--- imach096d/src/imach.c 2002/03/08 16:17:18 1.30 +++ imach096d/src/imach.c 2002/05/07 15:53:01 1.41 @@ -1,4 +1,4 @@ -/* $Id: imach.c,v 1.30 2002/03/08 16:17:18 lievre Exp $ +/* $Id: imach.c,v 1.41 2002/05/07 15:53:01 lievre Exp $ Interpolated Markov Chain Short summary of the programme: @@ -14,7 +14,7 @@ model. More health states you consider, more time is necessary to reach the Maximum Likelihood of the parameters involved in the model. The simplest model is the multinomial logistic model where pij is the - probabibility to be observed in state j at the second wave + probability to be observed in state j at the second wave conditional to be observed in state i at the first wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex' is a covariate. If you want to have a more @@ -56,7 +56,8 @@ #include #define MAXLINE 256 -#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot" +#define GNUPLOTPROGRAM "wgnuplot" +/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ #define FILENAMELENGTH 80 /*#define DEBUG*/ #define windows @@ -82,7 +83,7 @@ int cptcovn, cptcovage=0, cptcoveff=0,cp int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ -int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ +int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ int popbased=0; int *wav; /* Number of waves for this individuual 0 is possible */ @@ -135,6 +136,9 @@ int imx; int stepm; /* Stepm, step in month: minimum step interpolation*/ +int estepm; +/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/ + int m,nb; int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; @@ -686,16 +690,15 @@ double **prevalim(double **prlim, int nl for (k=1; k<=cptcovn;k++) { cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; - /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/ + /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/ } - for (k=1; k<=cptcovage;k++) - cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; for (k=1; k<=cptcovprod;k++) cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ - + /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); savm=oldm; @@ -1178,14 +1181,14 @@ void lubksb(double **a, int n, int *indx /************ Frequencies ********************/ void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) { /* Some frequencies */ - + int i, m, jk, k1,i1, j1, bool, z1,z2,j; double ***freq; /* Frequencies */ double *pp; double pos, k2, dateintsum=0,k2cpt=0; FILE *ficresp; char fileresp[FILENAMELENGTH]; - + pp=vector(1,nlstate); probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); strcpy(fileresp,"p"); @@ -1196,113 +1199,116 @@ void freqsummary(char fileres[], int ag } freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); j1=0; - + j=cptcoveff; if (cptcovn<1) {j=1;ncodemax[1]=1;} - + for(k1=1; k1<=j;k1++){ - for(i1=1; i1<=ncodemax[k1];i1++){ - j1++; - /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); - scanf("%d", i);*/ - for (i=-1; i<=nlstate+ndeath; i++) - for (jk=-1; jk<=nlstate+ndeath; jk++) - for(m=agemin; m <= agemax+3; m++) - freq[i][jk][m]=0; - - dateintsum=0; - k2cpt=0; - for (i=1; i<=imx; i++) { - bool=1; - if (cptcovn>0) { - for (z1=1; z1<=cptcoveff; z1++) - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) - bool=0; - } - if (bool==1) { - for(m=firstpass; m<=lastpass; m++){ - k2=anint[m][i]+(mint[m][i]/12.); - if ((k2>=dateprev1) && (k2<=dateprev2)) { - if(agev[m][i]==0) agev[m][i]=agemax+1; - if(agev[m][i]==1) agev[m][i]=agemax+2; - freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; - freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i]; - if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) { - dateintsum=dateintsum+k2; - k2cpt++; - } - - } - } - } - } + for(i1=1; i1<=ncodemax[k1];i1++){ + j1++; + /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); + scanf("%d", i);*/ + for (i=-1; i<=nlstate+ndeath; i++) + for (jk=-1; jk<=nlstate+ndeath; jk++) + for(m=agemin; m <= agemax+3; m++) + freq[i][jk][m]=0; + + dateintsum=0; + k2cpt=0; + for (i=1; i<=imx; i++) { + bool=1; + if (cptcovn>0) { + for (z1=1; z1<=cptcoveff; z1++) + if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) + bool=0; + } + if (bool==1) { + for(m=firstpass; m<=lastpass; m++){ + k2=anint[m][i]+(mint[m][i]/12.); + if ((k2>=dateprev1) && (k2<=dateprev2)) { + if(agev[m][i]==0) agev[m][i]=agemax+1; + if(agev[m][i]==1) agev[m][i]=agemax+2; + if (m1) && (agev[m][i]< (agemax+3))) { + dateintsum=dateintsum+k2; + k2cpt++; + } + } + } + } + } - fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); + fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); - if (cptcovn>0) { - fprintf(ficresp, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresp, "**********\n#"); - } - for(i=1; i<=nlstate;i++) - fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); - fprintf(ficresp, "\n"); - - for(i=(int)agemin; i <= (int)agemax+3; i++){ - if(i==(int)agemax+3) - printf("Total"); - else - printf("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) - printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); - else - printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - } + if (cptcovn>0) { + fprintf(ficresp, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficresp, "**********\n#"); + } + for(i=1; i<=nlstate;i++) + fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); + fprintf(ficresp, "\n"); + + for(i=(int)agemin; i <= (int)agemax+3; i++){ + if(i==(int)agemax+3) + printf("Total"); + else + printf("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) + printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); + else + printf(" %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; jk <=nlstate ; jk++){ + for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) + pp[jk] += freq[jk][m][i]; + } - for(jk=1,pos=0; jk <=nlstate ; jk++) - pos += pp[jk]; - for(jk=1; jk <=nlstate ; jk++){ - if(pos>=1.e-5) - printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - else - printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - if( i <= (int) agemax){ - if(pos>=1.e-5){ - fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); - 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]);*/ + for(jk=1,pos=0; jk <=nlstate ; jk++) + pos += pp[jk]; + for(jk=1; jk <=nlstate ; jk++){ + if(pos>=1.e-5) + printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + else + printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + if( i <= (int) agemax){ + if(pos>=1.e-5){ + fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); + probs[i][jk][j1]= pp[jk]/pos; + /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ + } + else + fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); + } } - else - fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); + + for(jk=-1; jk <=nlstate+ndeath; jk++) + for(m=-1; m <=nlstate+ndeath; m++) + if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); + if(i <= (int) agemax) + fprintf(ficresp,"\n"); + printf("\n"); } } - for(jk=-1; jk <=nlstate+ndeath; jk++) - for(m=-1; m <=nlstate+ndeath; m++) - if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); - if(i <= (int) agemax) - fprintf(ficresp,"\n"); - printf("\n"); - } - } - } + } dateintmean=dateintsum/k2cpt; fclose(ficresp); free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); free_vector(pp,1,nlstate); - + /* End of Freq */ } @@ -1346,8 +1352,11 @@ void prevalence(int agemin, float agemax if ((k2>=dateprev1) && (k2<=dateprev2)) { if(agev[m][i]==0) agev[m][i]=agemax+1; if(agev[m][i]==1) agev[m][i]=agemax+2; - freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; - /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i]; */ + if (m0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; + else + freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; + freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; } } } @@ -1380,7 +1389,7 @@ void prevalence(int agemin, float agemax } } } - + free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); free_vector(pp,1,nlstate); @@ -1497,6 +1506,7 @@ void tricode(int *Tvar, int **nbcode, in for (k=0; k<=19; k++) { if (Ndum[k] != 0) { nbcode[Tvar[j]][ij]=k; + ij++; } if (ij > ncodemax[j]) break; @@ -1513,7 +1523,7 @@ void tricode(int *Tvar, int **nbcode, in ij=1; for (i=1; i<=10; i++) { - if((Ndum[i]!=0) && (i<=ncov)){ + if((Ndum[i]!=0) && (i<=ncovcol)){ Tvaraff[ij]=i; ij++; } @@ -1524,71 +1534,191 @@ void tricode(int *Tvar, int **nbcode, in /*********** Health Expectancies ****************/ -void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij) +void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov ) + { /* Health expectancies */ - int i, j, nhstepm, hstepm, h; - double age, agelim,hf; - double ***p3mat; + int i, j, nhstepm, hstepm, h, nstepm, k, cptj; + double age, agelim, hf; + double ***p3mat,***varhe; + double **dnewm,**doldm; + double *xp; + double **gp, **gm; + double ***gradg, ***trgradg; + int theta; + + varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage); + xp=vector(1,npar); + dnewm=matrix(1,nlstate*2,1,npar); + doldm=matrix(1,nlstate*2,1,nlstate*2); fprintf(ficreseij,"# Health expectancies\n"); fprintf(ficreseij,"# Age"); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++) - fprintf(ficreseij," %1d-%1d",i,j); + fprintf(ficreseij," %1d-%1d (SE)",i,j); fprintf(ficreseij,"\n"); - hstepm=1*YEARM; /* Every j years of age (in month) */ - hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + /* We compute the life expectancy from trapezoids spaced every estepm months + * This is mainly to measure the difference between two models: for example + * if stepm=24 months pijx are given only every 2 years and by summing them + * we are calculating an estimate of the Life Expectancy assuming a linear + * progression inbetween and thus overestimating or underestimating according + * to the curvature of the survival function. If, for the same date, we + * estimate the model with stepm=1 month, we can keep estepm to 24 months + * to compare the new estimate of Life expectancy with the same linear + * hypothesis. A more precise result, taking into account a more precise + * curvature will be obtained if estepm is as small as stepm. */ + + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelin. + Look at hpijx to understand the reason of that which relies in memory size + and note for a fixed period like estepm months */ + /* We decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed only each two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ agelim=AGESUP; for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ /* nhstepm age range expressed in number of stepm */ - nhstepm=(int) rint((agelim-age)*YEARM/stepm); - /* Typically if 20 years = 20*12/6=40 stepm */ - /*if (stepm >= YEARM) hstepm=1;*/ -hstepm=1; - nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */ + nstepm=(int) rint((agelim-age)*YEARM/stepm); + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2); + gp=matrix(0,nhstepm,1,nlstate*2); + gm=matrix(0,nhstepm,1,nlstate*2); + /* Computed by stepm unit matrices, product of hstepm matrices, stored in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij); -hf=stepm/YEARM; -/*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/ + + + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ + + /* Computing Variances of health expectancies */ + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++){ + xp[i] = x[i] + (i==theta ?delti[theta]:0); + } + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + + cptj=0; + for(j=1; j<= nlstate; j++){ + for(i=1; i<=nlstate; i++){ + cptj=cptj+1; + for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){ + gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; + } + } + } + + + for(i=1; i<=npar; i++) + xp[i] = x[i] - (i==theta ?delti[theta]:0); + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + + cptj=0; + for(j=1; j<= nlstate; j++){ + for(i=1;i<=nlstate;i++){ + cptj=cptj+1; + for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ + gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; + } + } + } + + + + for(j=1; j<= nlstate*2; j++) + for(h=0; h<=nhstepm-1; h++){ + gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; + } + + } + +/* End theta */ + + trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar); + + for(h=0; h<=nhstepm-1; h++) + for(j=1; j<=nlstate*2;j++) + for(theta=1; theta <=npar; theta++) + trgradg[h][j][theta]=gradg[h][theta][j]; + + + for(i=1;i<=nlstate*2;i++) + for(j=1;j<=nlstate*2;j++) + varhe[i][j][(int)age] =0.; + + for(h=0;h<=nhstepm-1;h++){ + for(k=0;k<=nhstepm-1;k++){ + matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]); + for(i=1;i<=nlstate*2;i++) + for(j=1;j<=nlstate*2;j++) + varhe[i][j][(int)age] += doldm[i][j]*hf*hf; + } + } + + + /* Computing expectancies */ for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++) for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ - eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0; + eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; + +/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ + } - - /* hf=1; - if (stepm >= YEARM) hf=stepm/YEARM;*/ -hf=stepm/YEARM; - + fprintf(ficreseij,"%3.0f",age ); + cptj=0; for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ - fprintf(ficreseij," %9.4f", eij[i][j][(int)age]); + cptj++; + fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) ); } fprintf(ficreseij,"\n"); + + free_matrix(gm,0,nhstepm,1,nlstate*2); + free_matrix(gp,0,nhstepm,1,nlstate*2); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2); + free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar); free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); } + free_vector(xp,1,npar); + free_matrix(dnewm,1,nlstate*2,1,npar); + free_matrix(doldm,1,nlstate*2,1,nlstate*2); + free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage); } /************ Variance ******************/ -void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) +void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm) { /* Variance of health expectancies */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ double **newm; double **dnewm,**doldm; - int i, j, nhstepm, hstepm, h; + int i, j, nhstepm, hstepm, h, nstepm ; int k, cptcode; double *xp; double **gp, **gm; double ***gradg, ***trgradg; double ***p3mat; - double age,agelim; + double age,agelim, hf; int theta; fprintf(ficresvij,"# Covariances of life expectancies\n"); @@ -1602,13 +1732,27 @@ void varevsij(char fileres[], double *** 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 */ + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelin. + Look at hpijx to understand the reason of that which relies in memory size + and note for a fixed period like k years */ + /* We decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed only each two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 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 */ + 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); @@ -1663,24 +1807,25 @@ void varevsij(char fileres[], double *** for(theta=1; theta <=npar; theta++) trgradg[h][j][theta]=gradg[h][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]; + vareij[i][j][(int)age] += doldm[i][j]*hf*hf; } } - h=1; - if (stepm >= YEARM) h=stepm/YEARM; + fprintf(ficresvij,"%.0f ",age ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ - fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]); + fprintf(ficresvij," %.4f", vareij[i][j][(int)age]); } fprintf(ficresvij,"\n"); free_matrix(gp,0,nhstepm,1,nlstate); @@ -1780,9 +1925,9 @@ void varprevlim(char fileres[], double * } /************ Variance of one-step probabilities ******************/ -void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij) +void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax) { - int i, j; + int i, j, i1, k1, j1, z1; int k=0, cptcode; double **dnewm,**doldm; double *xp; @@ -1797,95 +1942,126 @@ void varprob(char fileres[], double **ma if((ficresprob=fopen(fileresprob,"w"))==NULL) { printf("Problem with resultfile: %s\n", fileresprob); } - printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob); + printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob); +fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n"); + fprintf(ficresprob,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=(nlstate+ndeath);j++) + fprintf(ficresprob," p%1d-%1d (SE)",i,j); + + + fprintf(ficresprob,"\n"); + xp=vector(1,npar); dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath)); cov[1]=1; - for (age=bage; age<=fage; age ++){ - cov[2]=age; - gradg=matrix(1,npar,1,9); - trgradg=matrix(1,9,1,npar); - gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath)); - gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath)); + j=cptcoveff; + if (cptcovn<1) {j=1;ncodemax[1]=1;} + j1=0; + for(k1=1; k1<=1;k1++){ + for(i1=1; i1<=ncodemax[k1];i1++){ + j1++; + + if (cptcovn>0) { + fprintf(ficresprob, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficresprob, "**********\n#"); + } - for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++) - xp[i] = x[i] + (i==theta ?delti[theta]:0); - - pmij(pmmij,cov,ncovmodel,xp,nlstate); - - k=0; - for(i=1; i<= (nlstate+ndeath); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - gp[k]=pmmij[i][j]; + for (age=bage; age<=fage; age ++){ + cov[2]=age; + for (k=1; k<=cptcovn;k++) { + cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; + } - } - - for(i=1; i<=npar; i++) - xp[i] = x[i] - (i==theta ?delti[theta]:0); + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; + for (k=1; k<=cptcovprod;k++) + cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + + gradg=matrix(1,npar,1,9); + trgradg=matrix(1,9,1,npar); + gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath)); + gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath)); + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++) + xp[i] = x[i] + (i==theta ?delti[theta]:0); + + pmij(pmmij,cov,ncovmodel,xp,nlstate); + + k=0; + for(i=1; i<= (nlstate+ndeath); 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]:0); - - pmij(pmmij,cov,ncovmodel,xp,nlstate); - k=0; - for(i=1; i<=(nlstate+ndeath); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - gm[k]=pmmij[i][j]; - } - } + pmij(pmmij,cov,ncovmodel,xp,nlstate); + k=0; + for(i=1; i<=(nlstate+ndeath); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gm[k]=pmmij[i][j]; + } + } - for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++) - gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; - } - - for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++) - for(theta=1; theta <=npar; theta++) - trgradg[j][theta]=gradg[theta][j]; - - matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg); - - pmij(pmmij,cov,ncovmodel,x,nlstate); + for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++) + gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; + } - k=0; - for(i=1; i<=(nlstate+ndeath); i++){ - for(j=1; j<=(nlstate+ndeath);j++){ - k=k+1; - gm[k]=pmmij[i][j]; + for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++) + for(theta=1; theta <=npar; theta++) + trgradg[j][theta]=gradg[theta][j]; + + matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg); + + pmij(pmmij,cov,ncovmodel,x,nlstate); + + k=0; + for(i=1; i<=(nlstate+ndeath); i++){ + for(j=1; j<=(nlstate+ndeath);j++){ + k=k+1; + gm[k]=pmmij[i][j]; + } } - } /*printf("\n%d ",(int)age); for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){ - - printf("%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); - - for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){ - if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]); -if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]); - } + fprintf(ficresprob,"\n%d ",(int)age); + for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++) + fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i])); + + } + } 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); -} - free_vector(xp,1,npar); -fclose(ficresprob); - + } + free_vector(xp,1,npar); + fclose(ficresprob); + } /******************* Printing html file ***********/ -void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){ +void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \ + int lastpass, int stepm, int weightopt, char model[],\ + int imx,int jmin, int jmax, double jmeanint,char optionfile[], \ + char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\ + char version[], int popforecast, int estepm ){ int jj1, k1, i1, cpt; FILE *fichtm; /*char optionfilehtm[FILENAMELENGTH];*/ @@ -1896,26 +2072,33 @@ void printinghtml(char fileres[], char t printf("Problem with %s \n",optionfilehtm), exit(0); } - fprintf(fichtm,"
    Imach, Version 0.71
    -Title=%s
    Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
    - -Total number of observations=%d
    -Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
    + fprintf(fichtm," %s
    \n +Title=%s
    Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
    \n +\n +Total number of observations=%d
    \n +Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
    \n
    -
  • Outputs files

    \n - - Observed prevalence in each state: p%s
    \n -- Estimated parameters and the covariance matrix: %s
    - - Stationary prevalence in each state: pl%s
    - - Transition probabilities: pij%s
    - - Copy of the parameter file: o%s
    - - Life expectancies by age and initial health status: e%s
    - - Variances of life expectancies by age and initial health status: v%s
    - - Health expectancies with their variances: t%s
    - - Standard deviation of stationary prevalences: vpl%s
    - - Prevalences forecasting: f%s
    - - Population forecasting (if popforecast=1): pop%s
    -
    ",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres); - +
    • Outputs files
      \n + - Copy of the parameter file: o%s
      \n + - Gnuplot file name: %s
      \n + - Observed prevalence in each state: p%s
      \n + - Stationary prevalence in each state: pl%s
      \n + - Transition probabilities: pij%s
      \n + - Life expectancies by age and initial health status (estepm=%2d months): e%s
      \n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres); + + fprintf(fichtm,"\n + - Parameter file with estimated parameters and the covariance matrix: %s
      \n + - Variance of one-step probabilities: prob%s
      \n + - Variances of life expectancies by age and initial health status (estepm=%d months): v%s
      \n + - Health expectancies with their variances: t%s
      \n + - Standard deviation of stationary prevalences: vpl%s
      \n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); + + if(popforecast==1) fprintf(fichtm,"\n + - Prevalences forecasting: f%s
      \n + - Population forecasting (if popforecast=1): pop%s
      \n +
      ",fileres,fileres,fileres,fileres); + else + fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)

      • \n",popforecast, stepm, model); fprintf(fichtm,"
    • Graphs

      • "); m=cptcoveff; @@ -1956,12 +2139,12 @@ fclose(fichtm); } /******************* Gnuplot file **************/ -void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){ +void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ int m,cpt,k1,i,k,j,jk,k2,k3,ij,l; strcpy(optionfilegnuplot,optionfilefiname); - strcat(optionfilegnuplot,".plt"); + strcat(optionfilegnuplot,".gp.txt"); if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { printf("Problem with file %s",optionfilegnuplot); } @@ -1976,10 +2159,10 @@ m=pow(2,cptcoveff); for (k1=1; k1<= m ; k1 ++) { #ifdef windows - fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1); #endif #ifdef unix -fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres); +fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres); #endif for (i=1; i<= nlstate ; i ++) { @@ -2006,7 +2189,7 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" /*2 eme*/ for (k1=1; k1<= m ; k1 ++) { - fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage); + fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage); for (i=1; i<= nlstate+1 ; i ++) { k=2*i; @@ -2038,10 +2221,19 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt<= nlstate ; cpt ++) { - k=2+nlstate*(cpt-1); - fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt); + k=2+nlstate*(2*cpt-2); + fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt); + /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); +fprintf(ficgp,"\" t \"e%d1\" w l",cpt); +fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); +fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + +*/ for (i=1; i< nlstate ; i ++) { - fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1); + fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1); + } fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1); } @@ -2051,7 +2243,7 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\" for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt=(agemin-((int)calagedate %12)/12.); agedeb--){ + for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); nhstepm = nhstepm/hstepm; @@ -2224,7 +2416,7 @@ calagedate=(anproj1+mproj1/12.+jproj1/36 for (h=0; h<=nhstepm; h++){ if (h==(int) (calagedate+YEARM*cpt)) { - fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm); + fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); } for(j=1; j<=nlstate+ndeath;j++) { kk1=0.;kk2=0; @@ -2253,7 +2445,7 @@ calagedate=(anproj1+mproj1/12.+jproj1/36 fclose(ficresf); } /************** Forecasting ******************/ -populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ +populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; int *popage; @@ -2267,7 +2459,7 @@ populforecast(char fileres[], double anp agelim=AGESUP; calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; - prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); + prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); strcpy(filerespop,"pop"); @@ -2281,7 +2473,7 @@ populforecast(char fileres[], double anp if (mobilav==1) { mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); - movingaverage(agedeb, fage, agemin, mobaverage); + movingaverage(agedeb, fage, ageminpar, mobaverage); } stepsize=(int) (stepm+YEARM-1)/YEARM; @@ -2322,7 +2514,7 @@ populforecast(char fileres[], double anp for (cpt=0; cpt<=0;cpt++) { fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); - for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){ + for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); nhstepm = nhstepm/hstepm; @@ -2368,7 +2560,7 @@ populforecast(char fileres[], double anp for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); - for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){ + for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); nhstepm = nhstepm/hstepm; @@ -2414,7 +2606,7 @@ int main(int argc, char *argv[]) int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod; double agedeb, agefin,hf; - double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; + double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; double fret; double **xi,tmp,delta; @@ -2441,7 +2633,7 @@ int main(int argc, char *argv[]) int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; int mobilav=0,popforecast=0; int hstepm, nhstepm; - double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1; + double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; double bage, fage, age, agelim, agebase; double ftolpl=FTOL; @@ -2459,7 +2651,7 @@ int main(int argc, char *argv[]) double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; - char version[80]="Imach version 0.71, February 2002, INED-EUROREVES "; + char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES "; char *alph[]={"a","a","b","c","d","e"}, str[4]; @@ -2472,7 +2664,7 @@ int main(int argc, char *argv[]) struct timeval start_time, end_time; gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - + getcwd(pathcd, size); printf("\n%s",version); if(argc <=1){ @@ -2520,9 +2712,9 @@ int main(int argc, char *argv[]) } ungetc(c,ficpar); - fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); - printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model); - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model); + 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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); + printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); @@ -2679,7 +2871,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); - for (j=ncov;j>=1;j--){ + for (j=ncovcol;j>=1;j--){ cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); } num[i]=atol(stra); @@ -2698,11 +2890,12 @@ while((c=getc(ficpar))=='#' && c!= EOF){ if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3; if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3; if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3; - } - - for (i=1; i<=imx; i++) - if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));*/ - + }*/ + /* for (i=1; i<=imx; i++){ + if (s[4][i]==9) s[4][i]=-1; + printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ + + /* Calculation of the number of parameter from char model*/ Tvar=ivector(1,15); Tprod=ivector(1,15); @@ -2717,7 +2910,6 @@ while((c=getc(ficpar))=='#' && c!= EOF){ cptcovn=j+1; cptcovprod=j1; - strcpy(modelsav,model); if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){ printf("Error. Non available option model=%s ",model); @@ -2748,7 +2940,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ } else { cutv(strb,stre,strc,'V'); - Tvar[i]=ncov+k1; + Tvar[i]=ncovcol+k1; cutv(strb,strc,strd,'V'); Tprod[k1]=i; Tvard[k1][1]=atoi(strc); @@ -2756,7 +2948,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ Tvar[cptcovn+k2]=Tvard[k1][1]; Tvar[cptcovn+k2+1]=Tvard[k1][2]; for (k=1; k<=lastobs;k++) - covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; + covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; k1++; k2=k2+2; } @@ -2773,7 +2965,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ } } - /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); printf("cptcovprod=%d ", cptcovprod); scanf("%d ",i);*/ fclose(fic); @@ -2785,22 +2977,26 @@ while((c=getc(ficpar))=='#' && c!= EOF){ /*-calculation of age at interview from date of interview and age at death -*/ agev=matrix(1,maxwav,1,imx); - for (i=1; i<=imx; i++) - for(m=2; (m<= maxwav); m++) + for (i=1; i<=imx; i++) { + for(m=2; (m<= maxwav); m++) { if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ anint[m][i]=9999; s[m][i]=-1; } - + if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; + } + } + for (i=1; i<=imx; i++) { agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); for(m=1; (m<= maxwav); m++){ if(s[m][i] >0){ - if (s[m][i] == nlstate+1) { + if (s[m][i] >= nlstate+1) { if(agedc[i]>0) if(moisdc[i]!=99 && andc[i]!=9999) - agev[m][i]=agedc[i]; - else { + agev[m][i]=agedc[i]; + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + else { if (andc[i]!=9999){ printf("Warning negative age at death: %d line:%d\n",num[i],i); agev[m][i]=-1; @@ -2875,20 +3071,21 @@ printf("Total number of individuals= %d, for(j=1; j <= ncodemax[k]; j++){ for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ h++; - if (h>m) h=1;codtab[h][k]=j; + if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j; + /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ } } } } - - - /*for(i=1; i <=m ;i++){ - for(k=1; k <=cptcovn; k++){ - printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff); - } - printf("\n"); - } - scanf("%d",i);*/ + /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); + codtab[1][2]=1;codtab[2][2]=2; */ + /* for(i=1; i <=m ;i++){ + for(k=1; k <=cptcovn; k++){ + printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); + } + printf("\n"); + } + scanf("%d",i);*/ /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ @@ -2910,12 +3107,12 @@ printf("Total number of individuals= %d, } /*--------- results files --------------*/ - fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model); + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); jk=1; - fprintf(ficres,"# Parameters\n"); - printf("# Parameters\n"); + fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); for(i=1,jk=1; i <=nlstate; i++){ for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) @@ -2937,8 +3134,8 @@ printf("Total number of individuals= %d, ftolhess=ftol; /* Usually correct */ hesscov(matcov, p, npar, delti, ftolhess, func); } - fprintf(ficres,"# Scales\n"); - printf("# Scales\n"); + fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); + printf("# Scales (for hessian or gradient estimation)\n"); for(i=1,jk=1; i <=nlstate; i++){ for(j=1; j <=nlstate+ndeath; j++){ if (j!=i) { @@ -2956,8 +3153,8 @@ printf("Total number of individuals= %d, } k=1; - fprintf(ficres,"# Covariance\n"); - printf("# Covariance\n"); + fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); for(i=1;i<=npar;i++){ /* if (k>nlstate) k=1; i1=(i-1)/(ncovmodel*nlstate)+1; @@ -2981,17 +3178,17 @@ printf("Total number of individuals= %d, fputs(line,ficparo); } ungetc(c,ficpar); - - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage); - + estepm=0; + fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if (estepm==0 || estepm < stepm) estepm=stepm; if (fage <= 2) { - bage = agemin; + bage = ageminpar; fage = agemaxpar; } fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); - fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage); - fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage); + fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); @@ -3049,7 +3246,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); /*------------ gnuplot -------------*/ - printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p); + printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p); /*------------ free_vector -------------*/ chdir(path); @@ -3065,7 +3262,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ /*--------- index.htm --------*/ - printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres); + printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm); /*--------------- Prevalence limit --------------*/ @@ -3088,7 +3285,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ k=0; - agebase=agemin; + agebase=ageminpar; agelim=agemaxpar; ftolpl=1.e-10; i1=cptcoveff; @@ -3149,34 +3346,32 @@ while((c=getc(ficpar))=='#' && c!= EOF){ for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespij," %1d-%1d",i,j); fprintf(ficrespij,"\n"); - for (h=0; h<=nhstepm; h++){ + for (h=0; h<=nhstepm; h++){ fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespij," %.5f", p3mat[i][j][h]); fprintf(ficrespij,"\n"); - } + } free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); fprintf(ficrespij,"\n"); } } } - /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/ + varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); fclose(ficrespij); /*---------- Forecasting ------------------*/ - if((stepm == 1) && (model==".")){ + if((stepm == 1) && (strcmp(model,".")==0)){ prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); -if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); - free_matrix(mint,1,maxwav,1,n); - free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n); - free_vector(weight,1,n);} + if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); + } else{ erreur=108; - printf("Error %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm); + printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); } @@ -3203,6 +3398,8 @@ if (popforecast==1) populforecast(filere printf("Problem with variance resultfile: %s\n", fileresv);exit(0); } printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + calagedate=-1; +prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); k=0; for(cptcov=1;cptcov<=i1;cptcov++){ @@ -3215,20 +3412,21 @@ if (popforecast==1) populforecast(filere fprintf(ficreseij,"\n#****** "); for(j=1;j<=cptcoveff;j++) - fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]); + fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); fprintf(ficreseij,"******\n"); fprintf(ficresvij,"\n#****** "); for(j=1;j<=cptcoveff;j++) - fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]); + fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); fprintf(ficresvij,"******\n"); eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; - evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k); + evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); + vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; - varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); + varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm); @@ -3236,8 +3434,6 @@ if (popforecast==1) populforecast(filere for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); fprintf(ficrest,"\n"); - hf=1; - if (stepm >= YEARM) hf=stepm/YEARM; epj=vector(1,nlstate+1); for(age=bage; age <=fage ;age++){ prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); @@ -3246,25 +3442,29 @@ if (popforecast==1) populforecast(filere prlim[i][i]=probs[(int)age][i][k]; } - fprintf(ficrest," %.0f",age); + fprintf(ficrest," %4.0f",age); for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ for(i=1, epj[j]=0.;i <=nlstate;i++) { - epj[j] += prlim[i][i]*hf*eij[i][j][(int)age]; + epj[j] += prlim[i][i]*eij[i][j][(int)age]; + /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ } epj[nlstate+1] +=epj[j]; } + for(i=1, vepp=0.;i <=nlstate;i++) for(j=1;j <=nlstate;j++) vepp += vareij[i][j][(int)age]; - fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp)); + fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); for(j=1;j <=nlstate;j++){ - fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age])); + fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); } fprintf(ficrest,"\n"); } } } - +free_matrix(mint,1,maxwav,1,n); + free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n); + free_vector(weight,1,n); fclose(ficreseij); fclose(ficresvij); fclose(ficrest); @@ -3316,7 +3516,7 @@ if (popforecast==1) populforecast(filere free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); if(erreur >0) - printf("End of Imach with error %d\n",erreur); + printf("End of Imach with error or warning %d\n",erreur); else printf("End of Imach\n"); /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ @@ -3340,14 +3540,12 @@ if (popforecast==1) populforecast(filere #ifdef windows while (z[0] != 'q') { - chdir(path); - printf("\nType e to edit output files, c to start again, and q for exiting: "); + /* chdir(path); */ + printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: "); scanf("%s",z); if (z[0] == 'c') system("./imach"); - else if (z[0] == 'e') { - chdir(path); - system(optionfilehtm); - } + else if (z[0] == 'e') system(optionfilehtm); + else if (z[0] == 'g') system(plotcmd); else if (z[0] == 'q') exit(0); } #endif