--- imach/src/imach.c	2017/04/04 13:01:16	1.259
+++ imach/src/imach.c	2017/04/05 10:14:09	1.261
@@ -1,6 +1,12 @@
-/* $Id: imach.c,v 1.259 2017/04/04 13:01:16 brouard Exp $
+/* $Id: imach.c,v 1.261 2017/04/05 10:14:09 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.261  2017/04/05 10:14:09  brouard
+  Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
+
+  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 +985,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.259 2017/04/04 13:01:16 brouard Exp $ */
+/* $Id: imach.c,v 1.261 2017/04/05 10:14:09 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: 1.261 $ $Date: 2017/04/05 10:14:09 $"; 
 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 +4665,8 @@ 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 +5029,7 @@ 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 +6688,26 @@ 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)");
@@ -6771,20 +6780,20 @@ void printinggnuplot(char fileresu[], ch
 	  fprintf(ficgp,"\nreplot ");
 	for (i=1; i<= nlstate+1 ; i ++) {
 	  k=2*i;
-	  fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
+	  fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
 	  for (j=1; j<= nlstate+1 ; j ++) {
 	    if (j==i) fprintf(ficgp," %%lf (%%lf)");
 	    else fprintf(ficgp," %%*lf (%%*lf)");
 	  }   
 	  if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
 	  else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-	  fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+	  fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
 	  for (j=1; j<= nlstate+1 ; j ++) {
 	    if (j==i) fprintf(ficgp," %%lf (%%lf)");
 	    else fprintf(ficgp," %%*lf (%%*lf)");
 	  }   
 	  fprintf(ficgp,"\" t\"\" w l lt 0,");
-	  fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+	  fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
 	  for (j=1; j<= nlstate+1 ; j ++) {
 	    if (j==i) fprintf(ficgp," %%lf (%%lf)");
 	    else fprintf(ficgp," %%*lf (%%*lf)");
@@ -6805,7 +6814,7 @@ void printinggnuplot(char fileresu[], ch
 	continue;
 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
-	fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
+	fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
 	for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
 	  lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
 	  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
@@ -6827,7 +6836,7 @@ void printinggnuplot(char fileresu[], ch
 	k=2+(nlstate+1)*(cpt-1);
 	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
 	fprintf(ficgp,"set ter svg size 640, 480\n\
-plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
 	/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 	  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 	  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
@@ -6837,11 +6846,11 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
 				
 	*/
 	for (i=1; i< nlstate ; i ++) {
-	  fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
+	  fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
 	  /*	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
 				
 	} 
-	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
+	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
       }
     } /* end nres */
   } /* end kl 3eme */
@@ -9108,13 +9117,13 @@ 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)++;