--- imach/src/imach.c	2014/06/10 21:23:15	1.145
+++ imach/src/imach.c	2014/08/25 20:10:10	1.156
@@ -1,6 +1,49 @@
-/* $Id: imach.c,v 1.145 2014/06/10 21:23:15 brouard Exp $
+/* $Id: imach.c,v 1.156 2014/08/25 20:10:10 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.156  2014/08/25 20:10:10  brouard
+  *** empty log message ***
+
+  Revision 1.155  2014/08/25 18:32:34  brouard
+  Summary: New compile, minor changes
+  Author: Brouard
+
+  Revision 1.154  2014/06/20 17:32:08  brouard
+  Summary: Outputs now all graphs of convergence to period prevalence
+
+  Revision 1.153  2014/06/20 16:45:46  brouard
+  Summary: If 3 live state, convergence to period prevalence on same graph
+  Author: Brouard
+
+  Revision 1.152  2014/06/18 17:54:09  brouard
+  Summary: open browser, use gnuplot on same dir than imach if not found in the path
+
+  Revision 1.151  2014/06/18 16:43:30  brouard
+  *** empty log message ***
+
+  Revision 1.150  2014/06/18 16:42:35  brouard
+  Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+  Author: brouard
+
+  Revision 1.149  2014/06/18 15:51:14  brouard
+  Summary: Some fixes in parameter files errors
+  Author: Nicolas Brouard
+
+  Revision 1.148  2014/06/17 17:38:48  brouard
+  Summary: Nothing new
+  Author: Brouard
+
+  Just a new packaging for OS/X version 0.98nS
+
+  Revision 1.147  2014/06/16 10:33:11  brouard
+  *** empty log message ***
+
+  Revision 1.146  2014/06/16 10:20:28  brouard
+  Summary: Merge
+  Author: Brouard
+
+  Merge, before building revised version.
+
   Revision 1.145  2014/06/10 21:23:15  brouard
   Summary: Debugging with valgrind
   Author: Nicolas Brouard
@@ -477,11 +520,11 @@ extern int errno;
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.145 2014/06/10 21:23:15 brouard Exp $ */
+/* $Id: imach.c,v 1.156 2014/08/25 20:10:10 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
-char fullversion[]="$Revision: 1.145 $ $Date: 2014/06/10 21:23:15 $"; 
+char version[]="Imach version 0.98nV, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
+char fullversion[]="$Revision: 1.156 $ $Date: 2014/08/25 20:10:10 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -3859,13 +3902,13 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
 <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Period (stable) prevalence in each health state */
-       for(cpt=1; cpt<nlstate;cpt++){
-	 fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
-<img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+       for(cpt=1; cpt<=nlstate;cpt++){
+	 fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
+<img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }
      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }
    } /* end i1 */
  }/* End k1 */
@@ -3961,6 +4004,7 @@ void printinggnuplot(char fileres[], cha
   strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");
  /* 1eme*/
+  fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {
     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
@@ -3988,7 +4032,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
    }
   }
   /*2 eme*/
-  
+  fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
   for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
@@ -4045,28 +4089,29 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
   }
   
   /* CV preval stable (period) */
-  for (k1=1; k1<= m ; k1 ++) { 
-    for (cpt=1; cpt<=nlstate ; cpt ++) {
+  for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+    for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;
+      fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter png small size 320, 240\n\
 unset log y\n\
-plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-      
-      for (i=1; i< nlstate ; i ++)
-	fprintf(ficgp,"+$%d",k+i+1);
-      fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-      
-      l=3+(nlstate+ndeath)*cpt;
-      fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-      for (i=1; i< nlstate ; i ++) {
-	l=3+(nlstate+ndeath)*cpt;
-	fprintf(ficgp,"+$%d",l+i+1);
-      }
-      fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
-    } 
-  }  
+plot [%.f:%.f]  ", ageminpar, agemaxpar);
+      for (i=1; i<= nlstate ; i ++){
+	if(i==1)
+	  fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+	else
+	  fprintf(ficgp,", '' ");
+	l=(nlstate+ndeath)*(i-1)+1;
+	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+	for (j=1; j<= (nlstate-1) ; j ++)
+	  fprintf(ficgp,"+$%d",k+l+j);
+	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+      } /* nlstate */
+      fprintf(ficgp,"\n");
+    } /* end cpt state*/ 
+  } /* end covariate */  
   
   /* proba elementaires */
   for(i=1,jk=1; i <=nlstate; i++){
@@ -5137,7 +5182,7 @@ calandcheckages(int imx, int maxwav, dou
 	  }
 	  else if(agev[m][i] >*agemax){
 	    *agemax=agev[m][i];
-	    printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
+	    /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
 	  }
 	  /*agev[m][i]=anint[m][i]-annais[i];*/
 	  /*	 agev[m][i] = age[i]+2*m;*/
@@ -5299,6 +5344,9 @@ int main(int argc, char *argv[])
     i=strlen(pathr);
     if(pathr[i-1]=='\n')
       pathr[i-1]='\0';
+    i=strlen(pathr);
+    if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+      pathr[i-1]='\0';
    for (tok = pathr; tok != NULL; ){
       printf("Pathr |%s|\n",pathr);
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
@@ -5354,7 +5402,7 @@ int main(int argc, char *argv[])
  path=%s \n\
  optionfile=%s\n\
  optionfilext=%s\n\
- optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+ optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
 
   printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);
@@ -5370,10 +5418,11 @@ int main(int argc, char *argv[])
   /*---------arguments file --------*/
 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-    printf("Problem with optionfile %s\n",optionfile);
-    fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+    printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+    fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
     fflush(ficlog);
-    goto end;
+    /* goto end; */
+    exit(70); 
   }
 
 
@@ -6624,9 +6673,9 @@ Interval (in months) between two waves:
   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
 #endif
   if(!stat(plotcmd,&info)){
-    printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+    printf("Error or gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     if(!stat(getenv("GNUPLOTBIN"),&info)){
-      printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+      printf("Error or gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
     }else
       strcpy(pplotcmd,plotcmd);
 #ifdef UNIX
@@ -6643,17 +6692,26 @@ Interval (in months) between two waves:
   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
 
   if((outcmd=system(plotcmd)) != 0){
-    printf("\n Problem with gnuplot\n");
+    printf("gnuplot command might not be in your path: %s, err=%d\n", plotcmd, outcmd);
+    printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+    sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+    if((outcmd=system(plotcmd)) != 0)
+      printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
   }
-  printf(" Wait...");
+  printf(" Successul, please wait...");
   while (z[0] != 'q') {
     /* chdir(path); */
-    printf("\nType e to edit output files, g to graph again and q for exiting: ");
+    printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
     scanf("%s",z);
 /*     if (z[0] == 'c') system("./imach"); */
     if (z[0] == 'e') {
-      printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
-      system(optionfilehtm);
+#ifdef OSX
+      sprintf(pplotcmd, "open %s", optionfilehtm);
+#else
+      sprintf(pplotcmd, "%s", optionfilehtm);
+#endif
+      printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+      system(pplotcmd);
     }
     else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);