--- imach096d/src/imach.c	2003/06/17 20:04:08	1.86
+++ imach096d/src/imach.c	2003/06/24 12:30:52	1.89
@@ -1,6 +1,17 @@
-/* $Id: imach.c,v 1.86 2003/06/17 20:04:08 brouard Exp $
+/* $Id: imach.c,v 1.89 2003/06/24 12:30:52 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.89  2003/06/24 12:30:52  brouard
+  (Module): Some bugs corrected for windows. Also, when
+  mle=-1 a template is output in file "or"mypar.txt with the design
+  of the covariance matrix to be input.
+
+  Revision 1.88  2003/06/23 17:54:56  brouard
+  * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
+
+  Revision 1.87  2003/06/18 12:26:01  brouard
+  Version 0.96
+
   Revision 1.86  2003/06/17 20:04:08  brouard
   (Module): Change position of html and gnuplot routines and added
   routine fileappend.
@@ -158,11 +169,11 @@
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.86 2003/06/17 20:04:08 brouard Exp $ */
+/* $Id: imach.c,v 1.89 2003/06/24 12:30:52 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.86 $ $Date: 2003/06/17 20:04:08 $"; 
+char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.89 $ $Date: 2003/06/24 12:30:52 $"; 
 int erreur; /* Error number */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
@@ -175,6 +186,8 @@ int popbased=0;
 int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */
 int jmin, jmax; /* min, max spacing between 2 waves */
+int gipmx, gsw; /* Global variables on the number of contributions 
+		   to the likelihood and the sum of weights (done by funcone)*/
 int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
@@ -203,8 +216,12 @@ char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+char tmpout[FILENAMELENGTH]; 
+char command[FILENAMELENGTH];
+int  outcmd=0;
 
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+char lfileres[FILENAMELENGTH];
 char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];
@@ -308,10 +325,10 @@ static	int split( char *path, char *dirc
 
 /******************************************/
 
-void replace(char *s, char*t)
+void replace_back_to_slash(char *s, char*t)
 {
   int i;
-  int lg=20;
+  int lg=0;
   i=0;
   lg=strlen(t);
   for(i=0; i<= lg; i++) {
@@ -1290,10 +1307,12 @@ double func( double *x)
 /*************** log-likelihood *************/
 double funcone( double *x)
 {
+  /* Same as likeli but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double **out;
   double lli; /* Individual log likelihood */
+  double llt;
   int s1, s2;
   double bbh, survp;
   /*extern weight */
@@ -1350,61 +1369,91 @@ double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){
-	fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
+	fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
  %10.6f %10.6f %10.6f ", \
 		num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 		2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-	for(k=1,l=0.; k<=nlstate; k++) 
-	  fprintf(ficresilk," %10.6f",ll[k]);
-	fprintf(ficresilk,"\n");
+	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+	  llt +=ll[k]*gipmx/gsw;
+	  fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+	}
+	fprintf(ficresilk," %10.6f\n", -llt);
       }
     } /* end of wave */
   } /* end of individual */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+  if(globpr==0){ /* First time we count the contributions and weights */
+    gipmx=ipmx;
+    gsw=sw;
+  }
   return -l;
 }
 
+char *subdirf(char fileres[])
+{
+  
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/"); /* Add to the right */
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+
+char *subdirf2(char fileres[], char *preop)
+{
+  
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/");
+  strcat(tmpout,preop);
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+char *subdirf3(char fileres[], char *preop, char *preop2)
+{
+  
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/");
+  strcat(tmpout,preop);
+  strcat(tmpout,preop2);
+  strcat(tmpout,fileres);
+  return tmpout;
+}
 
-void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 {
-  /* This routine should help understanding what is done with the selection of individuals/waves and
+  /* This routine should help understanding what is done with 
+     the selection of individuals/waves and
      to check the exact contribution to the likelihood.
      Plotting could be done.
    */
   int k;
-  if(globpr !=0){ /* Just counts and sums no printings */
+
+  if(*globpri !=0){ /* Just counts and sums, no printings */
     strcpy(fileresilk,"ilk"); 
     strcat(fileresilk,fileres);
     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     }
-    fprintf(ficresilk, "#individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state\n");
-    fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
+    fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+    fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     /* 	i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(k=1; k<=nlstate; k++) 
-      fprintf(ficresilk," ll[%d]",k);
-    fprintf(ficresilk,"\n");
+      fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+    fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }
 
   *fretone=(*funcone)(p);
-  if(globpr !=0){
+  if(*globpri !=0){
     fclose(ficresilk);
-    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
-      printf("Problem with html file: %s\n", optionfilehtm);
-      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
-      exit(0);
-    }
-    else{
-      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk);
-      fclose(fichtm);
-    }
-  }
+    fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+    fflush(fichtm); 
+  } 
   return;
 }
 
+
 /*********** Maximum Likelihood Estimation ***************/
 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
@@ -2360,23 +2409,10 @@ void varevsij(char optionfilefiname[], d
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   }  
   fprintf(ficresprobmorprev,"\n");
-  if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
-    printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
-    fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
-    exit(0);
-  }
-  else{
-    fprintf(ficgp,"\n# Routine varevsij");
-  }
-  if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
-    printf("Problem with html file: %s\n", optionfilehtm);
-    fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
-    exit(0);
-  }
-  else{
-    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-  }
+  fprintf(ficgp,"\n# Routine varevsij");
+  fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+  fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+/*   } */
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
@@ -2588,14 +2624,15 @@ void varevsij(char optionfilefiname[], d
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-  fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
-  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
-  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
-  fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
-  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
+  fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+  fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
 */
-  fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
+/*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+  fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
 
   free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);
@@ -2605,8 +2642,8 @@ void varevsij(char optionfilefiname[], d
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficresprobmorprev);
-  fclose(ficgp);
-  fclose(fichtm);
+  fflush(ficgp);
+  fflush(fichtm); 
 }  /* end varevsij */
 
 /************ Variance of prevlim ******************/
@@ -2763,28 +2800,13 @@ void varprob(char optionfilefiname[], do
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   first=1;
-  if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
-    printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
-    fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
-    exit(0);
-  }
-  else{
-    fprintf(ficgp,"\n# Routine varprob");
-  }
-  if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
-    printf("Problem with html file: %s\n", optionfilehtm);
-    fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
-    exit(0);
-  }
-  else{
-    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-    fprintf(fichtm,"\n");
-
-    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
-    fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-    fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
-
-  }
+  fprintf(ficgp,"\n# Routine varprob");
+  fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+  fprintf(fichtm,"\n");
+
+  fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
+  fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+  fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
 
   cov[1]=1;
   tj=cptcoveff;
@@ -2966,10 +2988,14 @@ void varprob(char optionfilefiname[], do
  		    fprintf(ficgp,"\nset parametric;unset label");
 		    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
 		    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
-		    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+ :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+		    fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 		    fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-		    fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+		    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
@@ -2986,7 +3012,7 @@ void varprob(char optionfilefiname[], do
 		  }/* if first */
 		} /* age mod 5 */
 	      } /* end loop age */
-	      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
+	      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 	      first=1;
 	    } /*l12 */
 	  } /* k12 */
@@ -3000,8 +3026,7 @@ void varprob(char optionfilefiname[], do
   fclose(ficresprob);
   fclose(ficresprobcov);
   fclose(ficresprobcor);
-  fclose(ficgp);
-  fclose(fichtm);
+  /*  fclose(ficgp);*/
 }
 
 
@@ -3014,18 +3039,21 @@ void printinghtml(char fileres[], char t
 		  double jprev2, double mprev2,double anprev2){
   int jj1, k1, i1, cpt;
   /*char optionfilehtm[FILENAMELENGTH];*/
-  if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
-    printf("Problem with %s \n",optionfilehtm), exit(0);
-    fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
-  }
+/*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
+/*     printf("Problem with %s \n",optionfilehtm), exit(0); */
+/*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
+/*   } */
 
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
- - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
- - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
- - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
+ - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
+ - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
+ - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
  - Life expectancies by age and initial health status (estepm=%2d months): \
-   <a href=\"e%s\">e%s</a> <br>\n</li>", \
-  jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+   <a href=\"%s\">%s</a> <br>\n</li>", \
+	   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
+	   stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
+	   subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
+	   estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
 
@@ -3043,24 +3071,24 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      /* Pij */
-     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
-<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
+<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
      /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
-<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
+<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Stable prevalence in each health state */
        for(cpt=1; cpt<nlstate;cpt++){
 	 fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
-<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }
      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
-<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
+<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-health expectancies in states (1) and (2): e%s%d.png<br>\
-<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+health expectancies in states (1) and (2): %s%d.png<br>\
+<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */
  }/* End k1 */
  fprintf(fichtm,"</ul>");
@@ -3068,12 +3096,19 @@ health expectancies in states (1) and (2
 
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
- - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
- - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
- - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
- - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
- - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
- - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+ - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
+ - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
+ - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
+ - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
+ - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
+ - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
+	 rfileres,rfileres,\
+	 subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
+	 subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
+	 subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
+	 estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
+	 subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
+	 subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
 
 /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
@@ -3098,75 +3133,83 @@ fprintf(fichtm," <ul><li><b>Graphs</b></
      }
      for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
-interval) in state (%d): v%s%d%d.png <br>\
-<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
+interval) in state (%d): %s%d%d.png <br>\
+<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"vr"),cpt,jj1,subdirf2(optionfilefiname,"vr"),cpt,jj1);  
      }
    } /* end i1 */
  }/* End k1 */
  fprintf(fichtm,"</ul>");
-fclose(fichtm);
+ fflush(fichtm);
 }
 
 /******************* Gnuplot file **************/
-void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 
+  char dirfileres[132],optfileres[132];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   int ng;
-  if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
-    printf("Problem with file %s",optionfilegnuplot);
-    fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
-  }
+/*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+/*     printf("Problem with file %s",optionfilegnuplot); */
+/*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+/*   } */
 
   /*#ifdef windows */
-    fprintf(ficgp,"cd \"%s\" \n",pathc);
+  fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */
-m=pow(2,cptcoveff);
-  
+  m=pow(2,cptcoveff);
+
+  strcpy(dirfileres,optionfilefiname);
+  strcpy(optfileres,"vpl");
  /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
-     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+     fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+     fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+     fprintf(ficgp,"set xlabel \"Age\" \n\
+set ylabel \"Probability\" \n\
+set ter png small\n\
+set size 0.65,0.65\n\
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
 
      for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");
      }
-     fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
+     fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      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 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
+     fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");
      }  
-     fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+     fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    }
   }
   /*2 eme*/
   
   for (k1=1; k1<= m ; k1 ++) { 
-    fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+    fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     
     for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;
-      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       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 ,");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {
 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 	else fprintf(ficgp," \%%*lf (\%%*lf)");
       }   
       fprintf(ficgp,"\" t\"\" w l 0,");
-      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+      fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {
 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 	else fprintf(ficgp," \%%*lf (\%%*lf)");
@@ -3181,8 +3224,10 @@ m=pow(2,cptcoveff);
   for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(2*cpt-2);
-      fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
-      fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+      fprintf(ficgp,"set ter png small\n\
+set size 0.65,0.65\n\
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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);
@@ -3192,7 +3237,7 @@ m=pow(2,cptcoveff);
 	
       */
       for (i=1; i< nlstate ; i ++) {
-	fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*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);
 	
       } 
     }
@@ -3202,15 +3247,18 @@ m=pow(2,cptcoveff);
   for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<=nlstate ; cpt ++) {
       k=3;
-      fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
-      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+      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\nset size 0.65,0.65\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,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+      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);
@@ -3234,7 +3282,7 @@ m=pow(2,cptcoveff);
 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      for(jk=1; jk <=m; jk++) {
-       fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
        if (ng==2)
 	 fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        else
@@ -3281,7 +3329,7 @@ m=pow(2,cptcoveff);
        } /* end k2 */
      } /* end jk */
    } /* end ng */
-   fclose(ficgp); 
+   fflush(ficgp); 
 }  /* end gnuplot */
 
 
@@ -3611,15 +3659,136 @@ populforecast(char fileres[], double anp
   fclose(ficrespop);
 } /* End of popforecast */
 
-int fileappend(FILE *fichier, char *optionfile)
+int fileappend(FILE *fichier, char *optionfich)
 {
-  if((fichier=fopen(optionfile,"a"))==NULL) {
-    printf("Problem with file: %s\n", optionfile);
-    fprintf(ficlog,"Problem with file: %s\n", optionfile);
-    return (1);
+  if((fichier=fopen(optionfich,"a"))==NULL) {
+    printf("Problem with file: %s\n", optionfich);
+    fprintf(ficlog,"Problem with file: %s\n", optionfich);
+    return (0);
   }
-
+  fflush(fichier);
+  return (1);
 }
+void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+{
+
+  char ca[32], cb[32], cc[32];
+  int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+  int numlinepar;
+
+  printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+  fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+  for(i=1; i <=nlstate; i++){
+    jj=0;
+    for(j=1; j <=nlstate+ndeath; j++){
+      if(j==i) continue;
+      jj++;
+      /*ca[0]= k+'a'-1;ca[1]='\0';*/
+      printf("%1d%1d",i,j);
+      fprintf(ficparo,"%1d%1d",i,j);
+      for(k=1; k<=ncovmodel;k++){
+	/* 	  printf(" %lf",param[i][j][k]); */
+	/* 	  fprintf(ficparo," %lf",param[i][j][k]); */
+	printf(" 0.");
+	fprintf(ficparo," 0.");
+      }
+      printf("\n");
+      fprintf(ficparo,"\n");
+    }
+  }
+  printf("# Scales (for hessian or gradient estimation)\n");
+  fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+  npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
+  for(i=1; i <=nlstate; i++){
+    jj=0;
+    for(j=1; j <=nlstate+ndeath; j++){
+      if(j==i) continue;
+      jj++;
+      fprintf(ficparo,"%1d%1d",i,j);
+      printf("%1d%1d",i,j);
+      fflush(stdout);
+      for(k=1; k<=ncovmodel;k++){
+	/* 	printf(" %le",delti3[i][j][k]); */
+	/* 	fprintf(ficparo," %le",delti3[i][j][k]); */
+	printf(" 0.");
+	fprintf(ficparo," 0.");
+      }
+      numlinepar++;
+      printf("\n");
+      fprintf(ficparo,"\n");
+    }
+  }
+  printf("# Covariance matrix\n");
+/* # 121 Var(a12)\n\ */
+/* # 122 Cov(b12,a12) Var(b12)\n\ */
+/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+  fflush(stdout);
+  fprintf(ficparo,"# Covariance matrix\n");
+  /* # 121 Var(a12)\n\ */
+  /* # 122 Cov(b12,a12) Var(b12)\n\ */
+  /* #   ...\n\ */
+  /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+  
+  for(itimes=1;itimes<=2;itimes++){
+    jj=0;
+    for(i=1; i <=nlstate; i++){
+      for(j=1; j <=nlstate+ndeath; j++){
+	if(j==i) continue;
+	for(k=1; k<=ncovmodel;k++){
+	  jj++;
+	  ca[0]= k+'a'-1;ca[1]='\0';
+	  if(itimes==1){
+	    printf("#%1d%1d%d",i,j,k);
+	    fprintf(ficparo,"#%1d%1d%d",i,j,k);
+	  }else{
+	    printf("%1d%1d%d",i,j,k);
+	    fprintf(ficparo,"%1d%1d%d",i,j,k);
+	    /* 	printf(" %.5le",matcov[i][j]); */
+	  }
+	  ll=0;
+	  for(li=1;li <=nlstate; li++){
+	    for(lj=1;lj <=nlstate+ndeath; lj++){
+	      if(lj==li) continue;
+	      for(lk=1;lk<=ncovmodel;lk++){
+		ll++;
+		if(ll<=jj){
+		  cb[0]= lk +'a'-1;cb[1]='\0';
+		  if(ll<jj){
+		    if(itimes==1){
+		      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+		      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+		    }else{
+		      printf(" 0.");
+		      fprintf(ficparo," 0.");
+		    }
+		  }else{
+		    if(itimes==1){
+		      printf(" Var(%s%1d%1d)",ca,i,j);
+		      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+		    }else{
+		      printf(" 0.");
+		      fprintf(ficparo," 0.");
+		    }
+		  }
+		}
+	      } /* end lk */
+	    } /* end lj */
+	  } /* end li */
+	  printf("\n");
+	  fprintf(ficparo,"\n");
+	  numlinepar++;
+	} /* end k*/
+      } /*end j */
+    } /* end i */
+  }
+
+} /* end of prwizard */
+
 /***********************************************/
 /**************** Main Program *****************/
 /***********************************************/
@@ -3628,8 +3797,10 @@ int main(int argc, char *argv[])
 {
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-  int jj;
+  int jj, imk;
   int numlinepar=0; /* Current linenumber of parameter file */
+  /*  FILE *fichtm; *//* Html File */
+  /* FILE *ficgp;*/ /*Gnuplot File */
   double agedeb, agefin,hf;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 
@@ -3641,7 +3812,8 @@ int main(int argc, char *argv[])
   double ***mobaverage;
   int *indx;
   char line[MAXLINE], linepar[MAXLINE];
-  char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
+  char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+  char pathr[MAXLINE]; 
   int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;
@@ -3675,7 +3847,7 @@ int main(int argc, char *argv[])
   char z[1]="c", occ;
 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-  char *strt, *strtend;
+  char strstart[80], *strt, strtend[80];
   char *stratrunc;
   int lstra;
 
@@ -3691,9 +3863,9 @@ int main(int argc, char *argv[])
   (void) gettimeofday(&start_time,&tzp);
   tm = *localtime(&start_time.tv_sec);
   tmg = *gmtime(&start_time.tv_sec);
-  strt=asctime(&tm);
+  strcpy(strstart,asctime(&tm));
 
-/*  printf("Localtime (at start)=%s",strt); */
+/*  printf("Localtime (at start)=%s",strstart); */
 /*  tp.tv_sec = tp.tv_sec +86400; */
 /*  tm = *localtime(&start_time.tv_sec); */
 /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
@@ -3701,12 +3873,12 @@ int main(int argc, char *argv[])
 /*   tmg.tm_hour=tmg.tm_hour + 1; */
 /*   tp.tv_sec = mktime(&tmg); */
 /*   strt=asctime(&tmg); */
-/*   printf("Time(after) =%s",strt);  */
+/*   printf("Time(after) =%s",strstart);  */
 /*  (void) time (&time_value);
 *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
 *  tm = *localtime(&time_value);
-*  strt=asctime(&tm);
-*  printf("tim_value=%d,asctime=%s\n",time_value,strt); 
+*  strstart=asctime(&tm);
+*  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
 */
 
   getcwd(pathcd, size);
@@ -3719,7 +3891,7 @@ int main(int argc, char *argv[])
   else{
     strcpy(pathtot,argv[1]);
   }
-  /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/
+  /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   /* cutv(path,optionfile,pathtot,'\\');*/
@@ -3727,7 +3899,17 @@ int main(int argc, char *argv[])
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);
-  replace(pathc,path);
+  strcpy(command,"mkdir ");
+  strcat(command,optionfilefiname);
+  if((outcmd=system(command)) != 0){
+    printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+    /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+    /* fclose(ficlog); */
+/*     exit(1); */
+  }
+/*   if((imk=mkdir(optionfilefiname))<0){ */
+/*     perror("mkdir"); */
+/*   } */
 
   /*-------- arguments in the command line --------*/
 
@@ -3741,10 +3923,14 @@ int main(int argc, char *argv[])
   fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s\n%s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: ");
-  fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  fprintf(ficlog,"pathtot=%s\n\
+ path=%s \n\
+ optionfile=%s\n\
+ optionfilext=%s\n\
+ optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
 
-  printf("Localtime (at start)=%s",strt);
-  fprintf(ficlog,"Localtime (at start)=%s",strt);
+  printf("Localtime (at start):%s",strstart);
+  fprintf(ficlog,"Localtime (at start): %s",strstart);
   fflush(ficlog);
 
   /* */
@@ -3761,9 +3947,11 @@ int main(int argc, char *argv[])
     goto end;
   }
 
+
+
   strcpy(filereso,"o");
   strcat(filereso,fileres);
-  if((ficparo=fopen(filereso,"w"))==NULL) {
+  if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
     fflush(ficlog);
@@ -3805,7 +3993,15 @@ int main(int argc, char *argv[])
 
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-  
+ 
+  if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+    prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+    printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+    fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+    fclose (ficparo);
+    fclose (ficlog);
+    exit(0);
+  }
   /* Read guess parameters */
   /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){
@@ -4265,16 +4461,16 @@ int main(int argc, char *argv[])
     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
     fprintf(ficgp,"set missing 'NaNq'\n");
   }
-  fclose(ficgp);
+  /*  fclose(ficgp);*/
   /*--------- index.htm --------*/
 
-  strcpy(optionfilehtm,optionfile);
+  strcpy(optionfilehtm,optionfilefiname);
   strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm), exit(0);
   }
 
-  fprintf(fichtm,"<body> <font size=\"2\">%s <br> %s</font> \
+  fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
 \n\
@@ -4282,25 +4478,31 @@ Title=%s <br>Datafile=%s Firstpass=%d La
  <ul><li><h4>Parameter files</h4>\n\
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
- - Gnuplot file name: <a href=\"%s\">%s</a>\n\
+ - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
  - Date and time at start: %s</ul>\n",\
-	  version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
+	  fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
 	  model,fileres,fileres,\
-	  filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
-  fclose(fichtm);
-
+	  filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+  /*fclose(fichtm);*/
+  fflush(fichtm);
+
+  strcpy(pathr,path);
+  strcat(pathr,optionfilefiname);
+  chdir(optionfilefiname); /* Move to directory named optionfile */
+  strcpy(lfileres,fileres);
+  strcat(lfileres,"/");
+  strcat(lfileres,optionfilefiname);
+  
   /* Calculates basic frequencies. Computes observed prevalence at single age
      and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
 
-  if(fileappend(fichtm, optionfilehtm)){
-    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+  fprintf(fichtm,"\n");
+  fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-	imx,agemin,agemax,jmin,jmax,jmean);
-    fclose(fichtm);
-  }
-    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+	  imx,agemin,agemax,jmin,jmax,jmean);
+  pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
@@ -4488,14 +4690,15 @@ Interval (in months) between two waves:
   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 
-  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
+  replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+  printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
 
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
 	       model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
 	       jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
  
   /*------------ free_vector  -------------*/
-  chdir(path);
+  /*  chdir(path); */
  
   free_ivector(wav,1,imx);
   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
@@ -4812,8 +5015,8 @@ ageminpar, agemax, s[lastpass][imx], age
   free_ivector(Tage,1,15);
   free_ivector(Tcode,1,100);
 
-  /*  fclose(fichtm);*/
-  /*  fclose(ficgp);*/ /* ALready done */
+  fflush(fichtm);
+  fflush(ficgp);
   
 
   if(erreur >0){
@@ -4829,24 +5032,25 @@ ageminpar, agemax, s[lastpass][imx], age
   (void) gettimeofday(&end_time,&tzp);
   tm = *localtime(&end_time.tv_sec);
   tmg = *gmtime(&end_time.tv_sec);
-  strtend=asctime(&tm);
-  printf("Localtime at start %s and at end=%s",strt, strtend); 
-  fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); 
+  strcpy(strtend,asctime(&tm));
+  printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
+  fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend); 
   /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
 
   printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
   fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
   /*  printf("Total time was %d uSec.\n", total_usecs);*/
-  if(fileappend(fichtm,optionfilehtm)){
-    fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
-    fclose(fichtm);
-  }
+/*   if(fileappend(fichtm,optionfilehtm)){ */
+  fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
+  fclose(fichtm);
+  fclose(ficgp);
   /*------ End -----------*/
 
   end:
 #ifdef windows
   /* chdir(pathcd);*/
 #endif 
+  chdir(path);
  /*system("wgnuplot graph.plt");*/
  /*system("../gp37mgw/wgnuplot graph.plt");*/
  /*system("cd ../gp37mgw");*/
@@ -4872,3 +5076,4 @@ ageminpar, agemax, s[lastpass][imx], age
 }
 
 
+