--- imach/src/imach.c 2004/09/15 10:38:38 1.101 +++ imach/src/imach.c 2006/01/05 20:23:19 1.105 @@ -1,6 +1,24 @@ -/* $Id: imach.c,v 1.101 2004/09/15 10:38:38 brouard Exp $ +/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.105 2006/01/05 20:23:19 lievre + *** empty log message *** + + Revision 1.104 2005/09/30 16:11:43 lievre + (Module): sump fixed, loop imx fixed, and simplifications. + (Module): If the status is missing at the last wave but we know + that the person is alive, then we can code his/her status as -2 + (instead of missing=-1 in earlier versions) and his/her + contributions to the likelihood is 1 - Prob of dying from last + health status (= 1-p13= p11+p12 in the easiest case of somebody in + the healthy state at last known wave). Version is 0.98 + + Revision 1.103 2005/09/30 15:54:49 lievre + (Module): sump fixed, loop imx fixed, and simplifications. + + Revision 1.102 2004/09/15 17:31:30 brouard + Add the possibility to read data file including tab characters. + Revision 1.101 2004/09/15 10:38:38 brouard Fix on curr_time @@ -241,11 +259,11 @@ #define ODIRSEPARATOR '/' #endif -/* $Id: imach.c,v 1.101 2004/09/15 10:38:38 brouard Exp $ */ +/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $ */ /* $State: Exp $ */ -char version[]="Imach version 0.97b, May 2004, INED-EUROREVES "; -char fullversion[]="$Revision: 1.101 $ $Date: 2004/09/15 10:38:38 $"; +char version[]="Imach version 0.98, September 2005, INED-EUROREVES "; +char fullversion[]="$Revision: 1.105 $ $Date: 2006/01/05 20:23:19 $"; int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ int nvar; int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; @@ -358,6 +376,7 @@ double *weight; int **s; /* Status */ double *agedc, **covar, idx; int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; +double *lsurv, *lpop, *tpop; double ftol=FTOL; /* Tolerance for computing Max Likelihood */ double ftolhess; /* Tolerance for computing hessian */ @@ -439,8 +458,8 @@ int nbocc(char *s, char occ) void cutv(char *u,char *v, char*t, char occ) { - /* cuts string t into u and v where u is ended by char occ excluding it - and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) + /* cuts string t into u and v where u ends before first occurence of char 'occ' + and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') gives u="abcedf" and v="ghi2j" */ int i,lg,j,p=0; i=0; @@ -1258,9 +1277,10 @@ double func( double *x) */ /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ if( s2 > nlstate){ - /* i.e. if s2 is a death state and if the date of death is known then the contribution - to the likelihood is the probability to die between last step unit time and current - step unit time, which is also equal to probability to die before dh + /* i.e. if s2 is a death state and if the date of death is known + then the contribution to the likelihood is the probability to + die between last step unit time and current step unit time, + which is also equal to probability to die before dh minus probability to die before dh-stepm . In version up to 0.92 likelihood was computed as if date of death was unknown. Death was treated as any other @@ -1281,7 +1301,28 @@ double func( double *x) lower mortality. */ lli=log(out[s1][s2] - savm[s1][s2]); - }else{ + + + } else if (s2==-2) { + for (j=1,survp=0. ; j<=nlstate; j++) + survp += out[s1][j]; + lli= 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{ 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 */ } @@ -1845,7 +1886,7 @@ 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) +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, char strstart[]) { /* Some frequencies */ int i, m, jk, k1,i1, j1, bool, z1,z2,j; @@ -1865,7 +1906,7 @@ void freqsummary(char fileres[], int ia fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); exit(0); } - freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3); + freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); j1=0; j=cptcoveff; @@ -1878,8 +1919,8 @@ void freqsummary(char fileres[], int ia j1++; /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); scanf("%d", i);*/ - for (i=-1; i<=nlstate+ndeath; i++) - for (jk=-1; jk<=nlstate+ndeath; jk++) + for (i=-5; i<=nlstate+ndeath; i++) + for (jk=-5; jk<=nlstate+ndeath; jk++) for(m=iagemin; m <= iagemax+3; m++) freq[i][jk][m]=0; @@ -1918,7 +1959,7 @@ void freqsummary(char fileres[], int ia } /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ - +fprintf(ficresp, "#Local time at start: %s", strstart); if (cptcovn>0) { fprintf(ficresp, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); @@ -2004,7 +2045,7 @@ void freqsummary(char fileres[], int ia dateintmean=dateintsum/k2cpt; fclose(ficresp); - free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3); + free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); free_vector(pp,1,nlstate); free_matrix(prop,1,nlstate,iagemin, iagemax+3); /* End of Freq */ @@ -2113,7 +2154,7 @@ void concatwav(int wav[], int **dh, int mi=0; m=firstpass; while(s[m][i] <= nlstate){ - if(s[m][i]>=1) + if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) mw[++mi][i]=m; if(m >=lastpass) break; @@ -2153,9 +2194,9 @@ void concatwav(int wav[], int **dh, int nberr++; 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; /* Temporary Dangerous 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(" 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. You MUST fix the contradiction between dates.\n",stepm); fprintf(ficlog,"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); + 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. You MUST fix the contradiction between dates.\n",stepm); } k=k+1; if (j >= jmax) jmax=j; @@ -2167,7 +2208,8 @@ void concatwav(int wav[], int **dh, int } else{ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); - /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ +/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */ + k=k+1; if (j >= jmax) jmax=j; else if (j <= jmin)jmin=j; @@ -2260,7 +2302,7 @@ void tricode(int *Tvar, int **nbcode, in for (k=0; k< maxncov; k++) Ndum[k]=0; for (i=1; i<=ncovmodel-2; i++) { - /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ + /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ ij=Tvar[i]; Ndum[ij]++; } @@ -2278,7 +2320,7 @@ void tricode(int *Tvar, int **nbcode, in /*********** Health Expectancies ****************/ -void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov ) +void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] ) { /* Health expectancies */ @@ -2296,6 +2338,7 @@ void evsij(char fileres[], double ***eij dnewm=matrix(1,nlstate*nlstate,1,npar); doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); + fprintf(ficreseij,"# Local time at start: %s", strstart); fprintf(ficreseij,"# Health expectancies\n"); fprintf(ficreseij,"# Age"); for(i=1; i<=nlstate;i++) @@ -2450,7 +2493,7 @@ void evsij(char fileres[], double ***eij } /************ 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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav) +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 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);*/ @@ -2501,7 +2544,9 @@ void varevsij(char optionfilefiname[], d 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); + fprintf(ficresprobmorprev, "#Local time at start: %s", strstart); 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); fprintf(ficresprobmorprev,"# Age cov=%-d",ij); for(j=nlstate+1; j<=(nlstate+ndeath);j++){ @@ -2511,11 +2556,12 @@ void varevsij(char optionfilefiname[], d } fprintf(ficresprobmorprev,"\n"); fprintf(ficgp,"\n# Routine varevsij"); + fprintf(fichtm, "#Local time at start: %s", strstart); fprintf(fichtm,"\n

  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); fprintf(fichtm,"\n
    %s
    \n",digitp); /* } */ varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - + fprintf(ficresvij, "#Local time at start: %s", strstart); fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n"); fprintf(ficresvij,"# Age"); for(i=1; i<=nlstate;i++) @@ -2748,7 +2794,7 @@ void varevsij(char optionfilefiname[], d } /* 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) +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, char strstart[]) { /* Variance of prevalence limit */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ @@ -2761,7 +2807,7 @@ void varprevlim(char fileres[], double * double **gradg, **trgradg; double age,agelim; int theta; - + fprintf(ficresvpl, "#Local time at start: %s", strstart); fprintf(ficresvpl,"# Standard deviation of stable prevalences \n"); fprintf(ficresvpl,"# Age"); for(i=1; i<=nlstate;i++) @@ -2831,7 +2877,7 @@ void varprevlim(char fileres[], double * } /************ Variance of one-step probabilities ******************/ -void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax) +void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[]) { int i, j=0, i1, k1, l1, t, tj; int k2, l2, j1, z1; @@ -2876,11 +2922,13 @@ void varprob(char optionfilefiname[], do fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); - + fprintf(ficresprob, "#Local time at start: %s", strstart); fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); fprintf(ficresprob,"# Age"); + fprintf(ficresprobcov, "#Local time at start: %s", strstart); fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); fprintf(ficresprobcov,"# Age"); + fprintf(ficresprobcor, "#Local time at start: %s", strstart); fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); fprintf(ficresprobcov,"# Age"); @@ -3918,24 +3966,22 @@ double gompertz(double x[]) int i,n=0; /* n is the size of the sample */ for (i=0;i<=imx-1 ; i++) { sump=sump+weight[i]; - sump=sump+1; + /* sump=sump+1;*/ num=num+1; } - /* for (i=1; i<=imx; i++) + /* for (i=0; i<=imx; i++) if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ - for (i=0;i<=imx-1 ; i++) + for (i=1;i<=imx ; i++) { if (cens[i]==1 & wav[i]>1) - A=-x[1]/(x[2])* - (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12))); + A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); if (cens[i]==0 & wav[i]>1) - A=-x[1]/(x[2])* - (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12))) - +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM); + A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) + +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); if (wav[i]>1 & agecens[i]>15) { L=L+A*weight[i]; @@ -3951,8 +3997,8 @@ double gompertz(double x[]) /******************* Printing html file ***********/ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ - int imx, double p[],double **matcov){ - int i; + int imx, double p[],double **matcov,double agemortsup){ + int i,k; fprintf(fichtm,""); + +fprintf(fichtm,"