version 1.119, 2006/03/15 17:42:26
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version 1.124, 2006/03/22 17:13:53
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.124 2006/03/22 17:13:53 lievre |
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Parameters are printed with %lf instead of %f (more numbers after the comma). |
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The log-likelihood is printed in the log file |
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Revision 1.123 2006/03/20 10:52:43 brouard |
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* imach.c (Module): <title> changed, corresponds to .htm file |
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name. <head> headers where missing. |
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* imach.c (Module): Weights can have a decimal point as for |
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English (a comma might work with a correct LC_NUMERIC environment, |
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otherwise the weight is truncated). |
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Modification of warning when the covariates values are not 0 or |
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1. |
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Version 0.98g |
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Revision 1.122 2006/03/20 09:45:41 brouard |
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(Module): Weights can have a decimal point as for |
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English (a comma might work with a correct LC_NUMERIC environment, |
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otherwise the weight is truncated). |
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Modification of warning when the covariates values are not 0 or |
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1. |
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Version 0.98g |
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Revision 1.121 2006/03/16 17:45:01 lievre |
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* imach.c (Module): Comments concerning covariates added |
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* imach.c (Module): refinements in the computation of lli if |
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status=-2 in order to have more reliable computation if stepm is |
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not 1 month. Version 0.98f |
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Revision 1.120 2006/03/16 15:10:38 lievre |
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(Module): refinements in the computation of lli if |
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status=-2 in order to have more reliable computation if stepm is |
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not 1 month. Version 0.98f |
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Revision 1.119 2006/03/15 17:42:26 brouard |
Revision 1.119 2006/03/15 17:42:26 brouard |
(Module): Bug if status = -2, the loglikelihood was |
(Module): Bug if status = -2, the loglikelihood was |
computed as likelihood omitting the logarithm. Version O.98e |
computed as likelihood omitting the logarithm. Version O.98e |
Line 329 extern int errno;
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Line 364 extern int errno;
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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char version[]="Imach version 0.98e, March 2006, INED-EUROREVES-Institut de longevite "; |
char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite "; |
char fullversion[]="$Revision$ $Date$"; |
char fullversion[]="$Revision$ $Date$"; |
char strstart[80]; |
char strstart[80]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
Line 404 char strcurr[80], strfor[80];
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Line 439 char strcurr[80], strfor[80];
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char *endptr; |
char *endptr; |
long lval; |
long lval; |
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double dval; |
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#define NR_END 1 |
#define NR_END 1 |
#define FREE_ARG char* |
#define FREE_ARG char* |
Line 969 void powell(double p[], double **xi, int
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Line 1005 void powell(double p[], double **xi, int
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last_time=curr_time; |
last_time=curr_time; |
(void) gettimeofday(&curr_time,&tzp); |
(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); |
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(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); |
/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */ |
*/ |
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for (i=1;i<=n;i++) { |
for (i=1;i<=n;i++) { |
printf(" %d %.12f",i, p[i]); |
printf(" %d %.12f",i, p[i]); |
fprintf(ficlog," %d %.12lf",i, p[i]); |
fprintf(ficlog," %d %.12lf",i, p[i]); |
Line 1386 double func( double *x)
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Line 1421 double func( double *x)
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} else if (s2==-2) { |
} else if (s2==-2) { |
for (j=1,survp=0. ; j<=nlstate; j++) |
for (j=1,survp=0. ; j<=nlstate; j++) |
survp += out[s1][j]; |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
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/*survp += out[s1][j]; */ |
lli= log(survp); |
lli= log(survp); |
} |
} |
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/* else if (s2==-4) { */ |
else if (s2==-4) { |
/* for (j=3,survp=0. ; j<=nlstate; j++) */ |
for (j=3,survp=0. ; j<=nlstate; j++) |
/* survp += out[s1][j]; */ |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
/* lli= survp; */ |
lli= log(survp); |
/* } */ |
} |
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/* else if (s2==-5) { */ |
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/* for (j=1,survp=0. ; j<=2; j++) */ |
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/* survp += out[s1][j]; */ |
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/* lli= survp; */ |
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/* } */ |
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else if (s2==-5) { |
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for (j=1,survp=0. ; j<=2; j++) |
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survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
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lli= log(survp); |
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} |
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else{ |
else{ |
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
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 */ |
/* 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 */ |
Line 1599 double funcone( double *x)
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Line 1634 double funcone( double *x)
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lli=log(out[s1][s2] - savm[s1][s2]); |
lli=log(out[s1][s2] - savm[s1][s2]); |
} else if (s2==-2) { |
} else if (s2==-2) { |
for (j=1,survp=0. ; j<=nlstate; j++) |
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); |
lli= log(survp); |
}else if (mle==1){ |
}else if (mle==1){ |
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
Line 2062 void freqsummary(char fileres[], int ia
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Line 2097 void freqsummary(char fileres[], int ia
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for(i=iagemin; i <= iagemax+3; i++){ |
for(i=iagemin; i <= iagemax+3; i++){ |
if(i==iagemax+3){ |
if(i==iagemax+3){ |
fprintf(ficlog,"Total"); |
fprintf(ficlog,"Total"); |
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fprintf(fichtm,"<br>Total<br>"); |
}else{ |
}else{ |
if(first==1){ |
if(first==1){ |
first=0; |
first=0; |
Line 3448 void printinghtml(char fileres[], char t
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Line 3484 void printinghtml(char fileres[], char t
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- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); |
subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); |
fprintf(fichtm,"\ |
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) 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</li>", |
<a href=\"%s\">%s</a> <br>\n</li>", |
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); |
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); |
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Line 4547 int main(int argc, char *argv[])
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Line 4583 int main(int argc, char *argv[])
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free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
fclose (ficparo); |
fclose (ficparo); |
fclose (ficlog); |
fclose (ficlog); |
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goto end; |
exit(0); |
exit(0); |
} |
} |
else if(mle==-3) { |
else if(mle==-3) { |
Line 4577 int main(int argc, char *argv[])
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Line 4614 int main(int argc, char *argv[])
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j++; |
j++; |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
if ((i1 != i) && (j1 != j)){ |
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 \ |
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It might be a problem of design; if ncovcol and the model are correct\n \ |
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run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); |
exit(1); |
exit(1); |
} |
} |
fprintf(ficparo,"%1d%1d",i1,j1); |
fprintf(ficparo,"%1d%1d",i1,j1); |
Line 4801 int main(int argc, char *argv[])
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Line 4840 int main(int argc, char *argv[])
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cutv(stra, strb,line,' '); |
cutv(stra, strb,line,' '); |
errno=0; |
errno=0; |
lval=strtol(strb,&endptr,10); |
dval=strtod(strb,&endptr); |
if( strb[0]=='\0' || (*endptr != '\0')){ |
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); |
exit(1); |
} |
} |
weight[i]=(double)(lval); |
weight[i]=dval; |
strcpy(line,stra); |
strcpy(line,stra); |
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for (j=ncovcol;j>=1;j--){ |
for (j=ncovcol;j>=1;j--){ |
Line 4818 int main(int argc, char *argv[])
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Line 4857 int main(int argc, char *argv[])
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exit(1); |
exit(1); |
} |
} |
if(lval <-1 || lval >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 \ |
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Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ |
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for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ |
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For example, for multinomial values like 1, 2 and 3,\n \ |
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build V1=0 V2=0 for the reference value (1),\n \ |
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V1=1 V2=0 for (2) \n \ |
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and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ |
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output of IMaCh is often meaningless.\n \ |
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Exiting.\n",lval,linei, i,line,j); |
exit(1); |
exit(1); |
} |
} |
covar[j][i]=(double)(lval); |
covar[j][i]=(double)(lval); |
Line 5114 int main(int argc, char *argv[])
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Line 5161 int main(int argc, char *argv[])
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printf("Problem with %s \n",optionfilehtmcov), exit(0); |
printf("Problem with %s \n",optionfilehtmcov), exit(0); |
} |
} |
else{ |
else{ |
fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \ |
fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\ |
fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); |
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); |
} |
} |
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fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \ |
fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
<hr size=\"2\" color=\"#EC5E5E\"> \n\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\ |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\ |
\n\ |
\n\ |
Line 5131 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 5178 Title=%s <br>Datafile=%s Firstpass=%d La
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- Log file of the run: <a href=\"%s\">%s</a><br>\n\ |
- Log file of the run: <a href=\"%s\">%s</a><br>\n\ |
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\ |
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\ |
- Date and time at start: %s</ul>\n",\ |
- Date and time at start: %s</ul>\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,\ |
optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ |
fileres,fileres,\ |
fileres,fileres,\ |
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); |
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); |
Line 5314 Interval (in months) between two waves:
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Line 5361 Interval (in months) between two waves:
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fprintf(ficlog,"%d%d ",i,k); |
fprintf(ficlog,"%d%d ",i,k); |
fprintf(ficres,"%1d%1d ",i,k); |
fprintf(ficres,"%1d%1d ",i,k); |
for(j=1; j <=ncovmodel; j++){ |
for(j=1; j <=ncovmodel; j++){ |
printf("%f ",p[jk]); |
printf("%lf ",p[jk]); |
fprintf(ficlog,"%f ",p[jk]); |
fprintf(ficlog,"%lf ",p[jk]); |
fprintf(ficres,"%f ",p[jk]); |
fprintf(ficres,"%lf ",p[jk]); |
jk++; |
jk++; |
} |
} |
printf("\n"); |
printf("\n"); |
Line 5896 Interval (in months) between two waves:
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Line 5943 Interval (in months) between two waves:
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fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec); |
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);*/ |
/* printf("Total time was %d uSec.\n", total_usecs);*/ |
/* if(fileappend(fichtm,optionfilehtm)){ */ |
/* if(fileappend(fichtm,optionfilehtm)){ */ |
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend); |
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend); |
fclose(fichtm); |
fclose(fichtm); |
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fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend); |
fclose(fichtmcov); |
fclose(fichtmcov); |
fclose(ficgp); |
fclose(ficgp); |
fclose(ficlog); |
fclose(ficlog); |