--- imach/src/imach.c	2005/09/30 15:54:49	1.103
+++ imach/src/imach.c	2005/09/30 16:11:43	1.104
@@ -1,6 +1,15 @@
-/* $Id: imach.c,v 1.103 2005/09/30 15:54:49 lievre Exp $
+/* $Id: imach.c,v 1.104 2005/09/30 16:11:43 lievre Exp $
   $State: Exp $
   $Log: imach.c,v $
+  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.
 
@@ -247,11 +256,11 @@
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.103 2005/09/30 15:54:49 lievre Exp $ */
+/* $Id: imach.c,v 1.104 2005/09/30 16:11:43 lievre Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.103 $ $Date: 2005/09/30 15:54:49 $"; 
+char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.104 $ $Date: 2005/09/30 16:11:43 $"; 
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
@@ -1264,9 +1273,10 @@ 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
@@ -1287,7 +1297,16 @@ 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{
 	  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 */
 	} 
@@ -1871,7 +1890,7 @@ 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(-2,nlstate+ndeath,-2,nlstate+ndeath,iagemin,iagemax+3);
   j1=0;
   
   j=cptcoveff;
@@ -1884,8 +1903,8 @@ 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=-2; i<=nlstate+ndeath; i++)  
+	for (jk=-2; jk<=nlstate+ndeath; jk++)  
 	  for(m=iagemin; m <= iagemax+3; m++)
 	    freq[i][jk][m]=0;
 
@@ -2010,7 +2029,7 @@ 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,-2,nlstate+ndeath,-2,nlstate+ndeath, iagemin, iagemax+3);
   free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /* End of Freq */
@@ -2119,7 +2138,7 @@ 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)
 	mw[++mi][i]=m;
       if(m >=lastpass)
 	break;
@@ -2173,7 +2192,8 @@ 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;
@@ -2266,7 +2286,7 @@ 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]++;
  }
@@ -4569,7 +4589,7 @@ int main(int argc, char *argv[])
   for (i=1; i<=imx; i++)  {
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
     for(m=firstpass; (m<= lastpass); m++){
-      if(s[m][i] >0){
+      if(s[m][i] >0 || s[m][i]==-2){
 	if (s[m][i] >= nlstate+1) {
 	  if(agedc[i]>0)
 	    if((int)moisdc[i]!=99 && (int)andc[i]!=9999)