--- imach/src/imach.c	2017/04/04 17:46:59	1.260
+++ imach/src/imach.c	2017/04/24 15:23:15	1.263
@@ -1,6 +1,15 @@
-/* $Id: imach.c,v 1.260 2017/04/04 17:46:59 brouard Exp $
+/* $Id: imach.c,v 1.263 2017/04/24 15:23:15 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.263  2017/04/24 15:23:15  brouard
+  Summary: to save
+
+  Revision 1.262  2017/04/18 16:48:12  brouard
+  *** empty log message ***
+
+  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)
 
@@ -982,12 +991,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.260 2017/04/04 17:46:59 brouard Exp $ */
+/* $Id: imach.c,v 1.263 2017/04/24 15:23:15 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: 1.260 $ $Date: 2017/04/04 17:46:59 $"; 
+char fullversion[]="$Revision: 1.263 $ $Date: 2017/04/24 15:23:15 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -4945,10 +4954,10 @@ void  concatwav(int wav[], int **dh, int
 #else
 	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
 	  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 pi. .\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);
+	    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 pi. .\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 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;
 	  mli=m;
 	}
@@ -6777,20 +6786,20 @@ 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)");
@@ -6811,7 +6820,7 @@ 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 */
@@ -6833,7 +6842,7 @@ 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);
@@ -6843,11 +6852,11 @@ 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 */
@@ -9119,13 +9128,13 @@ int calandcheckages(int imx, int maxwav,
 	  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 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 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 do not believe in a death, skipped.\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)++;
 	printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-	fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
+	fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
 	s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
       }
     }
@@ -10074,9 +10083,12 @@ int main(int argc, char *argv[])
       break;
   }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
-    if (num_filled == 0)
-            model[0]='\0';
-    else if (num_filled != 1){
+    if (num_filled == 0){
+      printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
+      fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
+      model[0]='\0';
+      goto end;
+    } else if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
       model[0]='\0';
@@ -11242,8 +11254,8 @@ Please run with mle=-1 to get a correct
 	/*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/
 	if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
 	  if (num_filled != 8) {
-	    printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-	    fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+	    printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+	    fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
 	    goto end;
 	  }
 	  printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);