--- imach/src/imach.c 2006/03/14 18:20:07 1.118
+++ imach/src/imach.c 2006/03/20 09:45:41 1.122
@@ -1,6 +1,30 @@
-/* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard Exp $
+/* $Id: imach.c,v 1.122 2006/03/20 09:45:41 brouard Exp $
$State: Exp $
$Log: imach.c,v $
+ 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
+
Revision 1.118 2006/03/14 18:20:07 brouard
(Module): varevsij Comments added explaining the second
table of variances if popbased=1 .
@@ -322,11 +346,11 @@ extern int errno;
#define ODIRSEPARATOR '/'
#endif
-/* $Id: imach.c,v 1.118 2006/03/14 18:20:07 brouard Exp $ */
+/* $Id: imach.c,v 1.122 2006/03/20 09:45:41 brouard Exp $ */
/* $State: Exp $ */
-char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
-char fullversion[]="$Revision: 1.118 $ $Date: 2006/03/14 18:20:07 $";
+char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+char fullversion[]="$Revision: 1.122 $ $Date: 2006/03/20 09:45:41 $";
char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
@@ -400,6 +424,7 @@ char strcurr[80], strfor[80];
char *endptr;
long lval;
+double dval;
#define NR_END 1
#define FREE_ARG char*
@@ -1382,23 +1407,23 @@ double func( double *x)
} 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;
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*survp += out[s1][j]; */
+ lli= log(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 */
@@ -1593,7 +1618,11 @@ double funcone( double *x)
*/
if( s2 > nlstate && (mle <5) ){ /* Jackson */
lli=log(out[s1][s2] - savm[s1][s2]);
- } else if (mle==1){
+ } else if (s2==-2) {
+ for (j=1,survp=0. ; j<=nlstate; 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 */
} 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 */
@@ -1609,8 +1638,8 @@ double funcone( double *x)
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,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
- %10.6f %10.6f %10.6f ", \
+ fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+ %11.6f %11.6f %11.6f ", \
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,llt=0.,l=0.; k<=nlstate; k++){
@@ -2475,23 +2504,21 @@ void evsij(char fileres[], double ***eij
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 */
-
+
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-
+
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
-
- /* Computing Variances of health expectancies */
- /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
- decrease memory allocation */
- printf("%d|",(int)age);fflush(stdout);
- fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+
+ printf("%d|",(int)age);fflush(stdout);
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+
/* Computing expectancies */
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+ /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
}
@@ -2505,12 +2532,12 @@ void evsij(char fileres[], double ***eij
fprintf(ficreseij,"%9.4f", eip );
}
fprintf(ficreseij,"\n");
-
+
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
printf("\n");
fprintf(ficlog,"\n");
-
+
}
void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
@@ -3442,7 +3469,7 @@ void printinghtml(char fileres[], char t
- Period (stable) prevalence in each health state: %s
\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) 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): \
%s
\n",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
@@ -4411,7 +4438,7 @@ int main(int argc, char *argv[])
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
printf("val= |%s| pathr=%s\n",val,pathr);
strcpy (pathtot, val);
- if(pathr[0] == '\0') break; /* Un peu sale */
+ if(pathr[0] == '\0') break; /* Dirty */
}
}
else{
@@ -4430,7 +4457,9 @@ int main(int argc, char *argv[])
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
- chdir(path);
+ chdir(path); /* Can be a relative path */
+ if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ printf("Current directory %s!\n",pathcd);
strcpy(command,"mkdir ");
strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){
@@ -4793,12 +4822,12 @@ 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--){
@@ -4810,7 +4839,15 @@ 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);
@@ -5263,7 +5300,7 @@ Interval (in months) between two waves:
printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
- replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
@@ -5500,7 +5537,7 @@ Interval (in months) between two waves:
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
/*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
@@ -5895,7 +5932,12 @@ Interval (in months) between two waves:
fclose(ficlog);
/*------ End -----------*/
- chdir(path);
+
+ printf("Before Current directory %s!\n",pathcd);
+ if(chdir(pathcd) != 0)
+ printf("Can't move to directory %s!\n",path);
+ if(getcwd(pathcd,MAXLINE) > 0)
+ printf("Current directory %s!\n",pathcd);
/*strcat(plotcmd,CHARSEPARATOR);*/
sprintf(plotcmd,"gnuplot");
#ifndef UNIX