--- imach/src/imach.c	2006/03/14 17:16:22	1.117
+++ imach/src/imach.c	2006/03/16 17:45:01	1.121
@@ -1,6 +1,29 @@
-/* $Id: imach.c,v 1.117 2006/03/14 17:16:22 brouard Exp $
+/* $Id: imach.c,v 1.121 2006/03/16 17:45:01 lievre Exp $
   $State: Exp $
   $Log: imach.c,v $
+  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 .
+  (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+  (Module): Function pstamp added
+  (Module): Version 0.98d
+
   Revision 1.117  2006/03/14 17:16:22  brouard
   (Module): varevsij Comments added explaining the second
   table of variances if popbased=1 .
@@ -315,11 +338,11 @@ extern int errno;
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.117 2006/03/14 17:16:22 brouard Exp $ */
+/* $Id: imach.c,v 1.121 2006/03/16 17:45:01 lievre Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
-char fullversion[]="$Revision: 1.117 $ $Date: 2006/03/14 17:16:22 $"; 
+char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
+char fullversion[]="$Revision: 1.121 $ $Date: 2006/03/16 17:45:01 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -1375,23 +1398,23 @@ double func( double *x)
 
 	} else if  (s2==-2) {
 	  for (j=1,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==-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 */
@@ -1586,7 +1609,11 @@ 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 */
@@ -1602,8 +1629,8 @@ 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++){
@@ -2468,23 +2495,21 @@ 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]);*/
 
 	}
 
@@ -2498,12 +2523,12 @@ 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[] )
@@ -3435,7 +3460,7 @@ 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) 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>",
 	   estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
 
@@ -4404,7 +4429,7 @@ 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{
@@ -4423,7 +4448,9 @@ 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){
@@ -4689,8 +4716,8 @@ int main(int argc, char *argv[])
 
   /*-------- data file ----------*/
   if((fic=fopen(datafile,"r"))==NULL)    {
-    printf("Problem with datafile: %s\n", datafile);goto end;
-    fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+    printf("Problem while opening datafile: %s\n", datafile);goto end;
+    fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
   }
 
   n= lastobs;
@@ -5256,7 +5283,7 @@ 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, \
@@ -5493,7 +5520,7 @@ 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,\
@@ -5748,7 +5775,7 @@ Interval (in months) between two waves:
 	}
 
 	pstamp(ficrest);
-	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state ( e.. (std) ");
+	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
 	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
 	fprintf(ficrest,"\n");
 
@@ -5888,7 +5915,12 @@ 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