--- imach/src/imach.c 2015/10/27 17:36:57 1.207 +++ imach/src/imach.c 2015/11/18 17:41:20 1.210 @@ -1,6 +1,22 @@ -/* $Id: imach.c,v 1.207 2015/10/27 17:36:57 brouard Exp $ +/* $Id: imach.c,v 1.210 2015/11/18 17:41:20 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.210 2015/11/18 17:41:20 brouard + Summary: Start working on projected prevalences + + Revision 1.209 2015/11/17 22:12:03 brouard + Summary: Adding ftolpl parameter + Author: N Brouard + + We had difficulties to get smoothed confidence intervals. It was due + to the period prevalence which wasn't computed accurately. The inner + parameter ftolpl is now an outer parameter of the .imach parameter + file after estepm. If ftolpl is small 1.e-4 and estepm too, + computation are long. + + Revision 1.208 2015/11/17 14:31:57 brouard + Summary: temporary + Revision 1.207 2015/10/27 17:36:57 brouard *** empty log message *** @@ -757,12 +773,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.207 2015/10/27 17:36:57 brouard Exp $ */ +/* $Id: imach.c,v 1.210 2015/11/18 17:41:20 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; -char fullversion[]="$Revision: 1.207 $ $Date: 2015/10/27 17:36:57 $"; +char fullversion[]="$Revision: 1.210 $ $Date: 2015/11/18 17:41:20 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -1985,13 +2001,17 @@ double **prevalim(double **prlim, int nl /* If we start from prlim again, prlim tends to a constant matrix */ int i, ii,j,k; - double min, max, maxmin, maxmax,sumnew=0.; + double *min, *max, *meandiff, maxmax,sumnew=0.; /* double **matprod2(); */ /* test */ double **out, cov[NCOVMAX+1], **pmij(); double **newm; - double agefin, delaymax=100 ; /* Max number of years to converge */ + double agefin, delaymax=200. ; /* 100 Max number of years to converge */ int ncvloop=0; + min=vector(1,nlstate); + max=vector(1,nlstate); + meandiff=vector(1,nlstate); + for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ oldm[ii][j]=(ii==j ? 1.0 : 0.0); @@ -2029,31 +2049,45 @@ double **prevalim(double **prlim, int nl savm=oldm; oldm=newm; - maxmax=0.; - for(j=1;j<=nlstate;j++){ - min=1.; - max=0.; - for(i=1; i<=nlstate; i++) { - sumnew=0; - for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; + + for(j=1; j<=nlstate; j++){ + max[j]=0.; + min[j]=1.; + } + for(i=1;i<=nlstate;i++){ + sumnew=0; + for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; + for(j=1; j<=nlstate; j++){ prlim[i][j]= newm[i][j]/(1-sumnew); - max=FMAX(max,prlim[i][j]); - min=FMIN(min,prlim[i][j]); - printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); + max[j]=FMAX(max[j],prlim[i][j]); + min[j]=FMIN(min[j],prlim[i][j]); } - maxmin=(max-min)/(max+min)*2; - maxmax=FMAX(maxmax,maxmin); + } + + maxmax=0.; + for(j=1; j<=nlstate; j++){ + meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */ + maxmax=FMAX(maxmax,meandiff[j]); + /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */ } /* j loop */ *ncvyear= (int)age- (int)agefin; - printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); + /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */ if(maxmax < ftolpl){ - /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */ + /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */ + free_vector(min,1,nlstate); + free_vector(max,1,nlstate); + free_vector(meandiff,1,nlstate); return prlim; } } /* age loop */ - printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\ -Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); -/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ + /* After some age loop it doesn't converge */ + printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ +Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); + /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ + free_vector(min,1,nlstate); + free_vector(max,1,nlstate); + free_vector(meandiff,1,nlstate); + return prlim; /* should not reach here */ } @@ -2686,16 +2720,16 @@ void likelione(FILE *ficres,double p[], fprintf(fichtm,"\n
File of contributions to the likelihood computed with optimized parameters mle = %d.",mle); fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: %s
\n",subdirf(fileresilk),subdirf(fileresilk)); - fprintf(fichtm,"
- The function drawn is -2Log(L) in Log scale: by state of origin %s-ori.png
\ -",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); - fprintf(fichtm,"
- and by state of destination %s-dest.png
\ -",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); - fflush(fichtm); for (k=1; k<= nlstate ; k++) { fprintf(fichtm,"
- Probability p%dj by origin %d and destination j %s-p%dj.png
\ ",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k); } + fprintf(fichtm,"
- The function drawn is -2Log(L) in Log scale: by state of origin %s-ori.png
\ +",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); + fprintf(fichtm,"
- and by state of destination %s-dest.png
\ +",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_")); + fflush(fichtm); } return; } @@ -2960,6 +2994,8 @@ double hessij( double x[], double **hess double p2[MAXPARM+1]; int k, kmax=1; double v1, v2, cv12, lc1, lc2; + + int firstime=0; fx=func(x); for (k=1; k<=kmax; k=k+10) { @@ -2981,13 +3017,14 @@ double hessij( double x[], double **hess k4=func(p2)-fx; res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */ if(k1*k2*k3*k4 <0.){ + firstime=1; kmax=kmax+10; - if(kmax >=10){ + } + if(kmax >=10 || firstime ==1){ printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol); printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); - } } #ifdef DEBUGHESSIJ v1=hess[thetai][thetai]; @@ -3187,7 +3224,7 @@ void freqsummary(char fileres[], int ia k2cpt=0; for (i=1; i<=imx; i++) { bool=1; - if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ + if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ for (z1=1; z1<=cptcoveff; z1++) if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* Tests if the value of each of the covariates of i is equal to filter j1 */ @@ -3197,7 +3234,7 @@ void freqsummary(char fileres[], int ia j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/ /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/ } - } + } /* cptcovn > 0 */ if (bool==1){ for(m=firstpass; m<=lastpass; m++){ @@ -3211,14 +3248,15 @@ void freqsummary(char fileres[], int ia freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; } - if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { + if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) { dateintsum=dateintsum+k2; k2cpt++; + /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ } /*}*/ - } - } - } /* end i */ + } /* end m */ + } /* end bool */ + } /* end i = 1 to imx */ /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ pstamp(ficresp); @@ -3304,9 +3342,9 @@ void freqsummary(char fileres[], int ia if(first==1) printf("Others in log...\n"); fprintf(ficlog,"\n"); - } + } /* end loop i */ /*}*/ - } + } /* end j1 */ dateintmean=dateintsum/k2cpt; fclose(ficresp); @@ -3993,7 +4031,7 @@ void cvevsij(double ***eij, double x[], } /************ Variance ******************/ - void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) + void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) { /* Variance of health expectancies */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ @@ -4047,7 +4085,6 @@ void cvevsij(double ***eij, double x[], fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); } printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); - fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); pstamp(ficresprobmorprev); fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); @@ -4058,6 +4095,7 @@ void cvevsij(double ***eij, double x[], fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j); } fprintf(ficresprobmorprev,"\n"); + fprintf(ficgp,"\n# Routine varevsij"); fprintf(ficgp,"\nunset title \n"); /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ @@ -4095,9 +4133,9 @@ void cvevsij(double ***eij, double x[], /* 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 function hpijx to understand why (it is linked to memory size questions) */ - /* We decided (b) to get a life expectancy respecting the most precise curvature of the + 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 @@ -4118,8 +4156,8 @@ void cvevsij(double ***eij, double x[], for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ xp[i] = x[i] + (i==theta ?delti[theta]:0); } - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); + + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); if (popbased==1) { if(mobilav ==0){ @@ -4131,13 +4169,14 @@ void cvevsij(double ***eij, double x[], } } + 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]; } } - /* This for computing probability of death (h=1 means + /* Next for computing probability of death (h=1 means computed over hstepm matrices product = hstepm*stepm months) as a weighted average of prlim. */ @@ -4149,8 +4188,8 @@ void cvevsij(double ***eij, double x[], for(i=1; i<=npar; i++) /* Computes gradient x - delta */ xp[i] = x[i] - (i==theta ?delti[theta]:0); - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij); + + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij); if (popbased==1) { if(mobilav ==0){ @@ -4162,6 +4201,8 @@ void cvevsij(double ***eij, double x[], } } + 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++) @@ -4224,8 +4265,8 @@ void cvevsij(double ***eij, double x[], varppt[j][i]=doldmp[j][i]; /* end ppptj */ /* x centered again */ - hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); - prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij); + + prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij); if (popbased==1) { if(mobilav ==0){ @@ -4241,6 +4282,7 @@ void cvevsij(double ***eij, double x[], 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]; @@ -4303,7 +4345,7 @@ void cvevsij(double ***eij, double x[], } /* 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 *ncvyear, int ij, char strstart[]) + 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);*/ @@ -4313,6 +4355,7 @@ void cvevsij(double ***eij, double x[], double *xp; double *gp, *gm; double **gradg, **trgradg; + double **mgm, **mgp; double age,agelim; int theta; @@ -4335,6 +4378,8 @@ void cvevsij(double ***eij, double x[], 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); @@ -4342,18 +4387,27 @@ void cvevsij(double ***eij, double x[], for(i=1; i<=npar; i++){ /* Computes gradient */ xp[i] = x[i] + (i==theta ?delti[theta]:0); } - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); - for(i=1;i<=nlstate;i++) + if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); + for(i=1;i<=nlstate;i++){ gp[i] = prlim[i][i]; - + mgp[theta][i] = prlim[i][i]; + } for(i=1; i<=npar; i++) /* Computes gradient */ xp[i] = x[i] - (i==theta ?delti[theta]:0); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij); - for(i=1;i<=nlstate;i++) + if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); + else + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij); + for(i=1;i<=nlstate;i++){ gm[i] = prlim[i][i]; - + mgm[theta][i] = prlim[i][i]; + } for(i=1;i<=nlstate;i++) gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; + /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */ } /* End theta */ trgradg =matrix(1,nlstate,1,npar); @@ -4361,10 +4415,28 @@ void cvevsij(double ***eij, double x[], 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==67 ||(int)age== 66 ){ + 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{ @@ -4380,6 +4452,8 @@ void cvevsij(double ***eij, double x[], 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 */ @@ -4791,7 +4865,7 @@ divided by h: hPij/h : \n- Survival functions from state %d in any different live states and total.\ + 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); } @@ -4903,6 +4977,11 @@ void printinggnuplot(char fileresu[], ch /*#endif */ m=pow(2,cptcoveff); + /* Projected Prevalences */ +/* plot "NAGI0w_V1V2_monthlyb2b-proj/F_NAGI0w_V1V2_monthlyb2b-proj.txt" u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0))? $7/(1-$13):1/0) t 'p11' w line */ +/* replot "" u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0))? $8/(1-$14):1/0) t 'p21' w line */ +/* replot "" u 6:((($1 == 1) && ($2==0) && ($3==2) &&($4==0)&&($9!=0))? $9/(1-$15):1/0) t 'p.1' w line */ + /* Contribution to likelihood */ /* Plot the probability implied in the likelihood */ fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); @@ -6510,7 +6589,7 @@ void syscompilerinfo(int logged) } - int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){ + 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; */ @@ -6566,7 +6645,7 @@ void syscompilerinfo(int logged) for (age=agebase; age<=agelim; age++){ /* for (age=agebase; age<=agebase; age++){ */ - prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); + 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)]); @@ -6575,7 +6654,7 @@ void syscompilerinfo(int logged) tot += prlim[i][i]; fprintf(ficrespl," %.5f", prlim[i][i]); } - fprintf(ficrespl," %.3f %d\n", tot, *ncvyear); + fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp); } /* Age */ /* was end of cptcod */ } /* cptcov */ @@ -6668,8 +6747,7 @@ int main(int argc, char *argv[]) #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 ncvyearnp=0; - int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */ + 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; @@ -6929,12 +7007,13 @@ int main(int argc, char *argv[]) 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\n"); + 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-3; /* 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 */ @@ -7870,17 +7949,40 @@ Please run with mle=-1 to get a correct fflush(ficlog); fflush(ficres); - - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; fputs(line,stdout); fputs(line,ficparo); - } - ungetc(c,ficpar); + fputs(line,ficlog); + continue; + }else + break; + } + + /* while((c=getc(ficpar))=='#' && c!= EOF){ */ + /* ungetc(c,ficpar); */ + /* fgets(line, MAXLINE, ficpar); */ + /* fputs(line,stdout); */ + /* fputs(line,ficparo); */ + /* } */ + /* ungetc(c,ficpar); */ estepm=0; - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){ + + if (num_filled != 6) { + printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n"); + printf("but line=%s\n",line); + goto end; + } + printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl); + } + /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ + /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ + + /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */ if (estepm==0 || estepm < stepm) estepm=stepm; if (fage <= 2) { bage = ageminpar; @@ -7979,7 +8081,7 @@ Please run with mle=-1 to get a correct /*--------------- Prevalence limit (period or stable prevalence) --------------*/ /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ prlim=matrix(1,nlstate,1,nlstate); - prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear); + prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear); fclose(ficrespl); #ifdef FREEEXIT2 @@ -8042,8 +8144,8 @@ Please run with mle=-1 to get a correct printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0); fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0); } - printf("Computing Health Expectancies: result on file '%s' \n", filerese); - fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); + printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout); + fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog); /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ @@ -8062,7 +8164,8 @@ Please run with mle=-1 to get a correct /*}*/ } fclose(ficreseij); - + printf("done evsij\n");fflush(stdout); + fprintf(ficlog,"done evsij\n");fflush(ficlog); /*---------- Health expectancies and variances ------------*/ @@ -8073,8 +8176,8 @@ Please run with mle=-1 to get a correct printf("Problem with total LE resultfile: %s\n", filerest);goto end; fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; } - printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); - fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); + printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout); + fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog); strcpy(fileresstde,"STDE_"); @@ -8083,8 +8186,8 @@ Please run with mle=-1 to get a correct printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); } - printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); - fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); + printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); + fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); strcpy(filerescve,"CVE_"); strcat(filerescve,fileresu); @@ -8092,8 +8195,8 @@ Please run with mle=-1 to get a correct printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); } - printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); - fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); + printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); + fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); strcpy(fileresv,"V_"); strcat(fileresv,fileresu); @@ -8101,97 +8204,109 @@ Please run with mle=-1 to get a correct printf("Problem with variance resultfile: %s\n", fileresv);exit(0); fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0); } - printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); - fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout); + fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog); /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ for (k=1; k <= (int) pow(2,cptcoveff); k++){ - fprintf(ficrest,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficrest,"******\n"); - - fprintf(ficresstdeij,"\n#****** "); - fprintf(ficrescveij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) { - fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - } - fprintf(ficresstdeij,"******\n"); - fprintf(ficrescveij,"******\n"); - - fprintf(ficresvij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficresvij,"******\n"); - - eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); - /* - */ - /* goto endfree; */ - - vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); - pstamp(ficrest); - - - for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ - oldm=oldms;savm=savms; /* ZZ Segmentation fault */ - cptcod= 0; /* To be deleted */ - varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ - fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); - if(vpopbased==1) - fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); - else - fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); - fprintf(ficrest,"# Age popbased mobilav e.. (std) "); - for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); - fprintf(ficrest,"\n"); - /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ - epj=vector(1,nlstate+1); - for(age=bage; age <=fage ;age++){ - prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */ - if (vpopbased==1) { - if(mobilav ==0){ - for(i=1; i<=nlstate;i++) - prlim[i][i]=probs[(int)age][i][k]; - }else{ /* mobilav */ - for(i=1; i<=nlstate;i++) - prlim[i][i]=mobaverage[(int)age][i][k]; - } - } - - fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); - /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */ - /* printf(" age %4.0f ",age); */ - for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ - for(i=1, epj[j]=0.;i <=nlstate;i++) { - epj[j] += prlim[i][i]*eij[i][j][(int)age]; - /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ - /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */ - } - epj[nlstate+1] +=epj[j]; + fprintf(ficrest,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrest,"******\n"); + + fprintf(ficresstdeij,"\n#****** "); + fprintf(ficrescveij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + fprintf(ficresstdeij,"******\n"); + fprintf(ficrescveij,"******\n"); + + fprintf(ficresvij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresvij,"******\n"); + + eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + printf(" cvevsij %d, ",k); + fprintf(ficlog, " cvevsij %d, ",k); + cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); + printf(" end cvevsij \n "); + fprintf(ficlog, " end cvevsij \n "); + + /* + */ + /* goto endfree; */ + + vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); + pstamp(ficrest); + + + for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ + oldm=oldms;savm=savms; /* ZZ Segmentation fault */ + cptcod= 0; /* To be deleted */ + printf("varevsij %d \n",vpopbased); + fprintf(ficlog, "varevsij %d \n",vpopbased); + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ + fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); + if(vpopbased==1) + fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); + else + fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); + fprintf(ficrest,"# Age popbased mobilav e.. (std) "); + for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); + fprintf(ficrest,"\n"); + /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ + epj=vector(1,nlstate+1); + printf("Computing age specific period (stable) prevalences in each health state \n"); + fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n"); + for(age=bage; age <=fage ;age++){ + prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */ + if (vpopbased==1) { + if(mobilav ==0){ + for(i=1; i<=nlstate;i++) + prlim[i][i]=probs[(int)age][i][k]; + }else{ /* mobilav */ + for(i=1; i<=nlstate;i++) + prlim[i][i]=mobaverage[(int)age][i][k]; } - /* printf(" age %4.0f \n",age); */ - - for(i=1, vepp=0.;i <=nlstate;i++) - for(j=1;j <=nlstate;j++) - vepp += vareij[i][j][(int)age]; - fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); - for(j=1;j <=nlstate;j++){ - fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); + } + + fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav); + /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */ + /* printf(" age %4.0f ",age); */ + for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){ + for(i=1, epj[j]=0.;i <=nlstate;i++) { + epj[j] += prlim[i][i]*eij[i][j][(int)age]; + /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/ + /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */ } - fprintf(ficrest,"\n"); + epj[nlstate+1] +=epj[j]; + } + /* printf(" age %4.0f \n",age); */ + + for(i=1, vepp=0.;i <=nlstate;i++) + for(j=1;j <=nlstate;j++) + vepp += vareij[i][j][(int)age]; + fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp)); + for(j=1;j <=nlstate;j++){ + fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age])); } + fprintf(ficrest,"\n"); } - free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); - free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); - free_vector(epj,1,nlstate+1); + } /* End vpopbased */ + free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_vector(epj,1,nlstate+1); + printf("done \n");fflush(stdout); + fprintf(ficlog,"done\n");fflush(ficlog); + /*}*/ - } + } /* End k */ free_vector(weight,1,n); free_imatrix(Tvard,1,NCOVMAX,1,2); free_imatrix(s,1,maxwav+1,1,n); @@ -8203,6 +8318,8 @@ Please run with mle=-1 to get a correct fclose(ficrescveij); fclose(ficresvij); fclose(ficrest); + printf("done Health expectancies\n");fflush(stdout); + fprintf(ficlog,"done Health expectancies\n");fflush(ficlog); fclose(ficpar); /*------- Variance of period (stable) prevalence------*/ @@ -8213,7 +8330,8 @@ Please run with mle=-1 to get a correct printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); exit(0); } - printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); + printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); + fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ @@ -8226,12 +8344,14 @@ Please run with mle=-1 to get a correct varpl=matrix(1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; - varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart); + varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart); free_matrix(varpl,1,nlstate,(int) bage, (int)fage); /*}*/ } fclose(ficresvpl); + printf("done variance-covariance of period prevalence\n");fflush(stdout); + fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); /*---------- End : free ----------------*/ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);