Summary: Version 0.99r24

diff --git a/CMakeLists.txt b/CMakeLists.txt
index cbcf5e8a87e54f317f01ba1f923bfc46ec5d3367..5d328d4a220302d11a6d3921555ef1b19efd22fa 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -8,7 +8,7 @@
 # SET (CMAKE_CONFIGURATION_TYPES "Debug;RelWithDebinfo" CACHE STRING "" FORCE)
 set(PACKAGE_NAME "imach")
 SET(IMACH_VERSION_MAJOR 0)
-SET(IMACH_VERSION_MINOR 99r23)
+SET(IMACH_VERSION_MINOR 99r24)
 SET(IMACH_VERSION_PATCH 0)
 SET(IMACH_VERSION_NOTE "")
 SET(IMACH_VERSION ${IMACH_VERSION_MAJOR}.${IMACH_VERSION_MINOR})

diff --git a/src/imach.c b/src/imach.c
index 5661d5b54a4f0d110957ef730a7c209f751592d3..128f5dfa0cd90a26248f715532b580e20dae07e9 100644 (file)
--- a/src/imach.c
+++ b/src/imach.c
@@ -1,6 +1,12 @@
 /* $Id$
   $State$
   $Log$
+  Revision 1.308  2021/03/31 13:11:57  brouard
+  Summary: Version 0.99r23
+
+
+  * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
+
   Revision 1.307  2021/03/08 18:11:32  brouard
   Summary: 0.99r22 fixed bug on result:
 
@@ -5265,33 +5271,33 @@ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc
   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);
          }
@@ -5316,34 +5322,35 @@ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc
 #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){