--- imach/src/imach.c	2006/04/28 18:11:50	1.127
+++ imach/src/imach.c	2007/08/31 13:49:27	1.129
@@ -1,6 +1,12 @@
-/* $Id: imach.c,v 1.127 2006/04/28 18:11:50 brouard Exp $
+/* $Id: imach.c,v 1.129 2007/08/31 13:49:27 lievre Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.129  2007/08/31 13:49:27  lievre
+  Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
+
+  Revision 1.128  2006/06/30 13:02:05  brouard
+  (Module): Clarifications on computing e.j
+
   Revision 1.127  2006/04/28 18:11:50  brouard
   (Module): Yes the sum of survivors was wrong since
   imach-114 because nhstepm was no more computed in the age
@@ -383,11 +389,11 @@ extern int errno;
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.127 2006/04/28 18:11:50 brouard Exp $ */
+/* $Id: imach.c,v 1.129 2007/08/31 13:49:27 lievre Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
-char fullversion[]="$Revision: 1.127 $ $Date: 2006/04/28 18:11:50 $"; 
+char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
+char fullversion[]="$Revision: 1.129 $ $Date: 2007/08/31 13:49:27 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -1344,10 +1350,11 @@ double ***hpxij(double ***po, int nhstep
     for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {
 	po[i][j][h]=newm[i][j];
-	/*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
-	 */
+	/*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }
+    /*printf("h=%d ",h);*/
   } /* end h */
+/*     printf("\n H=%d \n",h); */
   return po;
 }
 
@@ -2264,7 +2271,8 @@ void prevalence(double ***probs, double
  	  if( i <=  iagemax){ 
  	    if(posprop>=1.e-5){ 
  	      probs[i][jk][j1]= prop[jk][i]/posprop;
- 	    } 
+ 	    } else
+	      printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
  	  } 
  	}/* end jk */ 
       }/* end i */ 
@@ -2868,7 +2876,7 @@ void varevsij(char optionfilefiname[], d
   pstamp(ficresvij);
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   if(popbased==1)
-    fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+    fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   else
     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   fprintf(ficresvij,"# Age");
@@ -2896,8 +2904,7 @@ void varevsij(char optionfilefiname[], d
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin. 
-     Look at hpijx to understand the reason of that which relies in memory size
-     and note for a fixed period like k years */
+     Look at function hpijx to understand why (it is linked to memory size questions) */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      survival function given by stepm (the optimization length). Unfortunately it
      means that if the survival funtion is printed every two years of age and if
@@ -2963,7 +2970,7 @@ void varevsij(char optionfilefiname[], d
 	}
       }
 
-      for(j=1; j<= nlstate; j++){
+      for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
 	for(h=0; h<=nhstepm; h++){
 	  for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 	    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
@@ -3523,7 +3530,7 @@ 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 . 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) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates 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",
 	   estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
    fprintf(fichtm,"\
@@ -3588,11 +3595,11 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
    <a href=\"%s\">%s</a> <br>\n</li>",
 	   estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
  fprintf(fichtm,"\
- - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
 	 estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
  fprintf(fichtm,"\
- - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
-	 subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+ - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+	 estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
  fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
 	 subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
@@ -3625,7 +3632,10 @@ prevalence (with 95%% confidence interva
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-health expectancies in states (1) and (2): %s%d.png<br>\
+health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+true period expectancies (those weighted with period prevalences are also\
+ drawn in addition to the population based expectancies computed using\
+ observed and cahotic prevalences: %s%d.png<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */
  }/* End k1 */
@@ -4388,6 +4398,7 @@ int main(int argc, char *argv[])
   int numlinepar=0; /* Current linenumber of parameter file */
   int itimes;
   int NDIM=2;
+  int vpopbased=0;
 
   char ca[32], cb[32], cc[32];
   char dummy[]="                         ";
@@ -4907,13 +4918,13 @@ run imach with mle=-1 to get a correct t
  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);
+	goto end;
       }
       covar[j][i]=(double)(lval);
       strcpy(line,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);
@@ -5863,47 +5874,49 @@ Interval (in months) between two waves:
 	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
  
 	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-	oldm=oldms;savm=savms;
-	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
-	if(popbased==1){
-	  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
-	}
-
 	pstamp(ficrest);
-	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");
+	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+	  oldm=oldms;savm=savms;
+	  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);	  fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+	  if(vpopbased==1)
+	    fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+	  else
+	    fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+	  fprintf(ficrest,"# Age e.. (std) ");
+	  for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+	  fprintf(ficrest,"\n");
 
-	epj=vector(1,nlstate+1);
-	for(age=bage; age <=fage ;age++){
-	  prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-	  if (popbased==1) {
-	    if(mobilav ==0){
-	      for(i=1; i<=nlstate;i++)
-		prlim[i][i]=probs[(int)age][i][k];
-	    }else{ /* mobilav */ 
-	      for(i=1; i<=nlstate;i++)
-		prlim[i][i]=mobaverage[(int)age][i][k];
+	  epj=vector(1,nlstate+1);
+	  for(age=bage; age <=fage ;age++){
+	    prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+	    if (vpopbased==1) {
+	      if(mobilav ==0){
+		for(i=1; i<=nlstate;i++)
+		  prlim[i][i]=probs[(int)age][i][k];
+	      }else{ /* mobilav */ 
+		for(i=1; i<=nlstate;i++)
+		  prlim[i][i]=mobaverage[(int)age][i][k];
+	      }
 	    }
-	  }
 	
-	  fprintf(ficrest," %4.0f",age);
-	  for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-	    for(i=1, epj[j]=0.;i <=nlstate;i++) {
-	      epj[j] += prlim[i][i]*eij[i][j][(int)age];
-	      /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+	    fprintf(ficrest," %4.0f",age);
+	    for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+	      for(i=1, epj[j]=0.;i <=nlstate;i++) {
+		epj[j] += prlim[i][i]*eij[i][j][(int)age];
+		/*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+	      }
+	      epj[nlstate+1] +=epj[j];
 	    }
-	    epj[nlstate+1] +=epj[j];
-	  }
 
-	  for(i=1, vepp=0.;i <=nlstate;i++)
-	    for(j=1;j <=nlstate;j++)
-	      vepp += vareij[i][j][(int)age];
-	  fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-	  for(j=1;j <=nlstate;j++){
-	    fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+	    for(i=1, vepp=0.;i <=nlstate;i++)
+	      for(j=1;j <=nlstate;j++)
+		vepp += vareij[i][j][(int)age];
+	    fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+	    for(j=1;j <=nlstate;j++){
+	      fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+	    }
+	    fprintf(ficrest,"\n");
 	  }
-	  fprintf(ficrest,"\n");
 	}
 	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);