--- imach/src/imach.c	2003/06/05 15:17:23	1.79
+++ imach/src/imach.c	2003/06/25 15:30:29	1.91
@@ -1,4 +1,61 @@
-/* $Id: imach.c,v 1.79 2003/06/05 15:17:23 brouard Exp $
+/* $Id: imach.c,v 1.91 2003/06/25 15:30:29 brouard Exp $
+  $State: Exp $
+  $Log: imach.c,v $
+  Revision 1.91  2003/06/25 15:30:29  brouard
+  * imach.c (Repository): Duplicated warning errors corrected.
+  (Repository): Elapsed time after each iteration is now output. It
+  helps to forecast when convergence will be reached. Elapsed time
+  is stamped in powell.  We created a new html file for the graphs
+  concerning matrix of covariance. It has extension -cov.htm.
+
+  Revision 1.90  2003/06/24 12:34:15  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 1.89  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.
+
+  Revision 1.85  2003/06/17 13:12:43  brouard
+  * imach.c (Repository): Check when date of death was earlier that
+  current date of interview. It may happen when the death was just
+  prior to the death. In this case, dh was negative and likelihood
+  was wrong (infinity). We still send an "Error" but patch by
+  assuming that the date of death was just one stepm after the
+  interview.
+  (Repository): Because some people have very long ID (first column)
+  we changed int to long in num[] and we added a new lvector for
+  memory allocation. But we also truncated to 8 characters (left
+  truncation)
+  (Repository): No more line truncation errors.
+
+  Revision 1.84  2003/06/13 21:44:43  brouard
+  * imach.c (Repository): Replace "freqsummary" at a correct
+  place. It differs from routine "prevalence" which may be called
+  many times. Probs is memory consuming and must be used with
+  parcimony.
+  Version 0.95a3 (should output exactly the same maximization than 0.8a2)
+
+  Revision 1.83  2003/06/10 13:39:11  lievre
+  *** empty log message ***
+
+  Revision 1.82  2003/06/05 15:57:20  brouard
+  Add log in  imach.c and  fullversion number is now printed.
+
+*/
+/*
    Interpolated Markov Chain
 
   Short summary of the programme:
@@ -58,6 +115,7 @@
   read parameterfile
   read datafile
   concatwav
+  freqsummary
   if (mle >= 1)
     mlikeli
   print results files
@@ -91,12 +149,16 @@
 #include <stdlib.h>
 #include <unistd.h>
 
+#include <sys/time.h>
+#include <time.h>
+#include "timeval.h"
+
 #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
-#define FILENAMELENGTH 80
+#define FILENAMELENGTH 132
 /*#define DEBUG*/
-#define windows
+/*#define windows*/
 #define	GLOCK_ERROR_NOPATH		-1	/* empty path */
 #define	GLOCK_ERROR_GETCWD		-2	/* cannot get cwd */
 
@@ -111,21 +173,20 @@
 #define YEARM 12. /* Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
-#ifdef windows
-#define DIRSEPARATOR '\\'
-#define ODIRSEPARATOR '/'
-#else
+#ifdef unix
 #define DIRSEPARATOR '/'
 #define ODIRSEPARATOR '\\'
+#else
+#define DIRSEPARATOR '\\'
+#define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.79 2003/06/05 15:17:23 brouard Exp $ */
-/* $Log: imach.c,v $
- * Revision 1.79  2003/06/05 15:17:23  brouard
- * *** empty log message ***
- * */
-char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
-int erreur; /* Error number */
+/* $Id: imach.c,v 1.91 2003/06/25 15:30:29 brouard Exp $ */
+/* $State: Exp $ */
+
+char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.91 $ $Date: 2003/06/25 15:30:29 $"; 
+int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;
@@ -137,6 +198,8 @@ 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 */
@@ -147,9 +210,15 @@ double **oldm, **newm, **savm; /* Workin
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficlog, *ficrespow;
+int globpr; /* Global variable for printing or not */
+double fretone; /* Only one call to likelihood */
+long ipmx; /* Number of contributions */
+double sw; /* Sum of weights */
+char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+FILE *ficresilk;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE *ficresprobmorprev;
-FILE *fichtm; /* Html File */
+FILE *fichtm, *fichtmcov; /* Html File */
 FILE *ficreseij;
 char filerese[FILENAMELENGTH];
 FILE  *ficresvij;
@@ -159,14 +228,26 @@ 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];
 char popfile[FILENAMELENGTH];
 
-char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+
+struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+struct timezone tzp;
+extern int gettimeofday();
+struct tm tmg, tm, tmf, *gmtime(), *localtime();
+long time_value;
+extern long time();
+char strcurr[80], strfor[80];
 
 #define NR_END 1
 #define FREE_ARG char*
@@ -204,7 +285,8 @@ int estepm;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 
 int m,nb;
-int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+long *num;
+int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;
 double dateintmean=0;
@@ -244,11 +326,12 @@ static	int split( char *path, char *dirc
     dirc[l1-l2] = 0;			/* add zero */
   }
   l1 = strlen( dirc );			/* length of directory */
-#ifdef windows
+  /*#ifdef windows
   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 #else
   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 #endif
+  */
   ss = strrchr( name, '.' );		/* find last / */
   ss++;
   strcpy(ext,ss);			/* save extension */
@@ -262,10 +345,10 @@ 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++) {
@@ -332,31 +415,31 @@ void free_vector(double*v, int nl, int n
 }
 
 /************************ivector *******************************/
-char *cvector(long nl,long nh)
+int *ivector(long nl,long nh)
 {
-  char *v;
-  v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
-  if (!v) nrerror("allocation failure in cvector");
+  int *v;
+  v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+  if (!v) nrerror("allocation failure in ivector");
   return v-nl+NR_END;
 }
 
 /******************free ivector **************************/
-void free_cvector(char *v, long nl, long nh)
+void free_ivector(int *v, long nl, long nh)
 {
   free((FREE_ARG)(v+nl-NR_END));
 }
 
-/************************ivector *******************************/
-int *ivector(long nl,long nh)
+/************************lvector *******************************/
+long *lvector(long nl,long nh)
 {
-  int *v;
-  v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+  long *v;
+  v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   if (!v) nrerror("allocation failure in ivector");
   return v-nl+NR_END;
 }
 
-/******************free ivector **************************/
-void free_ivector(int *v, long nl, long nh)
+/******************free lvector **************************/
+void free_lvector(long *v, long nl, long nh)
 {
   free((FREE_ARG)(v+nl-NR_END));
 }
@@ -415,7 +498,7 @@ double **matrix(long nrl, long nrh, long
 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   return m;
-  /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
+  /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
    */
 }
 
@@ -645,6 +728,19 @@ void linmin(double p[], double xi[], int
   free_vector(pcom,1,n); 
 } 
 
+char *asc_diff_time(long time_sec, char ascdiff[])
+{
+  long sec_left, days, hours, minutes;
+  days = (time_sec) / (60*60*24);
+  sec_left = (time_sec) % (60*60*24);
+  hours = (sec_left) / (60*60) ;
+  sec_left = (sec_left) %(60*60);
+  minutes = (sec_left) /60;
+  sec_left = (sec_left) % (60);
+  sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
+  return ascdiff;
+}
+
 /*************** powell ************************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 	    double (*func)(double [])) 
@@ -655,6 +751,8 @@ void powell(double p[], double **xi, int
   double del,t,*pt,*ptt,*xit;
   double fp,fptt;
   double *xits;
+  int niterf, itmp;
+
   pt=vector(1,n); 
   ptt=vector(1,n); 
   xit=vector(1,n); 
@@ -665,9 +763,11 @@ void powell(double p[], double **xi, int
     fp=(*fret); 
     ibig=0; 
     del=0.0; 
-    printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
-    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
-    fprintf(ficrespow,"%d %.12f",*iter,*fret);
+    last_time=curr_time;
+    (void) gettimeofday(&curr_time,&tzp);
+    printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+    fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);
@@ -675,7 +775,28 @@ void powell(double p[], double **xi, int
     }
     printf("\n");
     fprintf(ficlog,"\n");
-    fprintf(ficrespow,"\n");
+    fprintf(ficrespow,"\n");fflush(ficrespow);
+    if(*iter <=3){
+      tm = *localtime(&curr_time.tv_sec);
+      asctime_r(&tm,strcurr);
+      forecast_time=curr_time;
+      itmp = strlen(strcurr);
+      if(strcurr[itmp-1]=='\n')
+	strcurr[itmp-1]='\0';
+      printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+      fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+      for(niterf=10;niterf<=30;niterf+=10){
+	forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+	tmf = *localtime(&forecast_time.tv_sec);
+	asctime_r(&tmf,strfor);
+/* 	strcpy(strfor,asctime(&tmf)); */
+	itmp = strlen(strfor);
+	if(strfor[itmp-1]=='\n')
+	strfor[itmp-1]='\0';
+	printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+	fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+      }
+    }
     for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret); 
@@ -1168,7 +1289,42 @@ double func( double *x)
 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       } /* end of wave */
     } /* end of individual */
-  }else{  /* ml=4 no inter-extrapolation */
+  }else if (mle==4){  /* ml=4 no inter-extrapolation */
+    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      for(mi=1; mi<= wav[i]-1; mi++){
+	for (ii=1;ii<=nlstate+ndeath;ii++)
+	  for (j=1;j<=nlstate+ndeath;j++){
+	    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+	    savm[ii][j]=(ii==j ? 1.0 : 0.0);
+	  }
+	for(d=0; d<dh[mi][i]; d++){
+	  newm=savm;
+	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  for (kk=1; kk<=cptcovage;kk++) {
+	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	  }
+	
+	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+	  savm=oldm;
+	  oldm=newm;
+	} /* end mult */
+      
+	s1=s[mw[mi][i]][i];
+	s2=s[mw[mi+1][i]][i];
+	if( s2 > nlstate){ 
+	  lli=log(out[s1][s2] - savm[s1][s2]);
+	}else{
+	  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+	}
+	ipmx +=1;
+	sw += weight[i];
+	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]); */
+      } /* end of wave */
+    } /* end of individual */
+  }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
@@ -1190,10 +1346,13 @@ double func( double *x)
 	  oldm=newm;
 	} /* end mult */
       
+	s1=s[mw[mi][i]][i];
+	s2=s[mw[mi+1][i]][i];
 	lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 	ipmx +=1;
 	sw += weight[i];
 	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]);*/
       } /* end of wave */
     } /* end of individual */
   } /* End of if */
@@ -1203,6 +1362,155 @@ double func( double *x)
   return -l;
 }
 
+/*************** 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 */
+  /* We are differentiating ll according to initial status */
+  /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+  /*for(i=1;i<imx;i++) 
+    printf(" %d\n",s[4][i]);
+  */
+  cov[1]=1.;
+
+  for(k=1; k<=nlstate; k++) ll[k]=0.;
+
+  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+    for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+    for(mi=1; mi<= wav[i]-1; mi++){
+      for (ii=1;ii<=nlstate+ndeath;ii++)
+	for (j=1;j<=nlstate+ndeath;j++){
+	  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+	  savm[ii][j]=(ii==j ? 1.0 : 0.0);
+	}
+      for(d=0; d<dh[mi][i]; d++){
+	newm=savm;
+	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	for (kk=1; kk<=cptcovage;kk++) {
+	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	}
+	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+	savm=oldm;
+	oldm=newm;
+      } /* end mult */
+      
+      s1=s[mw[mi][i]][i];
+      s2=s[mw[mi+1][i]][i];
+      bbh=(double)bh[mi][i]/(double)stepm; 
+      /* bias is positive if real duration
+       * is higher than the multiple of stepm and negative otherwise.
+       */
+      if( s2 > nlstate && (mle <5) ){  /* Jackson */
+	lli=log(out[s1][s2] - savm[s1][s2]);
+      } else if (mle==1){
+	lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+      } else if(mle==2){
+	lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+      } else if(mle==3){  /* exponential inter-extrapolation */
+	lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+      } else if (mle==4){  /* mle=4 no inter-extrapolation */
+	lli=log(out[s1][s2]); /* Original formula */
+      } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+	lli=log(out[s1][s2]); /* Original formula */
+      } /* End of if */
+      ipmx +=1;
+      sw += weight[i];
+      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,"%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,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[])
+{
+  /* Caution optionfilefiname is hidden */
+  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 *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
+     to check the exact contribution to the likelihood.
+     Plotting could be done.
+   */
+  int k;
+
+  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_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," -2*gipw/gsw*weight*ll[%d]++",k);
+    fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+  }
+
+  *fretone=(*funcone)(p);
+  if(*globpri !=0){
+    fclose(ficresilk);
+    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 ***************/
 
@@ -1211,6 +1519,7 @@ void mlikeli(FILE *ficres,double p[], in
   int i,j, iter;
   double **xi;
   double fret;
+  double fretone; /* Only one call to likelihood */
   char filerespow[FILENAMELENGTH];
   xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)
@@ -1228,6 +1537,7 @@ void mlikeli(FILE *ficres,double p[], in
     for(j=1;j<=nlstate+ndeath;j++)
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficrespow,"\n");
+
   powell(p,xi,npar,ftol,&iter,&fret,func);
 
   fclose(ficrespow);
@@ -1495,7 +1805,7 @@ void lubksb(double **a, int n, int *indx
 } 
 
 /************ Frequencies ********************/
-void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
+void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
 {  /* Some frequencies */
   
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
@@ -1549,7 +1859,7 @@ void  freqsummary(char fileres[], int ia
 	if (bool==1){
 	  for(m=firstpass; m<=lastpass; m++){
 	    k2=anint[m][i]+(mint[m][i]/12.);
-	    if ((k2>=dateprev1) && (k2<=dateprev2)) {
+	    /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 	      if(agev[m][i]==0) agev[m][i]=iagemax+1;
 	      if(agev[m][i]==1) agev[m][i]=iagemax+2;
 	      if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
@@ -1562,12 +1872,12 @@ void  freqsummary(char fileres[], int ia
 		dateintsum=dateintsum+k2;
 		k2cpt++;
 	      }
-	    }
+	      /*}*/
 	  }
 	}
       }
        
-      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 
       if  (cptcovn>0) {
 	fprintf(ficresp, "\n#********** Variable "); 
@@ -1628,7 +1938,7 @@ void  freqsummary(char fileres[], int ia
 	  if( i <= iagemax){
 	    if(pos>=1.e-5){
 	      fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-	      probs[i][jk][j1]= pp[jk]/pos;
+	      /*probs[i][jk][j1]= pp[jk]/pos;*/
 	      /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 	    }
 	    else
@@ -1661,7 +1971,7 @@ void  freqsummary(char fileres[], int ia
 }
 
 /************ Prevalence ********************/
-void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 {  
   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      in each health status at the date of interview (if between dateprev1 and dateprev2).
@@ -1779,12 +2089,13 @@ void  concatwav(int wav[], int **dh, int
 
     wav[i]=mi;
     if(mi==0){
+      nbwarn++;
       if(first==0){
-	printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
+	printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 	first=1;
       }
       if(first==1){
-	fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
+	fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       }
     } /* end mi==0 */
   } /* End individuals */
@@ -1796,15 +2107,22 @@ void  concatwav(int wav[], int **dh, int
       else{
 	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 	  if (agedc[i] < 2*AGESUP) {
-	  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
-	  if(j==0) j=1;  /* Survives at least one month after exam */
-	  k=k+1;
-	  if (j >= jmax) jmax=j;
-	  if (j <= jmin) jmin=j;
-	  sum=sum+j;
-	  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-	  /*	  printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-	  if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	    j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
+	    if(j==0) j=1;  /* Survives at least one month after exam */
+	    else if(j<0){
+	      nberr++;
+	      printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	      j=1; /* Temporary Dangerous patch */
+	      printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
+	      fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	      fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
+	    }
+	    k=k+1;
+	    if (j >= jmax) jmax=j;
+	    if (j <= jmin) jmin=j;
+	    sum=sum+j;
+	    /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+	    /*	  printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 	  }
 	}
 	else{
@@ -1815,13 +2133,17 @@ void  concatwav(int wav[], int **dh, int
 	  else if (j <= jmin)jmin=j;
 	  /*	    if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 	  /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-	  if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	  if(j<0){
+	    nberr++;
+	    printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	    fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	  }
 	  sum=sum+j;
 	}
 	jk= j/stepm;
 	jl= j -jk*stepm;
 	ju= j -(jk+1)*stepm;
-	if(mle <=1){ 
+	if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 	  if(jl==0){
 	    dh[mi][i]=jk;
 	    bh[mi][i]=0;
@@ -1846,8 +2168,8 @@ void  concatwav(int wav[], int **dh, int
 	    bh[mi][i]=ju; /* At least one step */
 	    /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
 	  }
-	}
-      } /* end if mle */
+	} /* end if mle */
+      }
     } /* end wave */
   }
   jmean=sum/k;
@@ -2148,23 +2470,10 @@ 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");
@@ -2376,14 +2685,15 @@ 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);
@@ -2393,9 +2703,9 @@ 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 ******************/
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
@@ -2551,28 +2861,23 @@ 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> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
+  fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
+  file %s<br>\n",optionfilehtmcov);
+  fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+and drawn. It helps understanding how is the covariance between two incidences.\
+ They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+  fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+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>\
+ Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+ and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
 
   cov[1]=1;
   tj=cptcoveff;
@@ -2754,10 +3059,14 @@ 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> 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(fichtmcov,"\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(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+		    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+		    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",\
@@ -2765,7 +3074,7 @@ void varprob(char optionfilefiname[], do
 			    mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
 		  }else{
 		    first=0;
-		    fprintf(fichtm," %d (%.3f),",(int) age, c12);
+		    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 		    fprintf(ficgp,"\nreplot %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",\
@@ -2774,7 +3083,7 @@ 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 */
@@ -2788,8 +3097,8 @@ void varprob(char optionfilefiname[], do
   fclose(ficresprob);
   fclose(ficresprobcov);
   fclose(ficresprobcor);
-  fclose(ficgp);
-  fclose(fichtm);
+  fflush(ficgp);
+  fflush(fichtmcov);
 }
 
 
@@ -2802,18 +3111,21 @@ 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);
-  }
-
-   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
- - 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);
+/*   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=\"%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=\"%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>");
 
@@ -2831,36 +3143,44 @@ 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); 
+     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: %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);
+	 fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
+<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);
+     fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+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>");
 
 
- 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);
+ 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=\"%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 */
@@ -2884,76 +3204,84 @@ fprintf(fichtm," <ul><li><b>Graphs</b></
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      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);  
+       fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
+interval) in state (%d): %s%d%d.png <br>\
+<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),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+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {
 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 	else fprintf(ficgp," \%%*lf (\%%*lf)");
@@ -2968,8 +3296,10 @@ m=pow(2,cptcoveff);
   for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(2*cpt-2);
-      fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
-      fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+      fprintf(ficgp,"set ter png small\n\
+set size 0.65,0.65\n\
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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);
@@ -2979,7 +3309,7 @@ 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);
 	
       } 
     }
@@ -2989,15 +3319,18 @@ 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 ++)
+      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);
@@ -3021,7 +3354,7 @@ 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
@@ -3068,7 +3401,7 @@ m=pow(2,cptcoveff);
        } /* end k2 */
      } /* end jk */
    } /* end ng */
-   fclose(ficgp); 
+   fflush(ficgp); 
 }  /* end gnuplot */
 
 
@@ -3131,7 +3464,7 @@ prevforecast(char fileres[], double anpr
   char fileresf[FILENAMELENGTH];
 
   agelim=AGESUP;
-  prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
  
   strcpy(fileresf,"f"); 
   strcat(fileresf,fileres);
@@ -3254,7 +3587,7 @@ populforecast(char fileres[], double anp
   agelim=AGESUP;
   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   
-  prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   
   
   strcpy(filerespop,"pop"); 
@@ -3396,7 +3729,138 @@ populforecast(char fileres[], double anp
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrespop);
+} /* End of popforecast */
+
+int fileappend(FILE *fichier, char *optionfich)
+{
+  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 *****************/
@@ -3406,6 +3870,10 @@ 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, 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;
 
@@ -3417,7 +3885,8 @@ int main(int argc, char *argv[])
   double ***mobaverage;
   int *indx;
   char line[MAXLINE], linepar[MAXLINE];
-  char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
+  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;
@@ -3449,17 +3918,42 @@ int main(int argc, char *argv[])
 
 
   char z[1]="c", occ;
-#include <sys/time.h>
-#include <time.h>
+
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+  char strstart[80], *strt, strtend[80];
+  char *stratrunc;
+  int lstra;
+
+  long total_usecs;
  
-  /* long total_usecs;
-     struct timeval start_time, end_time;
-  
-     gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+  /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+  (void) gettimeofday(&start_time,&tzp);
+  curr_time=start_time;
+  tm = *localtime(&start_time.tv_sec);
+  tmg = *gmtime(&start_time.tv_sec);
+  strcpy(strstart,asctime(&tm));
+
+/*  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; */
+/*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+/*   tmg.tm_hour=tmg.tm_hour + 1; */
+/*   tp.tv_sec = mktime(&tmg); */
+/*   strt=asctime(&tmg); */
+/*   printf("Time(after) =%s",strstart);  */
+/*  (void) time (&time_value);
+*  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+*  tm = *localtime(&time_value);
+*  strstart=asctime(&tm);
+*  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
+*/
+
+  nberr=0; /* Number of errors and warnings */
+  nbwarn=0;
   getcwd(pathcd, size);
 
-  printf("\n%s",version);
+  printf("\n%s\n%s",version,fullversion);
   if(argc <=1){
     printf("\nEnter the parameter file name: ");
     scanf("%s",pathtot);
@@ -3467,15 +3961,25 @@ int main(int argc, char *argv[])
   else{
     strcpy(pathtot,argv[1]);
   }
-  /*if(getcwd(pathcd, 80)!= 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,'\\');*/
 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-  printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",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 --------*/
 
@@ -3487,10 +3991,19 @@ int main(int argc, char *argv[])
     goto end;
   }
   fprintf(ficlog,"Log filename:%s\n",filelog);
-  fprintf(ficlog,"\n%s",version);
+  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",strstart);
+  fprintf(ficlog,"Localtime (at start): %s",strstart);
   fflush(ficlog);
+/*   (void) gettimeofday(&curr_time,&tzp); */
+/*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
 
   /* */
   strcpy(fileres,"r");
@@ -3502,37 +4015,49 @@ int main(int argc, char *argv[])
   if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile %s\n",optionfile);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+    fflush(ficlog);
     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);
     goto end;
   }
 
   /* Reads comments: lines beginning with '#' */
+  numlinepar=0;
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+  numlinepar++;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+  fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+  fflush(ficlog);
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
-  
+
    
   covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
@@ -3540,21 +4065,38 @@ 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){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
-  
+
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-  for(i=1; i <=nlstate; i++)
-    for(j=1; j <=nlstate+ndeath-1; j++){
+  for(i=1; i <=nlstate; i++){
+    j=0;
+    for(jj=1; jj <=nlstate+ndeath; jj++){
+      if(jj==i) continue;
+      j++;
       fscanf(ficpar,"%1d%1d",&i1,&j1);
+      if ((i1 != i) && (j1 != j)){
+	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+	exit(1);
+      }
       fprintf(ficparo,"%1d%1d",i1,j1);
       if(mle==1)
 	printf("%1d%1d",i,j);
@@ -3570,12 +4112,15 @@ int main(int argc, char *argv[])
 	fprintf(ficparo," %lf",param[i][j][k]);
       }
       fscanf(ficpar,"\n");
+      numlinepar++;
       if(mle==1)
 	printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
-  
+  }  
+  fflush(ficlog);
+
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
 
   p=param[1][1];
@@ -3584,8 +4129,10 @@ int main(int argc, char *argv[])
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
 
@@ -3594,18 +4141,28 @@ int main(int argc, char *argv[])
   for(i=1; i <=nlstate; i++){
     for(j=1; j <=nlstate+ndeath-1; j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);
+      if ((i1-i)*(j1-j)!=0){
+	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+	exit(1);
+      }
       printf("%1d%1d",i,j);
       fprintf(ficparo,"%1d%1d",i1,j1);
+      fprintf(ficlog,"%1d%1d",i1,j1);
       for(k=1; k<=ncovmodel;k++){
 	fscanf(ficpar,"%le",&delti3[i][j][k]);
 	printf(" %le",delti3[i][j][k]);
 	fprintf(ficparo," %le",delti3[i][j][k]);
+	fprintf(ficlog," %le",delti3[i][j][k]);
       }
       fscanf(ficpar,"\n");
+      numlinepar++;
       printf("\n");
       fprintf(ficparo,"\n");
+      fprintf(ficlog,"\n");
     }
   }
+  fflush(ficlog);
+
   delti=delti3[1][1];
 
 
@@ -3615,8 +4172,10 @@ int main(int argc, char *argv[])
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
   
@@ -3631,13 +4190,12 @@ int main(int argc, char *argv[])
       fscanf(ficpar," %le",&matcov[i][j]);
       if(mle==1){
 	printf(" %.5le",matcov[i][j]);
-	fprintf(ficlog," %.5le",matcov[i][j]);
       }
-      else
-	fprintf(ficlog," %.5le",matcov[i][j]);
+      fprintf(ficlog," %.5le",matcov[i][j]);
       fprintf(ficparo," %.5le",matcov[i][j]);
     }
     fscanf(ficpar,"\n");
+    numlinepar++;
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
@@ -3651,6 +4209,7 @@ int main(int argc, char *argv[])
     printf("\n");
   fprintf(ficlog,"\n");
 
+  fflush(ficlog);
 
   /*-------- Rewriting paramater file ----------*/
   strcpy(rfileres,"r");    /* "Rparameterfile */
@@ -3672,7 +4231,7 @@ int main(int argc, char *argv[])
   n= lastobs;
   severity = vector(1,maxwav);
   outcome=imatrix(1,maxwav+1,1,n);
-  num=ivector(1,n);
+  num=lvector(1,n);
   moisnais=vector(1,n);
   annais=vector(1,n);
   moisdc=vector(1,n);
@@ -3708,10 +4267,16 @@ int main(int argc, char *argv[])
       for (j=ncovcol;j>=1;j--){
 	cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
       } 
-      num[i]=atol(stra);
+      lstra=strlen(stra);
+      if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+	stratrunc = &(stra[lstra-9]);
+	num[i]=atol(stratrunc);
+      }
+      else
+	num[i]=atol(stra);
 	
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-	printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+	printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
 
       i=i+1;
     }
@@ -3727,7 +4292,7 @@ int main(int argc, char *argv[])
     }*/
    /*  for (i=1; i<=imx; i++){
      if (s[4][i]==9)  s[4][i]=-1; 
-     printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+     printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
   
  for (i=1; i<=imx; i++)
  
@@ -3830,14 +4395,16 @@ int main(int argc, char *argv[])
 	s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-	printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+	nberr++;
+	printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
 	s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-	printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
-	fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
-	s[m][i]=-1;
+	nberr++;
+	printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
+	fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
+	s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
       }
     }
   }
@@ -3853,8 +4420,9 @@ int main(int argc, char *argv[])
 	  /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
 	    else {
 	      if ((int)andc[i]!=9999){
-		printf("Warning negative age at death: %d line:%d\n",num[i],i);
-		fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
+		nbwarn++;
+		printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+		fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
 		agev[m][i]=-1;
 	      }
 	    }
@@ -3889,6 +4457,7 @@ int main(int argc, char *argv[])
   for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {
+	nberr++;
 	printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	
 	fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	
 	goto end;
@@ -3898,7 +4467,7 @@ int main(int argc, char *argv[])
 
   /*for (i=1; i<=imx; i++){
   for (m=firstpass; (m<lastpass); m++){
-     printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+     printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
 }
 
 }*/
@@ -3957,10 +4526,70 @@ int main(int argc, char *argv[])
      }
      scanf("%d",i);*/
     
+  /*------------ gnuplot -------------*/
+  strcpy(optionfilegnuplot,optionfilefiname);
+  strcat(optionfilegnuplot,".gp");
+  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+    printf("Problem with file %s",optionfilegnuplot);
+  }
+  else{
+    fprintf(ficgp,"\n# %s\n", version); 
+    fprintf(ficgp,"# %s\n", optionfilegnuplot); 
+    fprintf(ficgp,"set missing 'NaNq'\n");
+  }
+  /*  fclose(ficgp);*/
+  /*--------- index.htm --------*/
+
+  strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+  strcat(optionfilehtm,".htm");
+  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtm), exit(0);
+  }
+
+  strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+  strcat(optionfilehtmcov,"-cov.htm");
+  if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtmcov), exit(0);
+  }
+  else{
+  fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %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",\
+	  fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+  }
+
+  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\
+<hr  size=\"2\" color=\"#EC5E5E\">\
+ <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><br>\n\
+ - Date and time at start: %s</ul>\n",\
+	  fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+	  fileres,fileres,\
+	  filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+  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);
 
-    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+  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);
+  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 */
@@ -3971,6 +4600,18 @@ int main(int argc, char *argv[])
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
 
+  globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+  likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+  printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+  for (k=1; k<=npar;k++)
+    printf(" %d %8.5f",k,p[k]);
+  printf("\n");
+  globpr=1; /* to print the contributions */
+  likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+  printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+  for (k=1; k<=npar;k++)
+    printf(" %d %8.5f",k,p[k]);
+  printf("\n");
   if(mle>=1){ /* Could be 1 or 2 */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
   }
@@ -4002,7 +4643,7 @@ int main(int argc, char *argv[])
 	}
     }
   }
-  if(mle==1){
+  if(mle!=0){
     /* Computing hessian and covariance matrix */
     ftolhess=ftol; /* Usually correct */
     hesscov(matcov, p, npar, delti, ftolhess, func);
@@ -4133,53 +4774,24 @@ int main(int argc, char *argv[])
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
 
-  probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+  /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+  /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 
-  /*------------ gnuplot -------------*/
-  strcpy(optionfilegnuplot,optionfilefiname);
-  strcat(optionfilegnuplot,".gp");
-  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-    printf("Problem with file %s",optionfilegnuplot);
-  }
-  else{
-    fprintf(ficgp,"\n# %s\n", version); 
-    fprintf(ficgp,"# %s\n", optionfilegnuplot); 
-    fprintf(ficgp,"set missing 'NaNq'\n");
-  }
-  fclose(ficgp);
-  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
-  /*--------- index.htm --------*/
-
-  strcpy(optionfilehtm,optionfile);
-  strcat(optionfilehtm,".htm");
-  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-    printf("Problem with %s \n",optionfilehtm), exit(0);
-  }
+  replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+  printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
 
-  fprintf(fichtm,"<body> <font size=\"2\">%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
-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
-<hr  size=\"2\" color=\"#EC5E5E\">
- <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></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
-   fclose(fichtm);
-
-  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+  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);
   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
-  free_ivector(num,1,n);
+  free_lvector(num,1,n);
   free_vector(agedc,1,n);
   /*free_matrix(covar,0,NCOVMAX,1,n);*/
   /*free_matrix(covar,1,NCOVMAX,1,n);*/
@@ -4298,6 +4910,7 @@ Interval (in months) between two waves:
 
   fclose(ficrespij);
 
+  probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 
   /*---------- Forecasting ------------------*/
   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
@@ -4345,7 +4958,7 @@ Interval (in months) between two waves:
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
 
   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
-  prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
 ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
   */
@@ -4489,51 +5102,63 @@ 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){
-    printf("End of Imach with error or warning %d\n",erreur);
-    fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+  if((nberr >0) || (nbwarn>0)){
+    printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+    fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
   }else{
-   printf("End of Imach\n");
-   fprintf(ficlog,"End of Imach\n");
+    printf("End of Imach\n");
+    fprintf(ficlog,"End of Imach\n");
   }
   printf("See log file on %s\n",filelog);
-  fclose(ficlog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
-  
-  /* 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);*/
-  /*printf("Total time was %d uSec.\n", total_usecs);*/
+  (void) gettimeofday(&end_time,&tzp);
+  tm = *localtime(&end_time.tv_sec);
+  tmg = *gmtime(&end_time.tv_sec);
+  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\n",strstart, strtend); 
+  printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+
+  printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+  fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+  fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+  /*  printf("Total time was %d uSec.\n", total_usecs);*/
+/*   if(fileappend(fichtm,optionfilehtm)){ */
+  fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
+  fclose(fichtm);
+  fclose(fichtmcov);
+  fclose(ficgp);
+  fclose(ficlog);
   /*------ End -----------*/
 
-  end:
-#ifdef windows
-  /* chdir(pathcd);*/
-#endif 
- /*system("wgnuplot graph.plt");*/
- /*system("../gp37mgw/wgnuplot graph.plt");*/
- /*system("cd ../gp37mgw");*/
- /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
+  chdir(path);
   strcpy(plotcmd,GNUPLOTPROGRAM);
   strcat(plotcmd," ");
   strcat(plotcmd,optionfilegnuplot);
   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
-  system(plotcmd);
+  if((outcmd=system(plotcmd)) != 0){
+    printf(" Problem with gnuplot\n");
+  }
   printf(" Wait...");
-
- /*#ifdef windows*/
   while (z[0] != 'q') {
     /* chdir(path); */
-    printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+    printf("\nType e to edit output files, g to graph again and q for exiting: ");
     scanf("%s",z);
-    if (z[0] == 'c') system("./imach");
-    else if (z[0] == 'e') system(optionfilehtm);
+/*     if (z[0] == 'c') system("./imach"); */
+    if (z[0] == 'e') system(optionfilehtm);
     else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);
   }
-  /*#endif */
+  end:
+  while (z[0] != 'q') {
+    printf("\nType  q for exiting: ");
+    scanf("%s",z);
+  }
 }
 
 
+