********** Variable ");
fprintf(ficresphtmfr, "\n
********** Variable ");
for (z1=1; z1<=cptcoveff; z1++){
fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
}
fprintf(ficresp, "**********\n#");
fprintf(ficresphtm, "**********
\n");
fprintf(ficresphtmfr, "**********
\n");
fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "**********\n");
}
fprintf(ficresphtm,"| 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 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++){ for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) pp[jk] += freq[jk][m][i]; } for(jk=1; jk <=nlstate ; jk++){ for(m=-1, pos=0; m <=0 ; m++) pos += freq[jk][m][i]; if(pp[jk]>=1.e-10){ if(first==1){ printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); } fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); }else{ if(first==1) printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); } } for(jk=1; jk <=nlstate ; jk++){ for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) pp[jk] += freq[jk][m][i]; } for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ pos += pp[jk]; posprop += prop[jk][i]; } for(jk=1; jk <=nlstate ; jk++){ if(pos>=1.e-5){ if(first==1) printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); }else{ if(first==1) printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); } if( i <= iagemax){ if(pos>=1.e-5){ fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); fprintf(ficresphtm,"%d | %.5f | %.0f | %.0f | ",i,prop[jk][i]/posprop, prop[jk][i],posprop); /*probs[i][jk][j1]= pp[jk]/pos;*/ /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ } else{ fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); fprintf(ficresphtm,"%d | NaNq | %.0f | %.0f | ",i, prop[jk][i],posprop); } } } for(jk=-1; jk <=nlstate+ndeath; jk++){ for(m=-1; m <=nlstate+ndeath; m++){ if(freq[jk][m][i] !=0 ) { /* minimizing output */ if(first==1){ printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); } fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); } if(jk!=0 && m!=0) fprintf(ficresphtmfr,"%.0f | ",freq[jk][m][i]); } } fprintf(ficresphtmfr,"
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*/ 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); } 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); 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); 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 */ fprintf(ficresvpl,"%.0f ",age ); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); 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 */ free_vector(xp,1,npar); free_matrix(doldm,1,nlstate,1,npar); free_matrix(dnewm,1,nlstate,1,nlstate); } /************ Variance of one-step probabilities ******************/ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[]) { int i, j=0, k1, l1, tj; int k2, l2, j1, z1; int k=0, l; int first=1, first1, first2; double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; double **dnewm,**doldm; double *xp; double *gp, *gm; double **gradg, **trgradg; double **mu; double age, cov[NCOVMAX+1]; double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ int theta; char fileresprob[FILENAMELENGTH]; char fileresprobcov[FILENAMELENGTH]; char fileresprobcor[FILENAMELENGTH]; double ***varpij; strcpy(fileresprob,"PROB_"); strcat(fileresprob,fileres); if((ficresprob=fopen(fileresprob,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileresprob); fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob); } strcpy(fileresprobcov,"PROBCOV_"); strcat(fileresprobcov,fileresu); if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileresprobcov); fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov); } strcpy(fileresprobcor,"PROBCOR_"); strcat(fileresprobcor,fileresu); if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileresprobcor); fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor); } printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); pstamp(ficresprob); fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); fprintf(ficresprob,"# Age"); pstamp(ficresprobcov); fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); fprintf(ficresprobcov,"# Age"); pstamp(ficresprobcor); fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); fprintf(ficresprobcor,"# Age"); for(i=1; i<=nlstate;i++) for(j=1; j<=(nlstate+ndeath);j++){ fprintf(ficresprob," p%1d-%1d (SE)",i,j); fprintf(ficresprobcov," p%1d-%1d ",i,j); fprintf(ficresprobcor," p%1d-%1d ",i,j); } /* fprintf(ficresprob,"\n"); fprintf(ficresprobcov,"\n"); fprintf(ficresprobcor,"\n"); */ xp=vector(1,npar); dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage); first=1; fprintf(ficgp,"\n# Routine varprob"); fprintf(fichtm,"\n
Computing and drawing one step probabilities with their confidence intervals
Matrix of variance-covariance of one-step probabilities (drawings)
this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.\n\n
Matrix of variance-covariance of pairs of step probabilities
\n",optionfilehtmcov, optionfilehtmcov); fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p\n"); fprintf(fichtmcov,"\n
Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. \ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \ standard deviations wide on each axis.
\ Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\ and made the appropriate rotation to look at the uncorrelated principal directions.
\ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
\n"); cov[1]=1; /* tj=cptcoveff; */ tj = (int) pow(2,cptcoveff); if (cptcovn<1) {tj=1;ncodemax[1]=1;} j1=0; for(j1=1; j1<=tj;j1++){ /*for(i1=1; i1<=ncodemax[t];i1++){ */ /*j1++;*/ if (cptcovn>0) { fprintf(ficresprob, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); fprintf(ficresprob, "**********\n#\n"); fprintf(ficresprobcov, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); fprintf(ficresprobcov, "**********\n#\n"); fprintf(ficgp, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); fprintf(ficgp, "**********\n#\n"); fprintf(fichtmcov, "\n
********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); fprintf(fichtmcov, "**********\n
"); fprintf(ficresprobcor, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); fprintf(ficresprobcor, "**********\n#"); } gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); gp=vector(1,(nlstate)*(nlstate+ndeath)); gm=vector(1,(nlstate)*(nlstate+ndeath)); for (age=bage; age<=fage; age ++){ cov[2]=age; if(nagesqr==1) cov[3]= age*age; for (k=1; k<=cptcovn;k++) { cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4 * 1 1 1 1 1 * 2 2 1 1 1 * 3 1 2 1 1 */ /* nbcode[1][1]=0 nbcode[1][2]=1;*/ } /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; for (k=1; k<=cptcovprod;k++) cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; for(theta=1; theta <=npar; theta++){ for(i=1; i<=npar; i++) xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); pmij(pmmij,cov,ncovmodel,xp,nlstate); k=0; for(i=1; i<= (nlstate); i++){ for(j=1; j<=(nlstate+ndeath);j++){ k=k+1; gp[k]=pmmij[i][j]; } } for(i=1; i<=npar; i++) xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); pmij(pmmij,cov,ncovmodel,xp,nlstate); k=0; for(i=1; i<=(nlstate); i++){ for(j=1; j<=(nlstate+ndeath);j++){ k=k+1; gm[k]=pmmij[i][j]; } } for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; } for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) for(theta=1; theta <=npar; theta++) trgradg[j][theta]=gradg[theta][j]; matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); pmij(pmmij,cov,ncovmodel,x,nlstate); k=0; for(i=1; i<=(nlstate); i++){ for(j=1; j<=(nlstate+ndeath);j++){ k=k+1; mu[k][(int) age]=pmmij[i][j]; } } for(i=1;i<=(nlstate)*(nlstate+ndeath);i++) for(j=1;j<=(nlstate)*(nlstate+ndeath);j++) varpij[i][j][(int)age] = doldm[i][j]; /*printf("\n%d ",(int)age); for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); }*/ fprintf(ficresprob,"\n%d ",(int)age); fprintf(ficresprobcov,"\n%d ",(int)age); fprintf(ficresprobcor,"\n%d ",(int)age); for (i=1; i<=(nlstate)*(nlstate+ndeath);i++) fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age])); for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]); fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]); } i=0; for (k=1; k<=(nlstate);k++){ for (l=1; l<=(nlstate+ndeath);l++){ i++; fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); for (j=1; j<=i;j++){ /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); } } }/* end of loop for state */ } /* end of loop for age */ free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); /* Confidence intervalle of pij */ /* fprintf(ficgp,"\nunset parametric;unset label"); fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); fprintf(fichtm,"\n
Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); fprintf(fichtm,"\n
![](\"pijgr%s.png\")
",optionfilefiname);
fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
*/
/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
first1=1;first2=2;
for (k2=1; k2<=(nlstate);k2++){
for (l2=1; l2<=(nlstate+ndeath);l2++){
if(l2==k2) continue;
j=(k2-1)*(nlstate+ndeath)+l2;
for (k1=1; k1<=(nlstate);k1++){
for (l1=1; l1<=(nlstate+ndeath);l1++){
if(l1==k1) continue;
i=(k1-1)*(nlstate+ndeath)+l1;
if(i<=j) continue;
for (age=bage; age<=fage; age ++){
if ((int)age %5==0){
v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
mu1=mu[i][(int) age]/stepm*YEARM ;
mu2=mu[j][(int) age]/stepm*YEARM;
c12=cv12/sqrt(v1*v2);
/* Computing eigen value of matrix of covariance */
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
if ((lc2 <0) || (lc1 <0) ){
if(first2==1){
first1=0;
printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
}
fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
/* lc1=fabs(lc1); */ /* If we want to have them positive */
/* lc2=fabs(lc2); */
}
/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/*v21=sqrt(1.-v11*v11); *//* error */
v21=(lc1-v1)/cv12*v11;
v12=-v21;
v22=v11;
tnalp=v21/v11;
if(first1==1){
first1=0;
printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
}
fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
/*printf(fignu*/
/* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
/* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
if(first==1){
first=0;
fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter svg size 640, 480");
fprintf(fichtmcov,"\nEllipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ :\ %s_%d%1d%1d-%1d%1d.svg, ",k1,l1,k2,l2,\ subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\ subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); fprintf(fichtmcov,"\n
![](\"%s_%d%1d%1d-%1d%1d.svg\")
",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
fprintf(fichtmcov,"\nCorrelation at age %d (%.3f),",(int) age, c12); fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); }else{ first=0; fprintf(fichtmcov," %d (%.3f),",(int) age, c12); fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\ mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); }/* if first */ } /* age mod 5 */ } /* end loop age */ fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2); first=1; } /*l12 */ } /* k12 */ } /*l1 */ }/* k1 */ /* } */ /* loop covariates */ } free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); free_vector(xp,1,npar); fclose(ficresprob); fclose(ficresprobcov); fclose(ficresprobcor); fflush(ficgp); fflush(fichtmcov); } /******************* Printing html file ***********/ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ int popforecast, int prevfcast, int estepm , \ double jprev1, double mprev1,double anprev1, double dateprev1, \ double jprev2, double mprev2,double anprev2, double dateprev2){ int jj1, k1, i1, cpt; fprintf(fichtm,""); fprintf(fichtm,"
Result files (first order: no variance)
\n"); fprintf(fichtm,"- - Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file)
\n", jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm")); fprintf(fichtm," - - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file) ",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
fprintf(fichtm,", %s (text file)
\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); fprintf(fichtm,"\ - Estimated transition probabilities over %d (stepm) months: %s
\n ", stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_")); fprintf(fichtm,"\ - Period (stable) prevalence in each health state: %s
\n", subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); 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
\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):
"); fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year
",p[1],p[2],agegomp); for (i=1;i<=2;i++) fprintf(fichtm," p[%d] = %lf [%f ; %f]
\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); fprintf(fichtm,"![](\"graphmort.svg\")
");
fprintf(fichtm,"Life table
\n
"); fprintf(fichtm,"\nAge lx qx d(x,x+1) Lx Tx e
"); for (k=agegomp;k<(agemortsup-2);k++) fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf
\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]); fflush(fichtm); } /******************* Gnuplot file **************/ void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ char dirfileres[132],optfileres[132]; int ng; /*#ifdef windows */ fprintf(ficgp,"cd \"%s\" \n",pathc); /*#endif */ strcpy(dirfileres,optionfilefiname); strcpy(optfileres,"vpl"); fprintf(ficgp,"set out \"graphmort.svg\"\n "); fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); fprintf(ficgp, "set ter svg size 640, 480\n set log y\n"); /* fprintf(ficgp, "set size 0.65,0.65\n"); */ fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); } int readdata(char datafile[], int firstobs, int lastobs, int *imax) { /*-------- data file ----------*/ FILE *fic; char dummy[]=" "; int i=0, j=0, n=0; 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\n", datafile);fflush(stdout); fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);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; } } 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){ } 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){ } 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; } weight[i]=dval; 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 */ *imax=i-1; /* Number of individuals */ fclose(fic); return (0); /* endread: */ printf("Exiting readdata: "); fclose(fic); return (1); } 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=0, k2=-1, ks=0, cptcovn=0; if (strstr(model,"AGE") !=0){ printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model); fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog); return 1; } if (strstr(model,"v") !=0){ printf("Error. 'v' must be in upper case 'V' model=%s ",model); fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); return 1; } strcpy(modelsav,model); if ((strpt=strstr(model,"age*age")) !=0){ printf(" strpt=%s, model=%s\n",strpt, model); if(strpt != model){ printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ corresponding column of parameters.\n",model); fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ corresponding column of parameters.\n",model); fflush(ficlog); return 1; } nagesqr=1; if (strstr(model,"+age*age") !=0) substrchaine(modelsav, model, "+age*age"); else if (strstr(model,"age*age+") !=0) substrchaine(modelsav, model, "age*age+"); else substrchaine(modelsav, model, "age*age"); }else nagesqr=0; if (strlen(modelsav) >1){ j=nbocc(modelsav,'+'); /**< j=Number of '+' */ j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =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 */ /* 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--; 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*/ /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); printf("cptcovprod=%d ", cptcovprod); fprintf(ficlog,"cptcovprod=%d ", cptcovprod); scanf("%d ",i);*/ 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; 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; 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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); 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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); 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=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; } } } /* agedc > 0 */ } /* end if */ else if(s[m][i] !=9){ /* Standard case, age in fractional years but with the precision of a month */ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); if((int)mint[m][i]==99 || (int)anint[m][i]==9999) agev[m][i]=1; else if(agev[m][i] < *agemin){ *agemin=agev[m][i]; printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin); } else if(agev[m][i] >*agemax){ *agemax=agev[m][i]; /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ } /*agev[m][i]=anint[m][i]-annais[i];*/ /* agev[m][i] = age[i]+2*m;*/ } /* en if 9*/ else { /* =9 */ /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */ agev[m][i]=1; s[m][i]=-1; } } else if(s[m][i]==0) /*= 0 Unknown */ agev[m][i]=1; else{ printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); agev[m][i]=0; } } /* End for lastpass */ } for (i=1; i<=imx; i++) { for(m=firstpass; (m<=lastpass); m++){ if (s[m][i] > (nlstate+ndeath)) { (*nberr)++; printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); return 1; } } } /*for (i=1; i<=imx; i++){ for (m=firstpass; (m//#include //#include typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); LPFN_ISWOW64PROCESS fnIsWow64Process; BOOL IsWow64() { BOOL bIsWow64 = FALSE; //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) // (HANDLE, PBOOL); //LPFN_ISWOW64PROCESS fnIsWow64Process; HMODULE module = GetModuleHandle(_T("kernel32")); const char funcName[] = "IsWow64Process"; fnIsWow64Process = (LPFN_ISWOW64PROCESS) GetProcAddress(module, funcName); if (NULL != fnIsWow64Process) { if (!fnIsWow64Process(GetCurrentProcess(), &bIsWow64)) //throw std::exception("Unknown error"); printf("Unknown error\n"); } return bIsWow64 != FALSE; } #endif void syscompilerinfo(int logged) { /* #include "syscompilerinfo.h"*/ /* command line Intel compiler 32bit windows, XP compatible:*/ /* /GS /W3 /Gy /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" */ /* 64 bits */ /* /GS /W3 /Gy /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ /* Optimization are useless and O3 is slower than O2 */ /* /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ /* Link is */ /* /OUT:"visual studio 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT /PDB:"visual studio 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' uiAccess='false'" /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF /NOLOGO /TLBID:1 */ #if defined __INTEL_COMPILER #if defined(__GNUC__) struct utsname sysInfo; /* For Intel on Linux and OS/X */ #endif #elif defined(__GNUC__) #ifndef __APPLE__ #include /* Only on gnu */ #endif struct utsname sysInfo; int cross = CROSS; if (cross){ printf("Cross-"); if(logged) fprintf(ficlog, "Cross-"); } #endif #include printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); #if defined(__clang__) printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ #endif #if defined(__ICC) || defined(__INTEL_COMPILER) printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ #endif #if defined(__GNUC__) || defined(__GNUG__) printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ #endif #if defined(__HP_cc) || defined(__HP_aCC) printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ #endif #if defined(__IBMC__) || defined(__IBMCPP__) printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ #endif #if defined(_MSC_VER) printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ #endif #if defined(__PGI) printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ #endif #if defined(__SUNPRO_C) || defined(__SUNPRO_CC) printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ #endif printf(" for "); if (logged) fprintf(ficlog, " for "); // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros #ifdef _WIN32 // note the underscore: without it, it's not msdn official! // Windows (x64 and x86) printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) "); #elif __unix__ // all unices, not all compilers // Unix printf("Unix ");if(logged) fprintf(ficlog,"Unix "); #elif __linux__ // linux printf("linux ");if(logged) fprintf(ficlog,"linux "); #elif __APPLE__ // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS "); #endif /* __MINGW32__ */ /* __CYGWIN__ */ /* __MINGW64__ */ // http://msdn.microsoft.com/en-us/library/b0084kay.aspx /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ /* _WIN64 // Defined for applications for Win64. */ /* _M_X64 // Defined for compilations that target x64 processors. */ /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ #if UINTPTR_MAX == 0xffffffff printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */ #elif UINTPTR_MAX == 0xffffffffffffffff printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */ #else printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */ #endif #if defined(__GNUC__) # if defined(__GNUC_PATCHLEVEL__) # define __GNUC_VERSION__ (__GNUC__ * 10000 \ + __GNUC_MINOR__ * 100 \ + __GNUC_PATCHLEVEL__) # else # define __GNUC_VERSION__ (__GNUC__ * 10000 \ + __GNUC_MINOR__ * 100) # endif printf(" using GNU C version %d.\n", __GNUC_VERSION__); if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); if (uname(&sysInfo) != -1) { printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); } else perror("uname() error"); //#ifndef __INTEL_COMPILER #if !defined (__INTEL_COMPILER) && !defined(__APPLE__) printf("GNU libc version: %s\n", gnu_get_libc_version()); if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); #endif #endif // void main() // { #if defined(_MSC_VER) if (IsWow64()){ printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); } else{ printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n"); if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); } // printf("\nPress Enter to continue..."); // getchar(); // } #endif } int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){ /*--------------- Prevalence limit (period or stable prevalence) --------------*/ int i, j, k, i1 ; /* double ftolpl = 1.e-10; */ double age, agebase, agelim; double tot; strcpy(filerespl,"PL_"); strcat(filerespl,fileresu); if((ficrespl=fopen(filerespl,"w"))==NULL) { printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; } printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); pstamp(ficrespl); fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); fprintf(ficrespl,"#Age "); for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); fprintf(ficrespl,"\n"); /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */ agebase=ageminpar; agelim=agemaxpar; i1=pow(2,cptcoveff); if (cptcovn < 1){i1=1;} for(cptcov=1,k=0;cptcov<=i1;cptcov++){ /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */ //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ k=k+1; /* to clean */ //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov)); fprintf(ficrespl,"#******"); printf("#******"); fprintf(ficlog,"#******"); for(j=1;j<=cptcoveff;j++) { fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); } fprintf(ficrespl,"******\n"); printf("******\n"); fprintf(ficlog,"******\n"); fprintf(ficrespl,"#Age "); for(j=1;j<=cptcoveff;j++) { fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); } for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i); fprintf(ficrespl,"Total Years_to_converge\n"); for (age=agebase; age<=agelim; age++){ /* for (age=agebase; age<=agebase; age++){ */ prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k); fprintf(ficrespl,"%.0f ",age ); for(j=1;j<=cptcoveff;j++) fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); tot=0.; for(i=1; i<=nlstate;i++){ tot += prlim[i][i]; fprintf(ficrespl," %.5f", prlim[i][i]); } fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp); } /* Age */ /* was end of cptcod */ } /* cptcov */ return 0; } int hPijx(double *p, int bage, int fage){ /*------------- h Pij x at various ages ------------*/ int stepsize; int agelim; int hstepm; int nhstepm; int h, i, i1, j, k; double agedeb; double ***p3mat; strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu); if((ficrespij=fopen(filerespij,"w"))==NULL) { printf("Problem with Pij resultfile: %s\n", filerespij); return 1; fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1; } printf("Computing pij: result on file '%s' \n", filerespij); fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); stepsize=(int) (stepm+YEARM-1)/YEARM; /*if (stepm<=24) stepsize=2;*/ agelim=AGESUP; hstepm=stepsize*YEARM; /* Every year of age */ hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ /* hstepm=1; aff par mois*/ pstamp(ficrespij); fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); i1= pow(2,cptcoveff); /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ /* k=k+1; */ for (k=1; k <= (int) pow(2,cptcoveff); k++){ fprintf(ficrespij,"\n#****** "); for(j=1;j<=cptcoveff;j++) fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficrespij,"******\n"); for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ /* nhstepm=nhstepm*YEARM; aff par mois*/ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); oldm=oldms;savm=savms; hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespij," %1d-%1d",i,j); fprintf(ficrespij,"\n"); for (h=0; h<=nhstepm; h++){ /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespij," %.5f", p3mat[i][j][h]); fprintf(ficrespij,"\n"); } free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); fprintf(ficrespij,"\n"); } /*}*/ } return 0; } /***********************************************/ /**************** Main Program *****************/ /***********************************************/ int main(int argc, char *argv[]) { #ifdef GSL const gsl_multimin_fminimizer_type *T; size_t iteri = 0, it; int rval = GSL_CONTINUE; int status = GSL_SUCCESS; double ssval; #endif int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; int ncvyear=0; /* Number of years needed for the period prevalence to converge */ int jj, ll, li, lj, lk; int numlinepar=0; /* Current linenumber of parameter file */ int num_filled; int itimes; int NDIM=2; int vpopbased=0; char ca[32], cb[32]; /* FILE *fichtm; *//* Html File */ /* FILE *ficgp;*/ /*Gnuplot File */ struct stat info; double agedeb=0.; double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW; double fret; double dum=0.; /* Dummy variable */ double ***p3mat; double ***mobaverage; char line[MAXLINE]; char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE]; char model[MAXLINE], modeltemp[MAXLINE]; char pathr[MAXLINE], pathimach[MAXLINE]; char *tok, *val; /* pathtot */ int firstobs=1, lastobs=10; int c, h , cpt, c2; int jl=0; int i1, j1, jk, stepsize=0; int count=0; int *tab; int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ int mobilav=0,popforecast=0; int hstepm=0, nhstepm=0; int agemortsup; float sumlpop=0.; double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; double bage=0, fage=110., age, agelim=0., agebase=0.; double ftolpl=FTOL; double **prlim; double ***param; /* Matrix of parameters */ double *p; double **matcov; /* Matrix of covariance */ double **hess; /* Hessian matrix */ double ***delti3; /* Scale */ double *delti; /* Scale */ double ***eij, ***vareij; double **varpl; /* Variances of prevalence limits by age */ double *epj, vepp; double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; double **ximort; char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; int *dcwave; char z[1]="c"; /*char *strt;*/ char strtend[80]; /* setlocale (LC_ALL, ""); */ /* bindtextdomain (PACKAGE, LOCALEDIR); */ /* textdomain (PACKAGE); */ /* setlocale (LC_CTYPE, ""); */ /* setlocale (LC_MESSAGES, ""); */ /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ rstart_time = time(NULL); /* (void) gettimeofday(&start_time,&tzp);*/ start_time = *localtime(&rstart_time); curr_time=start_time; /*tml = *localtime(&start_time.tm_sec);*/ /* strcpy(strstart,asctime(&tml)); */ strcpy(strstart,asctime(&start_time)); /* printf("Localtime (at start)=%s",strstart); */ /* tp.tm_sec = tp.tm_sec +86400; */ /* tm = *localtime(&start_time.tm_sec); */ /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ /* tmg.tm_hour=tmg.tm_hour + 1; */ /* tp.tm_sec = mktime(&tmg); */ /* strt=asctime(&tmg); */ /* printf("Time(after) =%s",strstart); */ /* (void) time (&time_value); * printf("time=%d,t-=%d\n",time_value,time_value-86400); * tm = *localtime(&time_value); * strstart=asctime(&tm); * printf("tim_value=%d,asctime=%s\n",time_value,strstart); */ nberr=0; /* Number of errors and warnings */ nbwarn=0; #ifdef WIN32 _getcwd(pathcd, size); #else getcwd(pathcd, size); #endif syscompilerinfo(0); printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion); if(argc <=1){ printf("\nEnter the parameter file name: "); if(!fgets(pathr,FILENAMELENGTH,stdin)){ printf("ERROR Empty parameter file name\n"); goto end; } i=strlen(pathr); if(pathr[i-1]=='\n') pathr[i-1]='\0'; i=strlen(pathr); if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */ pathr[i-1]='\0'; } i=strlen(pathr); if( i==0 ){ printf("ERROR Empty parameter file name\n"); goto end; } for (tok = pathr; tok != NULL; ){ printf("Pathr |%s|\n",pathr); while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); printf("val= |%s| pathr=%s\n",val,pathr); strcpy (pathtot, val); if(pathr[0] == '\0') break; /* Dirty */ } } else{ strcpy(pathtot,argv[1]); } /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ /*cygwin_split_path(pathtot,path,optionfile); printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ /* cutv(path,optionfile,pathtot,'\\');*/ /* Split argv[0], imach program to get pathimach */ printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); /* strcpy(pathimach,argv[0]); */ /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ split(pathtot,path,optionfile,optionfilext,optionfilefiname); printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); #ifdef WIN32 _chdir(path); /* Can be a relative path */ if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ #else chdir(path); /* Can be a relative path */ if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ #endif printf("Current directory %s!\n",pathcd); strcpy(command,"mkdir "); strcat(command,optionfilefiname); if((outcmd=system(command)) != 0){ printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd); /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ /* fclose(ficlog); */ /* exit(1); */ } /* if((imk=mkdir(optionfilefiname))<0){ */ /* perror("mkdir"); */ /* } */ /*-------- arguments in the command line --------*/ /* Main Log file */ strcat(filelog, optionfilefiname); strcat(filelog,".log"); /* */ if((ficlog=fopen(filelog,"w"))==NULL) { printf("Problem with logfile %s\n",filelog); goto end; } fprintf(ficlog,"Log filename:%s\n",filelog); fprintf(ficlog,"Version %s %s",version,fullversion); fprintf(ficlog,"\nEnter the parameter file name: \n"); fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ path=%s \n\ optionfile=%s\n\ optionfilext=%s\n\ optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); syscompilerinfo(1); printf("Local time (at start):%s",strstart); fprintf(ficlog,"Local time (at start): %s",strstart); fflush(ficlog); /* (void) gettimeofday(&curr_time,&tzp); */ /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */ /* */ strcpy(fileres,"r"); strcat(fileres, optionfilefiname); strcat(fileresu, optionfilefiname); /* Without r in front */ strcat(fileres,".txt"); /* Other files have txt extension */ strcat(fileresu,".txt"); /* Other files have txt extension */ /* Main ---------arguments file --------*/ if((ficpar=fopen(optionfile,"r"))==NULL) { printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); fflush(ficlog); /* goto end; */ exit(70); } strcpy(filereso,"o"); strcat(filereso,fileresu); if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ printf("Problem with Output resultfile: %s\n", filereso); fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); fflush(ficlog); goto end; } /* Reads comments: lines beginning with '#' */ numlinepar=0; /* First parameter line */ while(fgets(line, MAXLINE, ficpar)) { /* If line starts with a # it is a comment */ if (line[0] == '#') { numlinepar++; fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); continue; }else break; } if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \ title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ if (num_filled != 5) { printf("Should be 5 parameters\n"); } numlinepar++; printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); } /* Second parameter line */ while(fgets(line, MAXLINE, ficpar)) { /* If line starts with a # it is a comment */ if (line[0] == '#') { numlinepar++; fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); continue; }else break; } if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \ &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){ if (num_filled != 8) { printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); printf("but line=%s\n",line); } printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt); } /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ /* Third parameter line */ while(fgets(line, MAXLINE, ficpar)) { /* If line starts with a # it is a comment */ if (line[0] == '#') { numlinepar++; fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); continue; }else break; } if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ if (num_filled == 0) model[0]='\0'; else if (num_filled != 1){ printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); model[0]='\0'; goto end; } else{ if (model[0]=='+'){ for(i=1; i<=strlen(model);i++) modeltemp[i-1]=model[i]; strcpy(model,modeltemp); } } /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ printf("model=1+age+%s\n",model);fflush(stdout); } /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ /* numlinepar=numlinepar+3; /\* In general *\/ */ /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); fflush(ficlog); /* if(model[0]=='#'|| model[0]== '\0'){ */ if(model[0]=='#'){ printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ if(mle != -1){ printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); exit(1); } } while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */ z[0]=line[1]; } /* printf("****line [1] = %c \n",line[1]); */ fputs(line, stdout); //puts(line); fputs(line,ficparo); fputs(line,ficlog); } ungetc(c,ficpar); covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 v1+v2*age+v2*v3 makes cptcovn = 3 */ if (strlen(model)>1) ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/ else ncovmodel=2; /* Constant and age */ nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ npar= nforce*ncovmodel; /* Number of parameters like aij*/ if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); fflush(stdout); fclose (ficlog); goto end; } delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); delti=delti3[1][1]; /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ if(mle==-1){ /* Print a wizard for help writing covariance matrix */ prwizard(ncovmodel, nlstate, ndeath, model, ficparo); printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); fclose (ficparo); fclose (ficlog); goto end; exit(0); } else if(mle==-3) { /* Main Wizard */ prwizard(ncovmodel, nlstate, ndeath, model, ficparo); printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); matcov=matrix(1,npar,1,npar); hess=matrix(1,npar,1,npar); } else{ /* Read guessed parameters */ /* Reads comments: lines beginning with '#' */ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); } ungetc(c,ficpar); param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); for(i=1; i <=nlstate; i++){ j=0; for(jj=1; jj <=nlstate+ndeath; jj++){ if(jj==i) continue; j++; fscanf(ficpar,"%1d%1d",&i1,&j1); if ((i1 != i) || (j1 != jj)){ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ It might be a problem of design; if ncovcol and the model are correct\n \ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); exit(1); } fprintf(ficparo,"%1d%1d",i1,j1); if(mle==1) printf("%1d%1d",i,jj); fprintf(ficlog,"%1d%1d",i,jj); for(k=1; k<=ncovmodel;k++){ fscanf(ficpar," %lf",¶m[i][j][k]); if(mle==1){ printf(" %lf",param[i][j][k]); fprintf(ficlog," %lf",param[i][j][k]); } else fprintf(ficlog," %lf",param[i][j][k]); fprintf(ficparo," %lf",param[i][j][k]); } fscanf(ficpar,"\n"); numlinepar++; if(mle==1) printf("\n"); fprintf(ficlog,"\n"); fprintf(ficparo,"\n"); } } fflush(ficlog); /* Reads scales values */ p=param[1][1]; /* Reads comments: lines beginning with '#' */ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); } ungetc(c,ficpar); for(i=1; i <=nlstate; i++){ for(j=1; j <=nlstate+ndeath-1; j++){ fscanf(ficpar,"%1d%1d",&i1,&j1); if ( (i1-i) * (j1-j) != 0){ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); exit(1); } printf("%1d%1d",i,j); fprintf(ficparo,"%1d%1d",i1,j1); fprintf(ficlog,"%1d%1d",i1,j1); for(k=1; k<=ncovmodel;k++){ fscanf(ficpar,"%le",&delti3[i][j][k]); printf(" %le",delti3[i][j][k]); fprintf(ficparo," %le",delti3[i][j][k]); fprintf(ficlog," %le",delti3[i][j][k]); } fscanf(ficpar,"\n"); numlinepar++; printf("\n"); fprintf(ficparo,"\n"); fprintf(ficlog,"\n"); } } fflush(ficlog); /* Reads covariance matrix */ delti=delti3[1][1]; /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ /* Reads comments: lines beginning with '#' */ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); } ungetc(c,ficpar); matcov=matrix(1,npar,1,npar); hess=matrix(1,npar,1,npar); for(i=1; i <=npar; i++) for(j=1; j <=npar; j++) matcov[i][j]=0.; /* Scans npar lines */ for(i=1; i <=npar; i++){ count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk); if(count != 3){ printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); exit(1); }else if(mle==1) printf("%1d%1d%1d",i1,j1,jk); fprintf(ficlog,"%1d%1d%1d",i1,j1,jk); fprintf(ficparo,"%1d%1d%1d",i1,j1,jk); for(j=1; j <=i; j++){ fscanf(ficpar," %le",&matcov[i][j]); if(mle==1){ printf(" %.5le",matcov[i][j]); } fprintf(ficlog," %.5le",matcov[i][j]); fprintf(ficparo," %.5le",matcov[i][j]); } fscanf(ficpar,"\n"); numlinepar++; if(mle==1) printf("\n"); fprintf(ficlog,"\n"); fprintf(ficparo,"\n"); } /* End of read covariance matrix npar lines */ for(i=1; i <=npar; i++) for(j=i+1;j<=npar;j++) matcov[i][j]=matcov[j][i]; if(mle==1) printf("\n"); fprintf(ficlog,"\n"); fflush(ficlog); /*-------- Rewriting parameter file ----------*/ strcpy(rfileres,"r"); /* "Rparameterfile */ strcat(rfileres,optionfilefiname); /* Parameter file first name*/ strcat(rfileres,"."); /* */ strcat(rfileres,optionfilext); /* Other files have txt extension */ if((ficres =fopen(rfileres,"w"))==NULL) { printf("Problem writing new parameter file: %s\n", rfileres);goto end; fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end; } fprintf(ficres,"#%s\n",version); } /* End of mle != -3 */ /* Main data */ n= lastobs; num=lvector(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); /* s[i][j] health state for wave i and individual j */ tab=ivector(1,NCOVMAX); ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ /* Reads data from file datafile */ if (readdata(datafile, firstobs, lastobs, &imx)==1) goto end; /* Calculation of the number of parameters from char model */ /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 k=3 V4 Tvar[k=3]= 4 (from V4) k=2 V1 Tvar[k=2]= 1 (from V1) k=1 Tvar[1]=2 (from V2) */ Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. */ /* For model-covariate k tells which data-covariate to use but because this model-covariate is a construction we invent a new column ncovcol + k1 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 Tvar[3=V1*V4]=4+1 etc */ Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */ Tvaraff=ivector(1,NCOVMAX); /* Unclear */ Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 4 covariates (3 plus signs) Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 */ /* Main decodemodel */ if(decodemodel(model, lastobs) == 1) goto end; if((double)(lastobs-imx)/(double)imx > 1.10){ nbwarn++; printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); } /* if(mle==1){*/ if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ } /*-calculation of age at interview from date of interview and age at death -*/ agev=matrix(1,maxwav,1,imx); if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) goto end; agegomp=(int)agemin; free_vector(moisnais,1,n); free_vector(annais,1,n); /* free_matrix(mint,1,maxwav,1,n); free_matrix(anint,1,maxwav,1,n);*/ /* free_vector(moisdc,1,n); */ /* free_vector(andc,1,n); */ /* */ wav=ivector(1,imx); /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */ /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */ /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */ dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/ bh=imatrix(1,lastpass-firstpass+2,1,imx); mw=imatrix(1,lastpass-firstpass+2,1,imx); /* Concatenates waves */ /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. Death is a valid wave (if date is known). mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] and mw[mi+1][i]. dh depends on stepm. */ concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); /* */ free_vector(moisdc,1,n); free_vector(andc,1,n); /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); ncodemax[1]=1; Ndum =ivector(-1,NCOVMAX); if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */ tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ /* 1 to ncodemax[j] which is the maximum value of this jth covariate */ /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/ /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded * (currently 0 or 1) in the data. * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of * corresponding modality (h,j). */ h=0; /*if (cptcovn > 0) */ m=pow(2,cptcoveff); /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 * For k=4 covariates, h goes from 1 to m=2**k * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1; * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 * h\k 1 2 3 4 *______________________________ * 1 i=1 1 i=1 1 i=1 1 i=1 1 * 2 2 1 1 1 * 3 i=2 1 2 1 1 * 4 2 2 1 1 * 5 i=3 1 i=2 1 2 1 * 6 2 1 2 1 * 7 i=4 1 2 2 1 * 8 2 2 2 1 * 9 i=5 1 i=3 1 i=2 1 2 * 10 2 1 1 2 * 11 i=6 1 2 1 2 * 12 2 2 1 2 * 13 i=7 1 i=4 1 2 2 * 14 2 1 2 2 * 15 i=8 1 2 2 2 * 16 2 2 2 2 */ /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */ /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4 * and the value of each covariate? * V1=1, V2=1, V3=2, V4=1 ? * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok. * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st. * In order to get the real value in the data, we use nbcode * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0 * We are keeping this crazy system in order to be able (in the future?) * to have more than 2 values (0 or 1) for a covariate. * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1 * bbbbbbbb * 76543210 * h-1 00000101 (6-1=5) *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift * & * 1 00000001 (1) * 00000001 = 1 & ((h-1) >> (k-1)) * +1= 00000010 =2 * * h=14, k=3 => h'=h-1=13, k'=k-1=2 * h' 1101 =2^3+2^2+0x2^1+2^0 * >>k' 11 * & 00000001 * = 00000001 * +1 = 00000010=2 = codtabm(14,3) * Reverse h=6 and m=16? * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1. * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff) * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 * decodtabm(h,j,cptcoveff)= (h <= (1< 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 日本学術振興会 (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; /* 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 -----------*/ 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 printf("Current directory %s!\n",pathcd); /*strcat(plotcmd,CHARSEPARATOR);*/ sprintf(plotcmd,"gnuplot"); #ifdef _WIN32 sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); #endif if(!stat(plotcmd,&info)){ printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); if(!stat(getenv("GNUPLOTBIN"),&info)){ printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); }else strcpy(pplotcmd,plotcmd); #ifdef __unix strcpy(plotcmd,GNUPLOTPROGRAM); if(!stat(plotcmd,&info)){ printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); }else strcpy(pplotcmd,plotcmd); #endif }else strcpy(pplotcmd,plotcmd); sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); if((outcmd=system(plotcmd)) != 0){ printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); if((outcmd=system(plotcmd)) != 0) printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); } printf(" Successful, please wait..."); while (z[0] != 'q') { /* chdir(path); */ printf("\nType e to edit results with your browser, g to graph again and q for exit: "); scanf("%s",z); /* if (z[0] == 'c') system("./imach"); */ 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); } end: while (z[0] != 'q') { printf("\nType q for exiting: "); fflush(stdout); scanf("%s",z); } }
"); m=pow(2,cptcoveff); if (cptcovn < 1) {m=1;ncodemax[1]=1;} jj1=0; for(k1=1; k1<=m;k1++){ /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; if (cptcovn > 0) { fprintf(fichtm,"
************ Results for covariates"); for (cpt=1; cpt<=cptcoveff;cpt++){ 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,"\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s_%d-2.svg
\
![](\"%s_%d-2.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Quasi-incidences */
fprintf(fichtm,"\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\ incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \ divided by h: hPij/h : %s_%d-3.svg
\
![](\"%s_%d-3.svg\")
",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
/* Survival functions (period) in state j */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
![%s%d_%d.svg](\"%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(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
\
", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
}
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d%d.svg
\
![](\"%s_%d%d.svg\")
",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
}
/* } /\* end i1 *\/ */
}/* End k1 */
fprintf(fichtm,"\n", estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_")); fprintf(fichtm,"\ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): %s
\n", estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_")); fprintf(fichtm,"\ - Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): %s
\n", estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_")); fprintf(fichtm,"\ - Standard deviation of period (stable) prevalences: %s
\n",\ subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); /* if(popforecast==1) fprintf(fichtm,"\n */ /* - Prevalences forecasting: f%s
\n */ /* - Population forecasting (if popforecast=1): pop%s
\n */ /*
",fileres,fileres,fileres,fileres); */ /* else */ /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)
\n",popforecast, stepm, model); */ fflush(fichtm); fprintf(fichtm,"
"); m=pow(2,cptcoveff); if (cptcovn < 1) {m=1;ncodemax[1]=1;} jj1=0; for(k1=1; k1<=m;k1++){ /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; if (cptcovn > 0) { fprintf(fichtm,"
************ Results for covariates"); for (cpt=1; cpt<=cptcoveff;cpt++) 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 (cross-sectional) and period (incidence based) \ prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d.svg
\
",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
}
fprintf(fichtm,"\n- Total life expectancy by age and \ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ true period expectancies (those weighted with period prevalences are also\ drawn in addition to the population based expectancies computed using\ observed and cahotic prevalences: %s_%d.svg
\
![](\"%s_%d.svg\")
",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
/* } /\* end i1 *\/ */
}/* End k1 */
fprintf(fichtm,"