--- imach/src/imach.c	2017/06/29 09:47:08	1.274
+++ imach/src/imach.c	2017/07/19 14:09:02	1.278
@@ -1,6 +1,18 @@
-/* $Id: imach.c,v 1.274 2017/06/29 09:47:08 brouard Exp $
+/* $Id: imach.c,v 1.278 2017/07/19 14:09:02 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.278  2017/07/19 14:09:02  brouard
+  Summary: Bug for mobil_average=0 and prevforecast fixed(?)
+
+  Revision 1.277  2017/07/17 08:53:49  brouard
+  Summary: BOM files can be read now
+
+  Revision 1.276  2017/06/30 15:48:31  brouard
+  Summary: Graphs improvements
+
+  Revision 1.275  2017/06/30 13:39:33  brouard
+  Summary: Saito's color
+
   Revision 1.274  2017/06/29 09:47:08  brouard
   Summary: Version 0.99r14
 
@@ -1025,12 +1037,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.274 2017/06/29 09:47:08 brouard Exp $ */
+/* $Id: imach.c,v 1.278 2017/07/19 14:09:02 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: 1.274 $ $Date: 2017/06/29 09:47:08 $"; 
+char fullversion[]="$Revision: 1.278 $ $Date: 2017/07/19 14:09:02 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -7049,7 +7061,8 @@ void printinggnuplot(char fileresu[], ch
       
 	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 label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+	/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
+	fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
 	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*/
@@ -7134,7 +7147,7 @@ void printinggnuplot(char fileresu[], ch
 	      if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
 	      else fprintf(ficgp," %%*lf (%%*lf)");
 	    } 
-	    fprintf(ficgp,"\" t\"95%% CI\" w l lt 5,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
+	    fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
 	    for (i=1; i<= nlstate ; i ++) {
 	      if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
 	      else fprintf(ficgp," %%*lf (%%*lf)");
@@ -7142,7 +7155,8 @@ void printinggnuplot(char fileresu[], ch
 	    fprintf(ficgp,"\" t\"\" w l lt 4");
 	  } /* end if backprojcast */
 	} /* end if backcast */
-	fprintf(ficgp,"\nset out ;unset label;\n");
+	/* fprintf(ficgp,"\nset out ;unset label;\n"); */
+	fprintf(ficgp,"\nset out ;unset title;\n");
       } /* nres */
     } /* k1 */
   } /* cpt */
@@ -7756,7 +7770,7 @@ set ter svg size 640, 480\nunset log y\n
 	continue;
       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
       strcpy(gplotlabel,"(");
-      sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);
+      /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
 	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
 	/* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
@@ -7773,7 +7787,9 @@ set ter svg size 640, 480\nunset log y\n
       strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
-      fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+      fprintf(ficgp,"\nset key outside ");
+      /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
+      fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
       fprintf(ficgp,"\nset ter svg size 640, 480 ");
       if (ng==1){
 	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
@@ -7893,12 +7909,12 @@ set ter svg size 640, 480\nunset log y\n
 	    }
 	    fprintf(ficgp,")");
 	    if(ng ==2)
-	      fprintf(ficgp," t \"p%d%d\" ", k2,k);
+	      fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
 	    else /* ng= 3 */
-	      fprintf(ficgp," t \"i%d%d\" ", k2,k);
+	      fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
 	  }else{ /* end ng <> 1 */
 	    if( k !=k2) /* logit p11 is hard to draw */
-	      fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+	      fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
 	  }
 	  if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
 	    fprintf(ficgp,",");
@@ -7907,7 +7923,8 @@ set ter svg size 640, 480\nunset log y\n
 	  i=i+ncovmodel;
 	} /* end k */
       } /* end k2 */
-      fprintf(ficgp,"\n set out; unset label;\n");
+      /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
+      fprintf(ficgp,"\n set out; unset title;set key default;\n");
     } /* end k1 */
   } /* end ng */
   /* avoid: */
@@ -7931,8 +7948,8 @@ set ter svg size 640, 480\nunset log y\n
    double *agemingoodr, *agemaxgoodr; 
   
   
-   /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
-   /* 		   a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
+   /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
+   /* 		   a covariate has 2 modalities, should be equal to ncovcombmax   */
 
    sumnewp = vector(1,ncovcombmax);
    sumnewm = vector(1,ncovcombmax);
@@ -8256,11 +8273,11 @@ set ter svg size 640, 480\nunset log y\n
 	for(j=1; j<=nlstate+ndeath;j++) {
 	  ppij=0.;
 	  for(i=1; i<=nlstate;i++) {
-	    /* if (mobilav>=1)  */
-	    ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
-	    /* else { */ /* even if mobilav==-1 we use mobaverage */
-	    /* 	ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
-	    /* } */
+	    if (mobilav>=1)
+	     ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
+	    else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
+	    	ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+	    }
 	    fprintf(ficresf," %.3f", p3mat[i][j][h]);
 	  } /* end i */
 	  fprintf(ficresf," %.3f", ppij);
@@ -10602,7 +10619,7 @@ int main(int argc, char *argv[])
   int vpopbased=0;
   int nres=0;
   int endishere=0;
-
+  int noffset=0;
   int ncurrv=0; /* Temporary variable */
   
   char ca[32], cb[32];
@@ -10828,17 +10845,52 @@ int main(int argc, char *argv[])
     fflush(ficlog);
     goto end;
   }
+      /*-------- Rewriting parameter file ----------*/
+  strcpy(rfileres,"r");    /* "Rparameterfile */
+  strcat(rfileres,optionfilefiname);    /* Parameter file first name */
+  strcat(rfileres,".");    /* */
+  strcat(rfileres,optionfilext);    /* Other files have txt extension */
+  if((ficres =fopen(rfileres,"w"))==NULL) {
+    printf("Problem writing new parameter file: %s\n", rfileres);goto end;
+    fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
+    fflush(ficlog);
+    goto end;
+  }
+  fprintf(ficres,"#IMaCh %s\n",version);
 
+				      
   /* Reads comments: lines beginning with '#' */
   numlinepar=0;
-
-    /* First parameter line */
+  /* Is it a BOM UTF-8 Windows file? */
+  /* First parameter line */
   while(fgets(line, MAXLINE, ficpar)) {
+    noffset=0;
+    if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
+    {
+      noffset=noffset+3;
+      printf("# File is an UTF8 Bom.\n"); // 0xBF
+    }
+    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
+    {
+      noffset=noffset+2;
+      printf("# File is an UTF16BE BOM file\n");
+    }
+    else if( line[0] == 0 && line[1] == 0)
+    {
+      if( line[2] == (char)0xFE && line[3] == (char)0xFF){
+	noffset=noffset+4;
+	printf("# File is an UTF16BE BOM file\n");
+      }
+    } else{
+      ;/*printf(" Not a BOM file\n");*/
+    }
+  
     /* If line starts with a # it is a comment */
-    if (line[0] == '#') {
+    if (line[noffset] == '#') {
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
+      fputs(line,ficres);
       fputs(line,ficlog);
       continue;
     }else
@@ -10859,6 +10911,7 @@ int main(int argc, char *argv[])
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
+      fputs(line,ficres);
       fputs(line,ficlog);
       continue;
     }else
@@ -10881,6 +10934,7 @@ int main(int argc, char *argv[])
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
+      fputs(line,ficres);
       fputs(line,ficlog);
       continue;
     }else
@@ -11142,16 +11196,6 @@ Please run with mle=-1 to get a correct
     
     fflush(ficlog);
     
-    /*-------- Rewriting parameter file ----------*/
-    strcpy(rfileres,"r");    /* "Rparameterfile */
-    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-    strcat(rfileres,".");    /* */
-    strcat(rfileres,optionfilext);    /* Other files have txt extension */
-    if((ficres =fopen(rfileres,"w"))==NULL) {
-      printf("Problem writing new parameter file: %s\n", rfileres);goto end;
-      fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
-    }
-    fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */
   
   /*  Main data