--- imach/src/imach.c 2006/03/15 17:42:26 1.119 +++ imach/src/imach.c 2006/04/28 17:23:28 1.126 @@ -1,6 +1,51 @@ -/* $Id: imach.c,v 1.119 2006/03/15 17:42:26 brouard Exp $ +/* $Id: imach.c,v 1.126 2006/04/28 17:23:28 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.126 2006/04/28 17:23:28 brouard + (Module): Yes the sum of survivors was wrong since + imach-114 because nhstepm was no more computed in the age + loop. Now we define nhstepma in the age loop. + Version 0.98h + + Revision 1.125 2006/04/04 15:20:31 lievre + Errors in calculation of health expectancies. Age was not initialized. + Forecasting file added. + + Revision 1.124 2006/03/22 17:13:53 lievre + Parameters are printed with %lf instead of %f (more numbers after the comma). + The log-likelihood is printed in the log file + + Revision 1.123 2006/03/20 10:52:43 brouard + * imach.c (Module): changed, corresponds to .htm file + name. <head> headers where missing. + + * imach.c (Module): Weights can have a decimal point as for + English (a comma might work with a correct LC_NUMERIC environment, + otherwise the weight is truncated). + Modification of warning when the covariates values are not 0 or + 1. + Version 0.98g + + Revision 1.122 2006/03/20 09:45:41 brouard + (Module): Weights can have a decimal point as for + English (a comma might work with a correct LC_NUMERIC environment, + otherwise the weight is truncated). + Modification of warning when the covariates values are not 0 or + 1. + Version 0.98g + + Revision 1.121 2006/03/16 17:45:01 lievre + * imach.c (Module): Comments concerning covariates added + + * imach.c (Module): refinements in the computation of lli if + status=-2 in order to have more reliable computation if stepm is + not 1 month. Version 0.98f + + Revision 1.120 2006/03/16 15:10:38 lievre + (Module): refinements in the computation of lli if + status=-2 in order to have more reliable computation if stepm is + not 1 month. Version 0.98f + Revision 1.119 2006/03/15 17:42:26 brouard (Module): Bug if status = -2, the loglikelihood was computed as likelihood omitting the logarithm. Version O.98e @@ -326,11 +371,11 @@ extern int errno; #define ODIRSEPARATOR '/' #endif -/* $Id: imach.c,v 1.119 2006/03/15 17:42:26 brouard Exp $ */ +/* $Id: imach.c,v 1.126 2006/04/28 17:23:28 brouard Exp $ */ /* $State: Exp $ */ -char version[]="Imach version 0.98e, March 2006, INED-EUROREVES-Institut de longevite "; -char fullversion[]="$Revision: 1.119 $ $Date: 2006/03/15 17:42:26 $"; +char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite "; +char fullversion[]="$Revision: 1.126 $ $Date: 2006/04/28 17:23:28 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -404,6 +449,7 @@ char strcurr[80], strfor[80]; char *endptr; long lval; +double dval; #define NR_END 1 #define FREE_ARG char* @@ -969,9 +1015,8 @@ void powell(double p[], double **xi, int last_time=curr_time; (void) gettimeofday(&curr_time,&tzp); printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout); - /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); - fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); - */ + fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog); +/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */ for (i=1;i<=n;i++) { printf(" %d %.12f",i, p[i]); fprintf(ficlog," %d %.12lf",i, p[i]); @@ -1386,23 +1431,23 @@ double func( double *x) } else if (s2==-2) { for (j=1,survp=0. ; j<=nlstate; j++) - survp += out[s1][j]; + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + /*survp += out[s1][j]; */ lli= log(survp); } -/* else if (s2==-4) { */ -/* for (j=3,survp=0. ; j<=nlstate; j++) */ -/* survp += out[s1][j]; */ -/* lli= survp; */ -/* } */ - -/* else if (s2==-5) { */ -/* for (j=1,survp=0. ; j<=2; j++) */ -/* survp += out[s1][j]; */ -/* lli= survp; */ -/* } */ - + else if (s2==-4) { + for (j=3,survp=0. ; j<=nlstate; j++) + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + lli= log(survp); + } + else if (s2==-5) { + for (j=1,survp=0. ; j<=2; j++) + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + lli= log(survp); + } + else{ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */ @@ -1599,7 +1644,7 @@ double funcone( double *x) lli=log(out[s1][s2] - savm[s1][s2]); } else if (s2==-2) { for (j=1,survp=0. ; j<=nlstate; j++) - survp += out[s1][j]; + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; lli= log(survp); }else if (mle==1){ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ @@ -2427,6 +2472,7 @@ void evsij(char fileres[], double ***eij { /* Health expectancies, no variances */ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2; + int nhstepma, nstepma; /* Decreasing with age */ double age, agelim, hf; double ***p3mat; double eip; @@ -2473,18 +2519,28 @@ void evsij(char fileres[], double ***eij hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ agelim=AGESUP; - /* nhstepm age range expressed in number of stepm */ - nstepm=(int) rint((agelim-age)*YEARM/stepm); + /* If stepm=6 months */ + /* Computed by stepm unit matrices, product of hstepm matrices, stored + in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ + +/* nhstepm age range expressed in number of stepm */ + nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ /* 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); - for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ - /* Computed by stepm unit matrices, product of hstepm matrices, stored - in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ + for (age=bage; age<=fage; age ++){ + nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ + + /* If stepm=6 months */ + /* Computed by stepm unit matrices, product of hstepma matrices, stored + in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ - hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); + hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij); hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ @@ -2526,6 +2582,7 @@ void cvevsij(char fileres[], double ***e to initial status i, ei. . */ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; + int nhstepma, nstepma; /* Decreasing with age */ double age, agelim, hf; double ***p3matp, ***p3matm, ***varhe; double **dnewm,**doldm; @@ -2599,7 +2656,7 @@ void cvevsij(char fileres[], double ***e /* If stepm=6 months */ /* nhstepm age range expressed in number of stepm */ agelim=AGESUP; - nstepm=(int) rint((agelim-age)*YEARM/stepm); + nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Typically if 20 years nstepm = 20*12/6=40 stepm */ /* if (stepm >= YEARM) hstepm=1;*/ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ @@ -2612,10 +2669,15 @@ void cvevsij(char fileres[], double ***e gm=matrix(0,nhstepm,1,nlstate*nlstate); for (age=bage; age<=fage; age ++){ - - /* Computed by stepm unit matrices, product of hstepm matrices, stored - in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ - + nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */ + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */ + + /* If stepm=6 months */ + /* Computed by stepm unit matrices, product of hstepma matrices, stored + in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */ + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ /* Computing Variances of health expectancies */ @@ -2666,6 +2728,7 @@ void cvevsij(char fileres[], double ***e varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; } } + /* Computing expectancies */ hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); for(i=1; i<=nlstate;i++) @@ -3448,10 +3511,12 @@ void printinghtml(char fileres[], char t - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); fprintf(fichtm,"\ - - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij (estepm=%2d months): \ - <a href=\"%s\">%s</a> <br>\n</li>", + - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ + <a href=\"%s\">%s</a> <br>\n", estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); - + fprintf(fichtm,"\ + - Population projections by age and states: \ + <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f")); fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>"); @@ -4547,6 +4612,7 @@ int main(int argc, char *argv[]) free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); fclose (ficparo); fclose (ficlog); + goto end; exit(0); } else if(mle==-3) { @@ -4577,7 +4643,9 @@ int main(int argc, char *argv[]) j++; fscanf(ficpar,"%1d%1d",&i1,&j1); if ((i1 != i) && (j1 != j)){ - printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); + 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); @@ -4801,12 +4869,12 @@ int main(int argc, char *argv[]) cutv(stra, strb,line,' '); errno=0; - lval=strtol(strb,&endptr,10); + dval=strtod(strb,&endptr); if( strb[0]=='\0' || (*endptr != '\0')){ - printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei); + printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); exit(1); } - weight[i]=(double)(lval); + weight[i]=dval; strcpy(line,stra); for (j=ncovcol;j>=1;j--){ @@ -4818,7 +4886,15 @@ int main(int argc, char *argv[]) exit(1); } if(lval <-1 || lval >1){ - printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j); + printf("Error reading data around '%d' at line number %ld 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); exit(1); } covar[j][i]=(double)(lval); @@ -5114,13 +5190,13 @@ int main(int argc, char *argv[]) printf("Problem with %s \n",optionfilehtmcov), exit(0); } else{ - fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s\n %s
%s \ + fprintf(fichtmcov,"\nIMaCh Cov %s\n %s
%s \
\n\ Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n",\ - fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); + optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(fichtm,"\nIMaCh %s\n %s
%s \ + fprintf(fichtm,"\nIMaCh %s\n %s
%s \
\n\ Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n\ \n\ @@ -5131,7 +5207,7 @@ Title=%s
Datafile=%s Firstpass=%d La - Log file of the run: %s
\n\ - Gnuplot file name: %s
\n\ - Date and time at start: %s\n",\ - fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ + optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ fileres,fileres,\ filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); @@ -5314,9 +5390,9 @@ Interval (in months) between two waves: fprintf(ficlog,"%d%d ",i,k); fprintf(ficres,"%1d%1d ",i,k); for(j=1; j <=ncovmodel; j++){ - printf("%f ",p[jk]); - fprintf(ficlog,"%f ",p[jk]); - fprintf(ficres,"%f ",p[jk]); + printf("%lf ",p[jk]); + fprintf(ficlog,"%lf ",p[jk]); + fprintf(ficres,"%lf ",p[jk]); jk++; } printf("\n"); @@ -5896,8 +5972,9 @@ Interval (in months) between two waves: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec); /* printf("Total time was %d uSec.\n", total_usecs);*/ /* if(fileappend(fichtm,optionfilehtm)){ */ - fprintf(fichtm,"
Local time at start %s
Local time at end %s
",strstart, strtend); + fprintf(fichtm,"
Local time at start %s
Local time at end %s
\n",strstart, strtend); fclose(fichtm); + fprintf(fichtmcov,"
Local time at start %s
Local time at end %s
\n",strstart, strtend); fclose(fichtmcov); fclose(ficgp); fclose(ficlog);