--- imach/src/imach.c	2015/12/16 08:52:24	1.215
+++ imach/src/imach.c	2015/12/18 17:32:11	1.216
@@ -1,6 +1,14 @@
-/* $Id: imach.c,v 1.215 2015/12/16 08:52:24 brouard Exp $
+/* $Id: imach.c,v 1.216 2015/12/18 17:32:11 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.216  2015/12/18 17:32:11  brouard
+  Summary: 0.98r4 Warning and status=-2
+
+  Version 0.98r4 is now:
+   - displaying an error when status is -1, date of interview unknown and date of death known;
+   - permitting a status -2 when the vital status is unknown at a known date of right truncation.
+  Older changes concerning s=-2, dating from 2005 have been supersed.
+
   Revision 1.215  2015/12/16 08:52:24  brouard
   Summary: 0.98r4 working
 
@@ -792,12 +800,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.215 2015/12/16 08:52:24 brouard Exp $ */
+/* $Id: imach.c,v 1.216 2015/12/18 17:32:11 brouard Exp $ */
 /* $State: Exp $ */
 #include "version.h"
 char version[]=__IMACH_VERSION__;
 char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
-char fullversion[]="$Revision: 1.215 $ $Date: 2015/12/16 08:52:24 $"; 
+char fullversion[]="$Revision: 1.216 $ $Date: 2015/12/18 17:32:11 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -2446,27 +2454,24 @@ double func( double *x)
 /* 	  else */
 /* 	    lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #endif */
-	    lli=log(out[s1][s2] - savm[s1][s2]);
-
-	} else if  (s2==-2) {
+	  lli=log(out[s1][s2] - savm[s1][s2]);
+	  
+	} else if  ( s2==-1 ) { /* alive */
 	  for (j=1,survp=0. ; j<=nlstate; j++) 
 	    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 += (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 */
@@ -2578,6 +2583,10 @@ double func( double *x)
 	s2=s[mw[mi+1][i]][i];
 	if( s2 > nlstate){ 
 	  lli=log(out[s1][s2] - savm[s1][s2]);
+	} else if  ( s2==-1 ) { /* alive */
+	  for (j=1,survp=0. ; j<=nlstate; j++) 
+	    survp += out[s1][j];
+	  lli= log(survp);
 	}else{
 	  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 	}
@@ -2685,13 +2694,17 @@ double funcone( double *x)
       
       s1=s[mw[mi][i]][i];
       s2=s[mw[mi+1][i]][i];
+      if(s2==-1){
+	printf(" s1=%d, s2=%d i=%d \n", s1, s2, i);
+	/* exit(1); */
+      }
       bbh=(double)bh[mi][i]/(double)stepm; 
       /* bias is positive if real duration
        * is higher than the multiple of stepm and negative otherwise.
        */
       if( s2 > nlstate && (mle <5) ){  /* Jackson */
 	lli=log(out[s1][s2] - savm[s1][s2]);
-      } else if  (s2==-2) {
+      } else if  ( s2==-1 ) { /* alive */
 	for (j=1,survp=0. ; j<=nlstate; j++) 
 	  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 	lli= log(survp);
@@ -3613,31 +3626,47 @@ void  concatwav(int wav[], int **dh, int
     mi=0;
     m=firstpass;
     while(s[m][i] <= nlstate){  /* a live state */
-      if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+      if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
 	mw[++mi][i]=m;
-      if(m >=lastpass)
+      }
+      if(m >=lastpass){
+	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+	  printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+	  fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+	  mw[++mi][i]=m;
+	}
+	if(s[m][i]==-2){ /* Vital status is really unknown */
+	  nbwarn++;
+	  if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
+	    printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+	    fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+	  }
+	  break;
+	}
 	break;
+      }
       else
 	m++;
     }/* end while */
+    
+    /* After last pass */
     if (s[m][i] > nlstate){  /* In a death state */
       mi++;	/* Death is another wave */
       /* if(mi==0)  never been interviewed correctly before death */
 	 /* Only death is a correct wave */
       mw[mi][i]=m;
-    }else if (andc[i] != 9999) { /* A death occured after lastpass */
-      m++;
-      mi++;
-      s[m][i]=nlstate+1;  /* We are setting the status to the last of non live state */
-      mw[mi][i]=m;
-      nbwarn++;
+    }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
+      /* m++; */
+      /* mi++; */
+      /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
+      /* mw[mi][i]=m; */
+      nberr++;
       if(firstwo==0){
-	printf("Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m);
-	fprintf(ficlog,"Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
+	printf("Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+	fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
 	firstwo=1;
-      }
-      if(firstwo==1){
-	fprintf(ficlog,"Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
+      }else if(firstwo==1){
+	fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
       }
     }
     wav[i]=mi;
@@ -6625,7 +6654,8 @@ int calandcheckages(int imx, int maxwav,
     for(m=2; (m<= maxwav); m++) {
       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
 	anint[m][i]=9999;
-	s[m][i]=-1;
+	if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
+	  s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
 	*nberr = *nberr + 1;
@@ -8784,8 +8814,8 @@ Please run with mle=-1 to get a correct
   
 
   if((nberr >0) || (nbwarn>0)){
-    printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
-    fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+    printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
+    fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
   }else{
     printf("End of Imach\n");
     fprintf(ficlog,"End of Imach\n");