintf(ficlog,"%f ",p[jk]); - fprintf(ficres,"%f ",p[jk]); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - } - } - } - if(mle==1){ - /* Computing hessian and covariance matrix */ - ftolhess=ftol; /* Usually correct */ - hesscov(matcov, p, npar, delti, ftolhess, func); - } - fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); - printf("# Scales (for hessian or gradient estimation)\n"); - fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(j=1; j <=nlstate+ndeath; j++){ - if (j!=i) { - fprintf(ficres,"%1d%1d",i,j); - printf("%1d%1d",i,j); - fprintf(ficlog,"%1d%1d",i,j); - for(k=1; k<=ncovmodel;k++){ - printf(" %.5e",delti[jk]); - fprintf(ficlog," %.5e",delti[jk]); - fprintf(ficres," %.5e",delti[jk]); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - } - } - } - - k=1; - fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - if(mle==1) - printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - for(i=1;i<=npar;i++){ - /* if (k>nlstate) k=1; - i1=(i-1)/(ncovmodel*nlstate)+1; - fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); - printf("%s%d%d",alph[k],i1,tab[i]);*/ - fprintf(ficres,"%3d",i); - if(mle==1) - printf("%3d",i); - fprintf(ficlog,"%3d",i); - for(j=1; j<=i;j++){ - fprintf(ficres," %.5e",matcov[i][j]); - if(mle==1) - printf(" %.5e",matcov[i][j]); - fprintf(ficlog," %.5e",matcov[i][j]); - } - fprintf(ficres,"\n"); - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - k++; - } - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - estepm=0; - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); - if (estepm==0 || estepm < stepm) estepm=stepm; - if (fage <= 2) { - bage = ageminpar; - fage = agemaxpar; - } - - fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); - fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - - fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); - fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); - fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - +LPFN_ISWOW64PROCESS fnIsWow64Process; - dateprev1=anprev1+mprev1/12.+jprev1/365.; - dateprev2=anprev2+mprev2/12.+jprev2/365.; +BOOL IsWow64() +{ + BOOL bIsWow64 = FALSE; - fscanf(ficpar,"pop_based=%d\n",&popbased); - fprintf(ficparo,"pop_based=%d\n",popbased); - fprintf(ficres,"pop_based=%d\n",popbased); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); + //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) + // (HANDLE, PBOOL); - fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2); -fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); -fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); + //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 -while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); +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 - fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1); - fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); - fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); - - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); - -/*------------ gnuplot -------------*/ - strcpy(optionfilegnuplot,optionfilefiname); - strcat(optionfilegnuplot,".gp"); - if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { - printf("Problem with file %s",optionfilegnuplot); - } - else{ - fprintf(ficgp,"\n# %s\n", version); - fprintf(ficgp,"# %s\n", optionfilegnuplot); - fprintf(ficgp,"set missing 'NaNq'\n"); -} - fclose(ficgp); - printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); -/*--------- index.htm --------*/ +#include - strcpy(optionfilehtm,optionfile); - strcat(optionfilehtm,".htm"); - if((fichtm=fopen(optionfilehtm,"w"))==NULL) { - printf("Problem with %s \n",optionfilehtm), exit(0); - } + 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 - fprintf(fichtm," %s
\n -Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n -\n -Total number of observations=%d
\n -Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
\n -
-Parameter files
\n - - Copy of the parameter file: o%s
\n - - Log file of the run: %s
\n - - Gnuplot file name: %s
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); + /* 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; - if(erreur >0){ - printf("End of Imach with error or warning %d\n",erreur); - fprintf(ficlog,"End of Imach with error or warning %d\n",erreur); + /* Initial vertex size vector */ + ss = gsl_vector_alloc (NDIM); + + if (ss == NULL){ + GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); + } + /* Set all step sizes to 1 */ + gsl_vector_set_all (ss, 0.001); + + /* Starting point */ + + x = gsl_vector_alloc (NDIM); + + if (x == NULL){ + gsl_vector_free(ss); + GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); + } + + /* Initialize method and iterate */ + /* p[1]=0.0268; p[NDIM]=0.083; */ + /* gsl_vector_set(x, 0, 0.0268); */ + /* gsl_vector_set(x, 1, 0.083); */ + gsl_vector_set(x, 0, p[1]); + gsl_vector_set(x, 1, p[2]); + + minex_func.f = &gompertz_f; + minex_func.n = NDIM; + minex_func.params = (void *)&p; /* ??? */ + + sfm = gsl_multimin_fminimizer_alloc (T, NDIM); + gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); + + printf("Iterations beginning .....\n\n"); + printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); + + iteri=0; + while (rval == GSL_CONTINUE){ + iteri++; + status = gsl_multimin_fminimizer_iterate(sfm); + + if (status) printf("error: %s\n", gsl_strerror (status)); + fflush(0); + + if (status) + break; + + rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); + ssval = gsl_multimin_fminimizer_size (sfm); + + if (rval == GSL_SUCCESS) + printf ("converged to a local maximum at\n"); + + printf("%5d ", iteri); + for (it = 0; it < NDIM; it++){ + printf ("%10.5f ", gsl_vector_get (sfm->x, it)); + } + printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); + } + + printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); + + gsl_vector_free(x); /* initial values */ + gsl_vector_free(ss); /* inital step size */ + for (it=0; it
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("wgnuplot graph.plt");*/ - /*system("../gp37mgw/wgnuplot graph.plt");*/ - /*system("cd ../gp37mgw");*/ - /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ - strcpy(plotcmd,GNUPLOTPROGRAM); - strcat(plotcmd," "); - strcat(plotcmd,optionfilegnuplot); - printf("Starting: %s\n",plotcmd);fflush(stdout); - system(plotcmd); + 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); - /*#ifdef windows*/ + 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(path); */ - printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: "); + printf("\nType e to edit results with your browser, g to graph again and q for exit: "); scanf("%s",z); - if (z[0] == 'c') system("./imach"); - else if (z[0] == 'e') system(optionfilehtm); +/* 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); + } } - -
"); - m=cptcoveff; + 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++){ + /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; if (cptcovn > 0) { fprintf(fichtm,"
************ Results for covariates"); - for (cpt=1; cpt<=cptcoveff;cpt++) - fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); + 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); + } fprintf(fichtm," ************\n
"); } + /* 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,"- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png
-
![](\"pe%s%d1.png\")
",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ 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,"- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png
-
![](\"pe%s%d2.png\")
",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
- /* Stable prevalence in each health state */
- for(cpt=1; cpt-
![](\"p%s%d%d.png\")
",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
- }
+ 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](\"%s%d_%d.svg\"){kind=link}
\ +
![](\"%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- Health life expectancies by age and initial health state (%d): exp%s%d%d.png
-
![](\"exp%s%d%d.png\")
",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ 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);
}
- fprintf(fichtm,"\n- Total life expectancy by age and -health expectancies in states (1) and (2): e%s%d.png
-
![](\"e%s%d.png\")
",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
- } /* end i1 */
+ /* } /\* end i1 *\/ */
}/* End k1 */
fprintf(fichtm,"\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,"
");
- fprintf(fichtm,"\n
"); - - m=cptcoveff; + 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++){ + /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; if (cptcovn > 0) { fprintf(fichtm,"
************ Results for covariates"); for (cpt=1; cpt<=cptcoveff;cpt++) - fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]); + fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); fprintf(fichtm," ************\n
"); } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"
- Observed and stationary prevalence (with confident -interval) in state (%d): v%s%d%d.png
-
![](\"v%s%d%d.png\")
",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ 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);
}
- } /* end i1 */
+ 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,"