--- imach/src/imach.c	2017/04/04 13:01:16	1.259
+++ imach/src/imach.c	2017/04/04 17:46:59	1.260
@@ -1,6 +1,9 @@
-/* $Id: imach.c,v 1.259 2017/04/04 13:01:16 brouard Exp $
+/* $Id: imach.c,v 1.260 2017/04/04 17:46:59 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.260  2017/04/04 17:46:59  brouard
+  Summary: Gnuplot indexations fixed (humm)
+
   Revision 1.259  2017/04/04 13:01:16  brouard
   Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
 
@@ -979,12 +982,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.259 2017/04/04 13:01:16 brouard Exp $ */
+/* $Id: imach.c,v 1.260 2017/04/04 17:46:59 brouard Exp $ */
 /* $State: Exp $ */
 #include "version.h"
 char version[]=__IMACH_VERSION__;
 char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
-char fullversion[]="$Revision: 1.259 $ $Date: 2017/04/04 13:01:16 $"; 
+char fullversion[]="$Revision: 1.260 $ $Date: 2017/04/04 17:46:59 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -4659,7 +4662,8 @@ Title=%s <br>Datafile=%s Firstpass=%d La
       if(posproptt < 1.e-5){
 	fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
 	fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-	fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+	fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
+	printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
 	invalidvarcomb[j1]=1;
       }else{
 	fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
@@ -5022,7 +5026,7 @@ void  concatwav(int wav[], int **dh, int
       if (stepm <=0)
 	dh[mi][i]=1;
       else{
-	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+	if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
 	  if (agedc[i] < 2*AGESUP) {
 	    j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 	    if(j==0) j=1;  /* Survives at least one month after exam */
@@ -6681,24 +6685,26 @@ void printinggnuplot(char fileresu[], ch
 	/* printf("\n#\n"); */
 	fprintf(ficgp,"\n#\n");
 	if(invalidvarcomb[k1]){
+          /*k1=k1-1;*/ /* To be checked */
 	  fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
 	  continue;
 	}
       
 	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
 	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
-	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
-      
+	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+	/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
+      /* k1-1 error should be nres-1*/
 	for (i=1; i<= nlstate ; i ++) {
 	  if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
 	  else        fprintf(ficgp," %%*lf (%%*lf)");
 	}
-	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
+	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
 	for (i=1; i<= nlstate ; i ++) {
 	  if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
 	  else fprintf(ficgp," %%*lf (%%*lf)");
 	} 
-	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); 
+	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); 
 	for (i=1; i<= nlstate ; i ++) {
 	  if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
 	  else fprintf(ficgp," %%*lf (%%*lf)");
@@ -9108,13 +9114,13 @@ int calandcheckages(int imx, int maxwav,
 	  s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-	*nbwarn = *nbwarn + 1;
+	*nberr = *nberr + 1;
 	if(firstone == 0){
 	  firstone=1;
-	printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we believe in a death.\nOther similar cases in log file\n", *nbwarn,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
+	printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
 	}
-	fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we believe in a death.\nOther similar cases in log file\n", *nbwarn,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
-	/* s[m][i]=-1; */ /* Keeping the death status */
+	fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
+	s[m][i]=-1;  /* Droping the death status */
       }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
 	(*nberr)++;