--- imach096d/src/imach.c 2003/06/05 15:41:51 1.81 +++ imach096d/src/imach.c 2003/06/17 20:04:08 1.86 @@ -1,4 +1,38 @@ -/* $Id: imach.c,v 1.81 2003/06/05 15:41:51 brouard Exp $ +/* $Id: imach.c,v 1.86 2003/06/17 20:04:08 brouard Exp $ + $State: Exp $ + $Log: imach.c,v $ + Revision 1.86 2003/06/17 20:04:08 brouard + (Module): Change position of html and gnuplot routines and added + routine fileappend. + + Revision 1.85 2003/06/17 13:12:43 brouard + * imach.c (Repository): Check when date of death was earlier that + current date of interview. It may happen when the death was just + prior to the death. In this case, dh was negative and likelihood + was wrong (infinity). We still send an "Error" but patch by + assuming that the date of death was just one stepm after the + interview. + (Repository): Because some people have very long ID (first column) + we changed int to long in num[] and we added a new lvector for + memory allocation. But we also truncated to 8 characters (left + truncation) + (Repository): No more line truncation errors. + + Revision 1.84 2003/06/13 21:44:43 brouard + * imach.c (Repository): Replace "freqsummary" at a correct + place. It differs from routine "prevalence" which may be called + many times. Probs is memory consuming and must be used with + parcimony. + Version 0.95a3 (should output exactly the same maximization than 0.8a2) + + Revision 1.83 2003/06/10 13:39:11 lievre + *** empty log message *** + + Revision 1.82 2003/06/05 15:57:20 brouard + Add log in imach.c and fullversion number is now printed. + +*/ +/* Interpolated Markov Chain Short summary of the programme: @@ -58,6 +92,7 @@ read parameterfile read datafile concatwav + freqsummary if (mle >= 1) mlikeli print results files @@ -91,12 +126,16 @@ #include #include +#include +#include +#include "timeval.h" + #define MAXLINE 256 #define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ -#define FILENAMELENGTH 80 +#define FILENAMELENGTH 132 /*#define DEBUG*/ -#define windows +/*#define windows*/ #define GLOCK_ERROR_NOPATH -1 /* empty path */ #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ @@ -111,31 +150,19 @@ #define YEARM 12. /* Number of months per year */ #define AGESUP 130 #define AGEBASE 40 -#ifdef windows -#define DIRSEPARATOR '\\' -#define ODIRSEPARATOR '/' -#else +#ifdef unix #define DIRSEPARATOR '/' #define ODIRSEPARATOR '\\' +#else +#define DIRSEPARATOR '\\' +#define ODIRSEPARATOR '/' #endif -/* $Id: imach.c,v 1.81 2003/06/05 15:41:51 brouard Exp $ */ -/* $Log: imach.c,v $ - * Revision 1.81 2003/06/05 15:41:51 brouard - * *** empty log message *** - * -/* Revision 1.80 2003/06/05 15:34:14 brouard -/* Trying to add the true revision in the program and log -/* -/* Revision 1.79 2003/06/05 15:17:23 brouard -/* *** empty log message *** -/* */ -/* $Revision: 1.81 $ */ -/* $Date: 2003/06/05 15:41:51 $ */ +/* $Id: imach.c,v 1.86 2003/06/17 20:04:08 brouard Exp $ */ /* $State: Exp $ */ -char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES "; -char fullversion[]="$Revision: 1.81 $ $Date: 2003/06/05 15:41:51 $"; +char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES "; +char fullversion[]="$Revision: 1.86 $ $Date: 2003/06/17 20:04:08 $"; int erreur; /* Error number */ int nvar; int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; @@ -158,6 +185,12 @@ double **oldm, **newm, **savm; /* Workin double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; FILE *ficlog, *ficrespow; +int globpr; /* Global variable for printing or not */ +double fretone; /* Only one call to likelihood */ +long ipmx; /* Number of contributions */ +double sw; /* Sum of weights */ +char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */ +FILE *ficresilk; FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; FILE *ficresprobmorprev; FILE *fichtm; /* Html File */ @@ -215,7 +248,8 @@ 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; +long *num; +int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; double **pmmij, ***probs; double dateintmean=0; @@ -255,11 +289,12 @@ static int split( char *path, char *dirc dirc[l1-l2] = 0; /* add zero */ } l1 = strlen( dirc ); /* length of directory */ -#ifdef windows + /*#ifdef windows if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } #else if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } #endif + */ ss = strrchr( name, '.' ); /* find last / */ ss++; strcpy(ext,ss); /* save extension */ @@ -343,31 +378,31 @@ void free_vector(double*v, int nl, int n } /************************ivector *******************************/ -char *cvector(long nl,long nh) +int *ivector(long nl,long nh) { - char *v; - v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char))); - if (!v) nrerror("allocation failure in cvector"); + int *v; + v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); + if (!v) nrerror("allocation failure in ivector"); return v-nl+NR_END; } /******************free ivector **************************/ -void free_cvector(char *v, long nl, long nh) +void free_ivector(int *v, long nl, long nh) { free((FREE_ARG)(v+nl-NR_END)); } -/************************ivector *******************************/ -int *ivector(long nl,long nh) +/************************lvector *******************************/ +long *lvector(long nl,long nh) { - int *v; - v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int))); + long *v; + v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long))); if (!v) nrerror("allocation failure in ivector"); return v-nl+NR_END; } -/******************free ivector **************************/ -void free_ivector(int *v, long nl, long nh) +/******************free lvector **************************/ +void free_lvector(long *v, long nl, long nh) { free((FREE_ARG)(v+nl-NR_END)); } @@ -426,7 +461,7 @@ double **matrix(long nrl, long nrh, long for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; return m; - /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) + /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) */ } @@ -1179,7 +1214,42 @@ double func( double *x) ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; } /* end of wave */ } /* end of individual */ - }else{ /* ml=4 no inter-extrapolation */ + }else if (mle==4){ /* ml=4 no inter-extrapolation */ + for (i=1,ipmx=0, sw=0.; i<=imx; i++){ + for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for(mi=1; mi<= wav[i]-1; mi++){ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } + for(d=0; d nlstate){ + lli=log(out[s1][s2] - savm[s1][s2]); + }else{ + lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ + } + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; +/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ + } /* end of wave */ + } /* end of individual */ + }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */ for (i=1,ipmx=0, sw=0.; i<=imx; i++){ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; for(mi=1; mi<= wav[i]-1; mi++){ @@ -1201,10 +1271,13 @@ double func( double *x) oldm=newm; } /* end mult */ + s1=s[mw[mi][i]][i]; + s2=s[mw[mi+1][i]][i]; lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ ipmx +=1; sw += weight[i]; ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/ } /* end of wave */ } /* end of individual */ } /* End of if */ @@ -1214,6 +1287,123 @@ double func( double *x) return -l; } +/*************** log-likelihood *************/ +double funcone( double *x) +{ + int i, ii, j, k, mi, d, kk; + double l, ll[NLSTATEMAX], cov[NCOVMAX]; + double **out; + double lli; /* Individual log likelihood */ + int s1, s2; + double bbh, survp; + /*extern weight */ + /* We are differentiating ll according to initial status */ + /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ + /*for(i=1;i nlstate && (mle <5) ){ /* Jackson */ + lli=log(out[s1][s2] - savm[s1][s2]); + } else if (mle==1){ + lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ + } else if(mle==2){ + 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 */ + } else if(mle==3){ /* exponential inter-extrapolation */ + lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ + } else if (mle==4){ /* mle=4 no inter-extrapolation */ + lli=log(out[s1][s2]); /* Original formula */ + } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */ + lli=log(out[s1][s2]); /* Original formula */ + } /* End of if */ + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; +/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ + if(globpr){ + fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\ + %10.6f %10.6f %10.6f ", \ + num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], + 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); + for(k=1,l=0.; k<=nlstate; k++) + fprintf(ficresilk," %10.6f",ll[k]); + fprintf(ficresilk,"\n"); + } + } /* end of wave */ + } /* end of individual */ + for(k=1,l=0.; k<=nlstate; k++) l += ll[k]; + /* printf("l1=%f l2=%f ",ll[1],ll[2]); */ + l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */ + return -l; +} + + +void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) +{ + /* This routine should help understanding what is done with the selection of individuals/waves and + to check the exact contribution to the likelihood. + Plotting could be done. + */ + int k; + if(globpr !=0){ /* Just counts and sums no printings */ + strcpy(fileresilk,"ilk"); + strcat(fileresilk,fileres); + if((ficresilk=fopen(fileresilk,"w"))==NULL) { + printf("Problem with resultfile: %s\n", fileresilk); + fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk); + } + fprintf(ficresilk, "#individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state\n"); + fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav "); + /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */ + for(k=1; k<=nlstate; k++) + fprintf(ficresilk," ll[%d]",k); + fprintf(ficresilk,"\n"); + } + + *fretone=(*funcone)(p); + if(globpr !=0){ + fclose(ficresilk); + if((fichtm=fopen(optionfilehtm,"a"))==NULL) { + printf("Problem with html file: %s\n", optionfilehtm); + fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); + exit(0); + } + else{ + fprintf(fichtm,"\n
File of contributions to the likelihood: %s
\n",fileresilk); + fclose(fichtm); + } + } + return; +} /*********** Maximum Likelihood Estimation ***************/ @@ -1222,6 +1412,7 @@ void mlikeli(FILE *ficres,double p[], in int i,j, iter; double **xi; double fret; + double fretone; /* Only one call to likelihood */ char filerespow[FILENAMELENGTH]; xi=matrix(1,npar,1,npar); for (i=1;i<=npar;i++) @@ -1239,6 +1430,7 @@ void mlikeli(FILE *ficres,double p[], in for(j=1;j<=nlstate+ndeath;j++) if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); fprintf(ficrespow,"\n"); + powell(p,xi,npar,ftol,&iter,&fret,func); fclose(ficrespow); @@ -1506,7 +1698,7 @@ void lubksb(double **a, int n, int *indx } /************ Frequencies ********************/ -void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) +void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint) { /* Some frequencies */ int i, m, jk, k1,i1, j1, bool, z1,z2,j; @@ -1560,7 +1752,7 @@ void freqsummary(char fileres[], int ia if (bool==1){ for(m=firstpass; m<=lastpass; m++){ k2=anint[m][i]+(mint[m][i]/12.); - if ((k2>=dateprev1) && (k2<=dateprev2)) { + /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ if(agev[m][i]==0) agev[m][i]=iagemax+1; if(agev[m][i]==1) agev[m][i]=iagemax+2; if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; @@ -1573,12 +1765,12 @@ void freqsummary(char fileres[], int ia 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 "); @@ -1639,7 +1831,7 @@ void freqsummary(char fileres[], int ia if( i <= iagemax){ if(pos>=1.e-5){ fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); - probs[i][jk][j1]= 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 @@ -1672,7 +1864,7 @@ void freqsummary(char fileres[], int ia } /************ Prevalence ********************/ -void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) +void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) { /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people in each health status at the date of interview (if between dateprev1 and dateprev2). @@ -1791,11 +1983,11 @@ void concatwav(int wav[], int **dh, int wav[i]=mi; if(mi==0){ if(first==0){ - printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i); + printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i); first=1; } if(first==1){ - fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i); + fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i); } } /* end mi==0 */ } /* End individuals */ @@ -1807,15 +1999,21 @@ void concatwav(int wav[], int **dh, int else{ if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ if (agedc[i] < 2*AGESUP) { - j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); - if(j==0) j=1; /* Survives at least one month after exam */ - k=k+1; - if (j >= jmax) jmax=j; - if (j <= jmin) jmin=j; - sum=sum+j; - /*if (j<0) printf("j=%d num=%d \n",j,i);*/ - /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ - if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); + if(j==0) j=1; /* Survives at least one month after exam */ + else if(j<0){ + printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + j=1; /* Careful Patch */ + printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm); + printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm); + } + k=k+1; + if (j >= jmax) jmax=j; + if (j <= jmin) jmin=j; + sum=sum+j; + /*if (j<0) printf("j=%d num=%d \n",j,i);*/ + /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ } } else{ @@ -1826,13 +2024,16 @@ void concatwav(int wav[], int **dh, int else if (j <= jmin)jmin=j; /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ - if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + if(j<0){ + printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + } sum=sum+j; } jk= j/stepm; jl= j -jk*stepm; ju= j -(jk+1)*stepm; - if(mle <=1){ + if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ if(jl==0){ dh[mi][i]=jk; bh[mi][i]=0; @@ -1857,8 +2058,8 @@ void concatwav(int wav[], int **dh, int bh[mi][i]=ju; /* At least one step */ /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/ } - } - } /* end if mle */ + } /* end if mle */ + } } /* end wave */ } jmean=sum/k; @@ -2406,7 +2607,7 @@ void varevsij(char optionfilefiname[], d fclose(ficresprobmorprev); fclose(ficgp); fclose(fichtm); -} +} /* end varevsij */ /************ Variance of prevlim ******************/ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) @@ -2818,11 +3019,11 @@ void printinghtml(char fileres[], char t fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); } - fprintf(fichtm,"

  • Result files (first order: no variance)

    \n - - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): p%s
    \n - - Estimated transition probabilities over %d (stepm) months: pij%s
    \n - - Stable prevalence in each health state: pl%s
    \n - - Life expectancies by age and initial health status (estepm=%2d months): + fprintf(fichtm,"

    • Result files (first order: no variance)

      \n \ + - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): p%s
      \n \ + - Estimated transition probabilities over %d (stepm) months: pij%s
      \n \ + - Stable prevalence in each health state: pl%s
      \n \ + - Life expectancies by age and initial health status (estepm=%2d months): \ e%s
      \n
      • ", \ jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres); @@ -2842,35 +3043,36 @@ fprintf(fichtm," \n
      • Graphs fprintf(fichtm," ************\n
        "); } /* Pij */ - fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png
        + fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png
        \ ",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); /* Quasi-incidences */ - fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png
        + fprintf(fichtm,"
        - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ + before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png
        \ ",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); /* Stable prevalence in each health state */ for(cpt=1; cpt- Stable prevalence in each health state : p%s%d%d.png
        + fprintf(fichtm,"
        - Stable prevalence in each health state : p%s%d%d.png
        \ ",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"\n
        - Health life expectancies by age and initial health state (%d): exp%s%d%d.png
        + fprintf(fichtm,"\n
        - Health life expectancies by age and initial health state (%d): exp%s%d%d.png
        \ ",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); } - fprintf(fichtm,"\n
        - Total life expectancy by age and -health expectancies in states (1) and (2): e%s%d.png
        + fprintf(fichtm,"\n
        - Total life expectancy by age and \ +health expectancies in states (1) and (2): e%s%d.png
        \ ",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); } /* end i1 */ }/* End k1 */ fprintf(fichtm,"
      "); - fprintf(fichtm,"\n

    • Result files (second order: variances)

      \n - - Parameter file with estimated parameters and covariance matrix: %s
      \n - - Variance of one-step probabilities: prob%s
      \n - - Variance-covariance of one-step probabilities: probcov%s
      \n - - Correlation matrix of one-step probabilities: probcor%s
      \n - - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): v%s
      \n - - Health expectancies with their variances (no covariance): t%s
      \n + fprintf(fichtm,"\n

    • Result files (second order: variances)

      \n\ + - Parameter file with estimated parameters and covariance matrix: %s
      \n\ + - Variance of one-step probabilities: prob%s
      \n\ + - Variance-covariance of one-step probabilities: probcov%s
      \n\ + - Correlation matrix of one-step probabilities: probcor%s
      \n\ + - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): v%s
      \n\ + - Health expectancies with their variances (no covariance): t%s
      \n\ - Standard deviation of stable prevalences: vpl%s
      \n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); /* if(popforecast==1) fprintf(fichtm,"\n */ @@ -2895,8 +3097,8 @@ fprintf(fichtm,"
      • Graphs"); } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"
        - Observed and period prevalence (with confident -interval) in state (%d): v%s%d%d.png
        + fprintf(fichtm,"
        - Observed and period prevalence (with confident\ +interval) in state (%d): v%s%d%d.png
        \ ",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); } } /* end i1 */ @@ -3003,7 +3205,7 @@ m=pow(2,cptcoveff); fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1); - for (i=1; i<= nlstate ; i ++) + for (i=1; i< nlstate ; i ++) fprintf(ficgp,"+$%d",k+i+1); fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); @@ -3142,7 +3344,7 @@ prevforecast(char fileres[], double anpr char fileresf[FILENAMELENGTH]; agelim=AGESUP; - prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); + prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); strcpy(fileresf,"f"); strcat(fileresf,fileres); @@ -3265,7 +3467,7 @@ populforecast(char fileres[], double anp agelim=AGESUP; calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; - prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); + prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); strcpy(filerespop,"pop"); @@ -3407,8 +3609,17 @@ populforecast(char fileres[], double anp free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); fclose(ficrespop); -} +} /* End of popforecast */ +int fileappend(FILE *fichier, char *optionfile) +{ + if((fichier=fopen(optionfile,"a"))==NULL) { + printf("Problem with file: %s\n", optionfile); + fprintf(ficlog,"Problem with file: %s\n", optionfile); + return (1); + } + +} /***********************************************/ /**************** Main Program *****************/ /***********************************************/ @@ -3417,6 +3628,8 @@ int main(int argc, char *argv[]) { int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; + int jj; + int numlinepar=0; /* Current linenumber of parameter file */ double agedeb, agefin,hf; double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; @@ -3428,7 +3641,7 @@ int main(int argc, char *argv[]) double ***mobaverage; int *indx; char line[MAXLINE], linepar[MAXLINE]; - char path[80],pathc[80],pathcd[80],pathtot[80],model[80]; + char path[132],pathc[132],pathcd[132],pathtot[132],model[132]; int firstobs=1, lastobs=10; int sdeb, sfin; /* Status at beginning and end */ int c, h , cpt,l; @@ -3460,14 +3673,42 @@ int main(int argc, char *argv[]) char z[1]="c", occ; -#include -#include + char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; + char *strt, *strtend; + char *stratrunc; + int lstra; + + long total_usecs; + struct timeval start_time, end_time, curr_time; + struct timezone tzp; + extern int gettimeofday(); + struct tm tmg, tm, *gmtime(), *localtime(); + long time_value; + extern long time(); - /* long total_usecs; - struct timeval start_time, end_time; - - gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ + /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ + (void) gettimeofday(&start_time,&tzp); + tm = *localtime(&start_time.tv_sec); + tmg = *gmtime(&start_time.tv_sec); + strt=asctime(&tm); + +/* printf("Localtime (at start)=%s",strt); */ +/* tp.tv_sec = tp.tv_sec +86400; */ +/* tm = *localtime(&start_time.tv_sec); */ +/* tmg.tm_year=tmg.tm_year +dsign*dyear; */ +/* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ +/* tmg.tm_hour=tmg.tm_hour + 1; */ +/* tp.tv_sec = mktime(&tmg); */ +/* strt=asctime(&tmg); */ +/* printf("Time(after) =%s",strt); */ +/* (void) time (&time_value); +* printf("time=%d,t-=%d\n",time_value,time_value-86400); +* tm = *localtime(&time_value); +* strt=asctime(&tm); +* printf("tim_value=%d,asctime=%s\n",time_value,strt); +*/ + getcwd(pathcd, size); printf("\n%s\n%s",version,fullversion); @@ -3478,13 +3719,13 @@ int main(int argc, char *argv[]) else{ strcpy(pathtot,argv[1]); } - /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/ + /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/ /*cygwin_split_path(pathtot,path,optionfile); printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ /* cutv(path,optionfile,pathtot,'\\');*/ split(pathtot,path,optionfile,optionfilext,optionfilefiname); - printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); + printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); chdir(path); replace(pathc,path); @@ -3498,9 +3739,12 @@ int main(int argc, char *argv[]) goto end; } fprintf(ficlog,"Log filename:%s\n",filelog); - fprintf(ficlog,"\n%s",version); + fprintf(ficlog,"\n%s\n%s",version,fullversion); fprintf(ficlog,"\nEnter the parameter file name: "); fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); + + printf("Localtime (at start)=%s",strt); + fprintf(ficlog,"Localtime (at start)=%s",strt); fflush(ficlog); /* */ @@ -3513,6 +3757,7 @@ int main(int argc, char *argv[]) if((ficpar=fopen(optionfile,"r"))==NULL) { printf("Problem with optionfile %s\n",optionfile); fprintf(ficlog,"Problem with optionfile %s\n",optionfile); + fflush(ficlog); goto end; } @@ -3521,29 +3766,38 @@ int main(int argc, char *argv[]) if((ficparo=fopen(filereso,"w"))==NULL) { printf("Problem with Output resultfile: %s\n", filereso); fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso); + fflush(ficlog); goto end; } /* Reads comments: lines beginning with '#' */ + numlinepar=0; while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); + numlinepar++; puts(line); fputs(line,ficparo); + fputs(line,ficlog); } ungetc(c,ficpar); fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); + numlinepar++; 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); + fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); + fflush(ficlog); while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); + numlinepar++; puts(line); fputs(line,ficparo); + fputs(line,ficlog); } ungetc(c,ficpar); - + covar=matrix(0,NCOVMAX,1,n); cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ @@ -3557,15 +3811,24 @@ int main(int argc, char *argv[]) while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); + numlinepar++; puts(line); fputs(line,ficparo); + fputs(line,ficlog); } ungetc(c,ficpar); - + param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); - for(i=1; i <=nlstate; i++) - for(j=1; j <=nlstate+ndeath-1; j++){ + for(i=1; i <=nlstate; i++){ + j=0; + for(jj=1; jj <=nlstate+ndeath; jj++){ + if(jj==i) continue; + j++; fscanf(ficpar,"%1d%1d",&i1,&j1); + if ((i1 != i) && (j1 != j)){ + printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); + exit(1); + } fprintf(ficparo,"%1d%1d",i1,j1); if(mle==1) printf("%1d%1d",i,j); @@ -3581,12 +3844,15 @@ int main(int argc, char *argv[]) fprintf(ficparo," %lf",param[i][j][k]); } fscanf(ficpar,"\n"); + numlinepar++; if(mle==1) printf("\n"); fprintf(ficlog,"\n"); fprintf(ficparo,"\n"); } - + } + fflush(ficlog); + npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ p=param[1][1]; @@ -3595,8 +3861,10 @@ int main(int argc, char *argv[]) while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); + numlinepar++; puts(line); fputs(line,ficparo); + fputs(line,ficlog); } ungetc(c,ficpar); @@ -3605,18 +3873,28 @@ int main(int argc, char *argv[]) for(i=1; i <=nlstate; i++){ for(j=1; j <=nlstate+ndeath-1; j++){ fscanf(ficpar,"%1d%1d",&i1,&j1); + if ((i1-i)*(j1-j)!=0){ + printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); + exit(1); + } printf("%1d%1d",i,j); fprintf(ficparo,"%1d%1d",i1,j1); + fprintf(ficlog,"%1d%1d",i1,j1); for(k=1; k<=ncovmodel;k++){ fscanf(ficpar,"%le",&delti3[i][j][k]); printf(" %le",delti3[i][j][k]); fprintf(ficparo," %le",delti3[i][j][k]); + fprintf(ficlog," %le",delti3[i][j][k]); } fscanf(ficpar,"\n"); + numlinepar++; printf("\n"); fprintf(ficparo,"\n"); + fprintf(ficlog,"\n"); } } + fflush(ficlog); + delti=delti3[1][1]; @@ -3626,8 +3904,10 @@ int main(int argc, char *argv[]) while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); + numlinepar++; puts(line); fputs(line,ficparo); + fputs(line,ficlog); } ungetc(c,ficpar); @@ -3642,13 +3922,12 @@ int main(int argc, char *argv[]) fscanf(ficpar," %le",&matcov[i][j]); if(mle==1){ printf(" %.5le",matcov[i][j]); - fprintf(ficlog," %.5le",matcov[i][j]); } - else - fprintf(ficlog," %.5le",matcov[i][j]); + fprintf(ficlog," %.5le",matcov[i][j]); fprintf(ficparo," %.5le",matcov[i][j]); } fscanf(ficpar,"\n"); + numlinepar++; if(mle==1) printf("\n"); fprintf(ficlog,"\n"); @@ -3662,6 +3941,7 @@ int main(int argc, char *argv[]) printf("\n"); fprintf(ficlog,"\n"); + fflush(ficlog); /*-------- Rewriting paramater file ----------*/ strcpy(rfileres,"r"); /* "Rparameterfile */ @@ -3683,7 +3963,7 @@ int main(int argc, char *argv[]) n= lastobs; severity = vector(1,maxwav); outcome=imatrix(1,maxwav+1,1,n); - num=ivector(1,n); + num=lvector(1,n); moisnais=vector(1,n); annais=vector(1,n); moisdc=vector(1,n); @@ -3719,10 +3999,16 @@ int main(int argc, char *argv[]) for (j=ncovcol;j>=1;j--){ cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); } - num[i]=atol(stra); + lstra=strlen(stra); + if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ + stratrunc = &(stra[lstra-9]); + num[i]=atol(stratrunc); + } + else + num[i]=atol(stra); /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ - printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ + printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ i=i+1; } @@ -3738,7 +4024,7 @@ int main(int argc, char *argv[]) }*/ /* 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]));}*/ + printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ for (i=1; i<=imx; i++) @@ -3841,14 +4127,14 @@ int main(int argc, char *argv[]) s[m][i]=-1; } if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ - printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); - fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); + printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); + fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); s[m][i]=-1; } if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ - printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); - fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); - s[m][i]=-1; + printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); + fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); + s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ } } } @@ -3864,8 +4150,8 @@ int main(int argc, char *argv[]) /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ else { if ((int)andc[i]!=9999){ - printf("Warning negative age at death: %d line:%d\n",num[i],i); - fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); + printf("Warning negative age at death: %ld line:%d\n",num[i],i); + fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); agev[m][i]=-1; } } @@ -3909,7 +4195,7 @@ int main(int argc, char *argv[]) /*for (i=1; i<=imx; i++){ for (m=firstpass; (m %s
        %s         \ +
        \n\ +Title=%s
        Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
        \n\ +\n\ +
        \ +

        • Parameter files

          \n\ + - Copy of the parameter file: o%s
          \n\ + - Log file of the run: %s
          \n\ + - Gnuplot file name: %s\n\ + - Date and time at start: %s
        \n",\ + version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\ + model,fileres,fileres,\ + filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt); + fclose(fichtm); + /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); + if(fileappend(fichtm, optionfilehtm)){ + fprintf(fichtm,"
        Total number of observations=%d
        \n\ +Youngest age at first (selected) pass %.2f, oldest age %.2f
        \n\ +Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
        \n",\ + imx,agemin,agemax,jmin,jmax,jmean); + fclose(fichtm); + } pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ @@ -3982,6 +4311,18 @@ int main(int argc, char *argv[]) so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ p=param[1][1]; /* *(*(*(param +1)+1)+0) */ + globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ + likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ + printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); + for (k=1; k<=npar;k++) + printf(" %d %8.5f",k,p[k]); + printf("\n"); + globpr=1; /* to print the contributions */ + likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ + printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); + for (k=1; k<=npar;k++) + printf(" %d %8.5f",k,p[k]); + printf("\n"); if(mle>=1){ /* Could be 1 or 2 */ mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); } @@ -4013,7 +4354,7 @@ int main(int argc, char *argv[]) } } } - if(mle==1){ + if(mle!=0){ /* Computing hessian and covariance matrix */ ftolhess=ftol; /* Usually correct */ hesscov(matcov, p, npar, delti, ftolhess, func); @@ -4144,44 +4485,14 @@ int main(int argc, char *argv[]) fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); - probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); + /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/ + /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ - /*------------ gnuplot -------------*/ - strcpy(optionfilegnuplot,optionfilefiname); - strcat(optionfilegnuplot,".gp"); - if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { - printf("Problem with file %s",optionfilegnuplot); - } - else{ - fprintf(ficgp,"\n# %s\n", version); - fprintf(ficgp,"# %s\n", optionfilegnuplot); - fprintf(ficgp,"set missing 'NaNq'\n"); - } - fclose(ficgp); printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); - /*--------- index.htm --------*/ - strcpy(optionfilehtm,optionfile); - strcat(optionfilehtm,".htm"); - if((fichtm=fopen(optionfilehtm,"w"))==NULL) { - printf("Problem with %s \n",optionfilehtm), exit(0); - } - - 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 -Youngest age at first (selected) pass %.2f, oldest age %.2f
        \n -Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
        \n -
        -

        • Parameter files

          \n - - Copy of the parameter file: o%s
          \n - - Log file of the run: %s
          \n - - Gnuplot file name: %s
        \n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); - fclose(fichtm); - - printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); + printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ + model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ + jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); /*------------ free_vector -------------*/ chdir(path); @@ -4190,7 +4501,7 @@ Interval (in months) between two waves: free_imatrix(dh,1,lastpass-firstpass+1,1,imx); free_imatrix(bh,1,lastpass-firstpass+1,1,imx); free_imatrix(mw,1,lastpass-firstpass+1,1,imx); - free_ivector(num,1,n); + free_lvector(num,1,n); free_vector(agedc,1,n); /*free_matrix(covar,0,NCOVMAX,1,n);*/ /*free_matrix(covar,1,NCOVMAX,1,n);*/ @@ -4309,6 +4620,7 @@ Interval (in months) between two waves: fclose(ficrespij); + probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); /*---------- Forecasting ------------------*/ /*if((stepm == 1) && (strcmp(model,".")==0)){*/ @@ -4356,7 +4668,7 @@ Interval (in months) between two waves: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ - prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); + prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\ ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); */ @@ -4514,9 +4826,21 @@ ageminpar, agemax, s[lastpass][imx], age printf("See log file on %s\n",filelog); fclose(ficlog); /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ - - /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/ - /*printf("Total time was %d uSec.\n", total_usecs);*/ + (void) gettimeofday(&end_time,&tzp); + tm = *localtime(&end_time.tv_sec); + tmg = *gmtime(&end_time.tv_sec); + strtend=asctime(&tm); + printf("Localtime at start %s and at end=%s",strt, strtend); + fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); + /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/ + + printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec); + fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec); + /* printf("Total time was %d uSec.\n", total_usecs);*/ + if(fileappend(fichtm,optionfilehtm)){ + fprintf(fichtm,"
        Localtime at start %s and at end=%s
        ",strt, strtend); + fclose(fichtm); + } /*------ End -----------*/ end: