--- imach/src/imach.c	2016/08/30 15:01:20	1.242
+++ imach/src/imach.c	2016/09/02 07:25:01	1.245
@@ -1,6 +1,15 @@
-/* $Id: imach.c,v 1.242 2016/08/30 15:01:20 brouard Exp $
+/* $Id: imach.c,v 1.245 2016/09/02 07:25:01 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.245  2016/09/02 07:25:01  brouard
+  *** empty log message ***
+
+  Revision 1.244  2016/09/02 07:17:34  brouard
+  *** empty log message ***
+
+  Revision 1.243  2016/09/02 06:45:35  brouard
+  *** empty log message ***
+
   Revision 1.242  2016/08/30 15:01:20  brouard
   Summary: Fixing a lots
 
@@ -928,12 +937,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.242 2016/08/30 15:01:20 brouard Exp $ */
+/* $Id: imach.c,v 1.245 2016/09/02 07:25:01 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: 1.242 $ $Date: 2016/08/30 15:01:20 $"; 
+char fullversion[]="$Revision: 1.245 $ $Date: 2016/09/02 07:25:01 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -2222,7 +2231,8 @@ void powell(double p[], double **xi, int
 				/* printf("\n"); */
 				/* fprintf(ficlog,"\n"); */
 			}
-    if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
+    /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
+    if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
@@ -3213,7 +3223,7 @@ double func( double *x)
 	 Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
 	 to be observed in j being in i according to the model.
       */
-      ioffset=2+nagesqr+cptcovage;
+      ioffset=2+nagesqr ;
    /* Fixed */
       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
 	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
@@ -3532,7 +3542,8 @@ double funcone( double *x)
   for(k=1; k<=nlstate; k++) ll[k]=0.;
   ioffset=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-    ioffset=2+nagesqr+cptcovage;
+    /* ioffset=2+nagesqr+cptcovage; */
+    ioffset=2+nagesqr;
     /* Fixed */
     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
@@ -6436,7 +6447,7 @@ void printinggnuplot(char fileresu[], ch
 	  /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
 	  fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
 	  if(cptcoveff ==0){
-	    fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",	 2+(cpt-1),  cpt );
+	    fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",	 2+(cpt-1),  cpt );
 	  }else{
 	    kl=0;
 	    for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
@@ -6451,7 +6462,7 @@ void printinggnuplot(char fileresu[], ch
 	      /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
 	      /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
 	      if(k==cptcoveff){
-		fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+		fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
 			2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
 	      }else{
 		fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
@@ -6521,7 +6532,7 @@ void printinggnuplot(char fileresu[], ch
 	  else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
 	} /* state */
       } /* vpopbased */
-      fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
+      fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
     } /* end nres */
   } /* k1 end 2 eme*/