--- imach/src/imach.c	2021/03/31 13:11:57	1.308
+++ imach/src/imach.c	2021/05/20 12:39:14	1.309
@@ -1,6 +1,9 @@
-/* $Id: imach.c,v 1.308 2021/03/31 13:11:57 brouard Exp $
+/* $Id: imach.c,v 1.309 2021/05/20 12:39:14 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.309  2021/05/20 12:39:14  brouard
+  Summary: Version 0.99r24
+
   Revision 1.308  2021/03/31 13:11:57  brouard
   Summary: Version 0.99r23
 
@@ -1150,12 +1153,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.308 2021/03/31 13:11:57 brouard Exp $ */
+/* $Id: imach.c,v 1.309 2021/05/20 12:39:14 brouard Exp $ */
 /* $State: Exp $ */
 #include "version.h"
 char version[]=__IMACH_VERSION__;
 char copyright[]="March 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021, INED 2000-2021";
-char fullversion[]="$Revision: 1.308 $ $Date: 2021/03/31 13:11:57 $"; 
+char fullversion[]="$Revision: 1.309 $ $Date: 2021/05/20 12:39:14 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -5271,33 +5274,33 @@ void  concatwav(int wav[], int **dh, int
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;  /* First valid wave */
     mli=0; /* Last valid wave */
-    m=firstpass;
-    while(s[m][i] <= nlstate){  /* a live state */
+    m=firstpass;  /* Loop on waves */
+    while(s[m][i] <= nlstate){  /* a live state or unknown state  */
       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
 	mli=m-1;/* mw[++mi][i]=m-1; */
       }else 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;
+	mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
 	mli=m;
       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
       if(m < lastpass){ /* m < lastpass, standard case */
 	m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
       }
-      else{ /* m >= lastpass, eventual special issue with warning */
+      else{ /* m = lastpass, eventual special issue with warning */
 #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
 	break;
 #else
-	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* case -2 (vital status unknown is warned later */
 	  if(firsthree == 0){
 	    printf("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 as 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
 	    firsthree=1;
 	  }
 	  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 as 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
-	  mw[++mi][i]=m;
+	  mw[++mi][i]=m; /* Valid transition with unknown status */
 	  mli=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? */
+	  if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
 	    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.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
 	  }
@@ -5322,34 +5325,35 @@ void  concatwav(int wav[], int **dh, int
 #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     else if ((int) andc[i] != 9999) {  /* Date of death is known */
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-	if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
+	if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
 	  nbwarn++;
 	  if(firstfiv==0){
-	    printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing 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], s[m][i], i,m );
+	    printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing 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], s[m][i], i,m );
 	    firstfiv=1;
 	  }else{
-	    fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+	    fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
 	  }
-	}else{ /* Death occured afer last wave potential bias */
+	    s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
+	}else{ /* Month of Death occured afer last wave month, potential bias */
 	  nberr++;
 	  if(firstwo==0){
-	    printf("Error! Death for individual %ld line=%d occurred at %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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\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 );
+	    printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
 	    firstwo=1;
 	  }
-	  fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\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 at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
 	}
       }else{ /* if date of interview is unknown */
 	/* death is known but not confirmed by death status at any wave */
 	if(firstfour==0){
-	  printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %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 );
+	  printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %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], s[m][i], i,m );
 	  firstfour=1;
 	}
-	fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %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.\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 but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d  with status %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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
       }
     } /* end if date of death is known */
 #endif
-    wav[i]=mi; /* mi should be the last effective wave (or mli) */
-    /* wav[i]=mw[mi][i]; */
+    wav[i]=mi; /* mi should be the last effective wave (or mli),  */
+    /* wav[i]=mw[mi][i];   */
     if(mi==0){
       nbwarn++;
       if(first==0){