--- imach/src/imach.c	2003/06/24 12:34:15	1.90
+++ imach/src/imach.c	2006/01/19 16:20:37	1.107
@@ -1,6 +1,93 @@
-/* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $
+/* $Id: imach.c,v 1.107 2006/01/19 16:20:37 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.107  2006/01/19 16:20:37  brouard
+  Test existence of gnuplot in imach path
+
+  Revision 1.106  2006/01/19 13:24:36  brouard
+  Some cleaning and links added in html output
+
+  Revision 1.105  2006/01/05 20:23:19  lievre
+  *** empty log message ***
+
+  Revision 1.104  2005/09/30 16:11:43  lievre
+  (Module): sump fixed, loop imx fixed, and simplifications.
+  (Module): If the status is missing at the last wave but we know
+  that the person is alive, then we can code his/her status as -2
+  (instead of missing=-1 in earlier versions) and his/her
+  contributions to the likelihood is 1 - Prob of dying from last
+  health status (= 1-p13= p11+p12 in the easiest case of somebody in
+  the healthy state at last known wave). Version is 0.98
+
+  Revision 1.103  2005/09/30 15:54:49  lievre
+  (Module): sump fixed, loop imx fixed, and simplifications.
+
+  Revision 1.102  2004/09/15 17:31:30  brouard
+  Add the possibility to read data file including tab characters.
+
+  Revision 1.101  2004/09/15 10:38:38  brouard
+  Fix on curr_time
+
+  Revision 1.100  2004/07/12 18:29:06  brouard
+  Add version for Mac OS X. Just define UNIX in Makefile
+
+  Revision 1.99  2004/06/05 08:57:40  brouard
+  *** empty log message ***
+
+  Revision 1.98  2004/05/16 15:05:56  brouard
+  New version 0.97 . First attempt to estimate force of mortality
+  directly from the data i.e. without the need of knowing the health
+  state at each age, but using a Gompertz model: log u =a + b*age .
+  This is the basic analysis of mortality and should be done before any
+  other analysis, in order to test if the mortality estimated from the
+  cross-longitudinal survey is different from the mortality estimated
+  from other sources like vital statistic data.
+
+  The same imach parameter file can be used but the option for mle should be -3.
+
+  Agnès, who wrote this part of the code, tried to keep most of the
+  former routines in order to include the new code within the former code.
+
+  The output is very simple: only an estimate of the intercept and of
+  the slope with 95% confident intervals.
+
+  Current limitations:
+  A) Even if you enter covariates, i.e. with the
+  model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
+  B) There is no computation of Life Expectancy nor Life Table.
+
+  Revision 1.97  2004/02/20 13:25:42  lievre
+  Version 0.96d. Population forecasting command line is (temporarily)
+  suppressed.
+
+  Revision 1.96  2003/07/15 15:38:55  brouard
+  * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
+  rewritten within the same printf. Workaround: many printfs.
+
+  Revision 1.95  2003/07/08 07:54:34  brouard
+  * imach.c (Repository):
+  (Repository): Using imachwizard code to output a more meaningful covariance
+  matrix (cov(a12,c31) instead of numbers.
+
+  Revision 1.94  2003/06/27 13:00:02  brouard
+  Just cleaning
+
+  Revision 1.93  2003/06/25 16:33:55  brouard
+  (Module): On windows (cygwin) function asctime_r doesn't
+  exist so I changed back to asctime which exists.
+  (Module): Version 0.96b
+
+  Revision 1.92  2003/06/25 16:30:45  brouard
+  (Module): On windows (cygwin) function asctime_r doesn't
+  exist so I changed back to asctime which exists.
+
+  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
@@ -140,12 +227,21 @@
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 #include <unistd.h>
 
-#include <sys/time.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+extern int errno;
+
+/* #include <sys/time.h> */
 #include <time.h>
 #include "timeval.h"
 
+/* #include <libintl.h> */
+/* #define _(String) gettext (String) */
+
 #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
@@ -166,20 +262,23 @@
 #define YEARM 12. /* Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
-#ifdef unix
+#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+#ifdef UNIX
 #define DIRSEPARATOR '/'
+#define CHARSEPARATOR "/"
 #define ODIRSEPARATOR '\\'
 #else
 #define DIRSEPARATOR '\\'
+#define CHARSEPARATOR "\\"
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $ */
+/* $Id: imach.c,v 1.107 2006/01/19 16:20:37 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.90 $ $Date: 2003/06/24 12:34:15 $"; 
-int erreur; /* Error number */
+char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.107 $ $Date: 2006/01/19 16:20:37 $"; 
+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;
@@ -207,11 +306,12 @@ int globpr; /* Global variable for print
 double fretone; /* Only one call to likelihood */
 long ipmx; /* Number of contributions */
 double sw; /* Sum of weights */
+char filerespow[FILENAMELENGTH];
 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;
@@ -221,18 +321,26 @@ char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
-char tmpout[FILENAMELENGTH]; 
+char tmpout[FILENAMELENGTH],  tmpout2[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*
@@ -261,9 +369,10 @@ static double maxarg1,maxarg2;
 static double sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
+int agegomp= AGEGOMP;
 
 int imx; 
-int stepm;
+int stepm=1;
 /* Stepm, step in month: minimum step interpolation*/
 
 int estepm;
@@ -271,15 +380,17 @@ int estepm;
 
 int m,nb;
 long *num;
-int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;
+double *ageexmed,*agecens;
 double dateintmean=0;
 
 double *weight;
 int **s; /* Status */
 double *agedc, **covar, idx;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+double *lsurv, *lpop, *tpop;
 
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 double ftolhess; /* Tolerance for computing hessian */
@@ -287,13 +398,17 @@ double ftolhess; /* Tolerance for comput
 /**************** split *************************/
 static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {
+  /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+     the name of the file (name), its extension only (ext) and its first part of the name (finame)
+  */ 
   char	*ss;				/* pointer */
   int	l1, l2;				/* length counters */
 
   l1 = strlen(path );			/* length of path */
   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   ss= strrchr( path, DIRSEPARATOR );		/* find last / */
-  if ( ss == NULL ) {			/* no directory, so use current */
+  if ( ss == NULL ) {			/* no directory, so determine current directory */
+    strcpy( name, path );		/* we got the fullname name because no directory */
     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /* get current working directory */
@@ -301,7 +416,8 @@ static	int split( char *path, char *dirc
     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       return( GLOCK_ERROR_GETCWD );
     }
-    strcpy( name, path );		/* we've got it */
+    /* got dirc from getcwd*/
+    printf(" DIRC = %s \n",dirc);
   } else {				/* strip direcotry from path */
     ss++;				/* after this, the filename */
     l2 = strlen( ss );			/* length of filename */
@@ -309,21 +425,25 @@ static	int split( char *path, char *dirc
     strcpy( name, ss );		/* save file name */
     strncpy( dirc, path, l1 - l2 );	/* now the directory */
     dirc[l1-l2] = 0;			/* add zero */
+    printf(" DIRC2 = %s \n",dirc);
   }
+  /* We add a separator at the end of dirc if not exists */
   l1 = strlen( dirc );			/* length of directory */
-  /*#ifdef windows
-  if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
-#else
-  if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
-#endif
-  */
+  if( dirc[l1-1] != DIRSEPARATOR ){
+    dirc[l1] =  DIRSEPARATOR;
+    dirc[l1+1] = 0; 
+    printf(" DIRC3 = %s \n",dirc);
+  }
   ss = strrchr( name, '.' );		/* find last / */
-  ss++;
-  strcpy(ext,ss);			/* save extension */
-  l1= strlen( name);
-  l2= strlen(ss)+1;
-  strncpy( finame, name, l1-l2);
-  finame[l1-l2]= 0;
+  if (ss >0){
+    ss++;
+    strcpy(ext,ss);			/* save extension */
+    l1= strlen( name);
+    l2= strlen(ss)+1;
+    strncpy( finame, name, l1-l2);
+    finame[l1-l2]= 0;
+  }
+
   return( 0 );				/* we're done */
 }
 
@@ -356,8 +476,8 @@ int nbocc(char *s, char occ)
 
 void cutv(char *u,char *v, char*t, char occ)
 {
-  /* cuts string t into u and v where u is ended by char occ excluding it
-     and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+  /* cuts string t into u and v where u ends before first occurence of char 'occ' 
+     and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
      gives u="abcedf" and v="ghi2j" */
   int i,lg,j,p=0;
   i=0;
@@ -538,6 +658,41 @@ void free_ma3x(double ***m, long nrl, lo
   free((FREE_ARG)(m+nrl-NR_END));
 }
 
+/*************** function subdirf ***********/
+char *subdirf(char fileres[])
+{
+  /* Caution optionfilefiname is hidden */
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/"); /* Add to the right */
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+
+/*************** function subdirf2 ***********/
+char *subdirf2(char fileres[], char *preop)
+{
+  
+  /* Caution optionfilefiname is hidden */
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/");
+  strcat(tmpout,preop);
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+
+/*************** function subdirf3 ***********/
+char *subdirf3(char fileres[], char *preop, char *preop2)
+{
+  
+  /* Caution optionfilefiname is hidden */
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/");
+  strcat(tmpout,preop);
+  strcat(tmpout,preop2);
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+
 /***************** f1dim *************************/
 extern int ncom; 
 extern double *pcom,*xicom;
@@ -713,6 +868,19 @@ 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 [])) 
@@ -723,6 +891,8 @@ 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); 
@@ -733,17 +903,42 @@ 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);
-    for (i=1;i<=n;i++) {
+    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]);
       fprintf(ficrespow," %.12lf", p[i]);
     }
     printf("\n");
     fprintf(ficlog,"\n");
-    fprintf(ficrespow,"\n");
+    fprintf(ficrespow,"\n");fflush(ficrespow);
+    if(*iter <=3){
+      tm = *localtime(&curr_time.tv_sec);
+      strcpy(strcurr,asctime(&tm));
+/*       asctime_r(&tm,strcurr); */
+      forecast_time=curr_time; 
+      itmp = strlen(strcurr);
+      if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+	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 i.e.\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 i.e.\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); 
@@ -906,57 +1101,57 @@ double **pmij(double **ps, double *cov,
   int i,j,j1, nc, ii, jj;
 
     for(i=1; i<= nlstate; i++){
-    for(j=1; j<i;j++){
-      for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-	/*s2 += param[i][j][nc]*cov[nc];*/
-	s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-	/*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
-      }
-      ps[i][j]=s2;
-      /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
-    }
-    for(j=i+1; j<=nlstate+ndeath;j++){
-      for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-	s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-	/*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
+      for(j=1; j<i;j++){
+	for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+	  /*s2 += param[i][j][nc]*cov[nc];*/
+	  s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+/* 	 printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+	}
+	ps[i][j]=s2;
+/* 	printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+      }
+      for(j=i+1; j<=nlstate+ndeath;j++){
+	for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+	  s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+/* 	  printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+	}
+	ps[i][j]=s2;
       }
-      ps[i][j]=s2;
     }
-  }
     /*ps[3][2]=1;*/
-
-  for(i=1; i<= nlstate; i++){
-     s1=0;
-    for(j=1; j<i; j++)
-      s1+=exp(ps[i][j]);
-    for(j=i+1; j<=nlstate+ndeath; j++)
-      s1+=exp(ps[i][j]);
-    ps[i][i]=1./(s1+1.);
-    for(j=1; j<i; j++)
-      ps[i][j]= exp(ps[i][j])*ps[i][i];
-    for(j=i+1; j<=nlstate+ndeath; j++)
-      ps[i][j]= exp(ps[i][j])*ps[i][i];
-    /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-  } /* end i */
-
-  for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-    for(jj=1; jj<= nlstate+ndeath; jj++){
-      ps[ii][jj]=0;
-      ps[ii][ii]=1;
+    
+    for(i=1; i<= nlstate; i++){
+      s1=0;
+      for(j=1; j<i; j++)
+	s1+=exp(ps[i][j]);
+      for(j=i+1; j<=nlstate+ndeath; j++)
+	s1+=exp(ps[i][j]);
+      ps[i][i]=1./(s1+1.);
+      for(j=1; j<i; j++)
+	ps[i][j]= exp(ps[i][j])*ps[i][i];
+      for(j=i+1; j<=nlstate+ndeath; j++)
+	ps[i][j]= exp(ps[i][j])*ps[i][i];
+      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+    } /* end i */
+    
+    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+      for(jj=1; jj<= nlstate+ndeath; jj++){
+	ps[ii][jj]=0;
+	ps[ii][ii]=1;
+      }
     }
-  }
-
+    
 
-  /*   for(ii=1; ii<= nlstate+ndeath; ii++){
-    for(jj=1; jj<= nlstate+ndeath; jj++){
-     printf("%lf ",ps[ii][jj]);
-   }
-    printf("\n ");
-    }
-    printf("\n ");printf("%lf ",cov[2]);*/
-/*
-  for(i=1; i<= npar; i++) printf("%f ",x[i]);
-  goto end;*/
+/*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+/* 	 for(jj=1; jj<= nlstate+ndeath; jj++){ */
+/* 	   printf("ddd %lf ",ps[ii][jj]); */
+/* 	 } */
+/* 	 printf("\n "); */
+/*        } */
+/*        printf("\n ");printf("%lf ",cov[2]); */
+       /*
+      for(i=1; i<= npar; i++) printf("%f ",x[i]);
+      goto end;*/
     return ps;
 }
 
@@ -1080,14 +1275,14 @@ double func( double *x)
 	} /* end mult */
       
 	/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-	/* But now since version 0.9 we anticipate for bias and large stepm.
+	/* But now since version 0.9 we anticipate for bias at large stepm.
 	 * If stepm is larger than one month (smallest stepm) and if the exact delay 
 	 * (in months) between two waves is not a multiple of stepm, we rounded to 
 	 * the nearest (and in case of equal distance, to the lowest) interval but now
 	 * we keep into memory the bias bh[mi][i] and also the previous matrix product
-	 * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
+	 * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 	 * probability in order to take into account the bias as a fraction of the way
-	 * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
+	 * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 	 * -stepm/2 to stepm/2 .
 	 * For stepm=1 the results are the same as for previous versions of Imach.
 	 * For stepm > 1 the results are less biased than in previous versions. 
@@ -1095,15 +1290,16 @@ double func( double *x)
 	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
+	/* bias bh is positive if real duration
 	 * is higher than the multiple of stepm and negative otherwise.
 	 */
 	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 	if( s2 > nlstate){ 
-	  /* i.e. if s2 is a death state and if the date of death is known then the contribution
-	     to the likelihood is the probability to die between last step unit time and current 
-	     step unit time, which is also the differences between probability to die before dh 
-	     and probability to die before dh-stepm . 
+	  /* i.e. if s2 is a death state and if the date of death is known 
+	     then the contribution to the likelihood is the probability to 
+	     die between last step unit time and current  step unit time, 
+	     which is also equal to probability to die before dh 
+	     minus probability to die before dh-stepm . 
 	     In version up to 0.92 likelihood was computed
 	as if date of death was unknown. Death was treated as any other
 	health state: the date of the interview describes the actual state
@@ -1123,7 +1319,28 @@ double func( double *x)
 	lower mortality.
 	  */
 	  lli=log(out[s1][s2] - savm[s1][s2]);
-	}else{
+
+
+	} else if  (s2==-2) {
+	  for (j=1,survp=0. ; j<=nlstate; j++) 
+	    survp += out[s1][j];
+	  lli= survp;
+	}
+	
+	else if  (s2==-4) {
+	  for (j=3,survp=0. ; j<=nlstate; j++) 
+	    survp += out[s1][j];
+	  lli= survp;
+	}
+	
+	else if  (s2==-5) {
+	  for (j=1,survp=0. ; j<=2; j++) 
+	    survp += out[s1][j];
+	  lli= survp;
+	}
+
+
+	else{
 	  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 	  /*  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 */
 	} 
@@ -1156,31 +1373,10 @@ double func( double *x)
 	  oldm=newm;
 	} /* end mult */
       
-	/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-	/* But now since version 0.9 we anticipate for bias and large stepm.
-	 * If stepm is larger than one month (smallest stepm) and if the exact delay 
-	 * (in months) between two waves is not a multiple of stepm, we rounded to 
-	 * the nearest (and in case of equal distance, to the lowest) interval but now
-	 * we keep into memory the bias bh[mi][i] and also the previous matrix product
-	 * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-	 * probability in order to take into account the bias as a fraction of the way
-	 * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-	 * -stepm/2 to stepm/2 .
-	 * For stepm=1 the results are the same as for previous versions of Imach.
-	 * For stepm > 1 the results are less biased than in previous versions. 
-	 */
 	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.
-	 */
 	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 */
-	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-	/*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
-	/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-	/*if(lli ==000.0)*/
-	/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 	ipmx +=1;
 	sw += weight[i];
 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
@@ -1207,30 +1403,10 @@ double func( double *x)
 	  oldm=newm;
 	} /* end mult */
       
-	/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-	/* But now since version 0.9 we anticipate for bias and large stepm.
-	 * If stepm is larger than one month (smallest stepm) and if the exact delay 
-	 * (in months) between two waves is not a multiple of stepm, we rounded to 
-	 * the nearest (and in case of equal distance, to the lowest) interval but now
-	 * we keep into memory the bias bh[mi][i] and also the previous matrix product
-	 * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-	 * probability in order to take into account the bias as a fraction of the way
-	 * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-	 * -stepm/2 to stepm/2 .
-	 * For stepm=1 the results are the same as for previous versions of Imach.
-	 * For stepm > 1 the results are less biased than in previous versions. 
-	 */
 	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.
-	 */
-	/* 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 */
 	lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-	/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-	/*if(lli ==000.0)*/
-	/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 	ipmx +=1;
 	sw += weight[i];
 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
@@ -1396,35 +1572,8 @@ double funcone( double *x)
   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;
-}
 
+/*************** function likelione ***********/
 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 
@@ -1467,7 +1616,7 @@ void mlikeli(FILE *ficres,double p[], in
   double **xi;
   double fret;
   double fretone; /* Only one call to likelihood */
-  char filerespow[FILENAMELENGTH];
+  /*  char filerespow[FILENAMELENGTH];*/
   xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++)
@@ -1502,11 +1651,11 @@ void hesscov(double **matcov, double p[]
   int i, j,jk;
   int *indx;
 
-  double hessii(double p[], double delta, int theta, double delti[]);
-  double hessij(double p[], double delti[], int i, int j);
+  double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+  double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;
-
+  double gompertz(double p[]);
   hess=matrix(1,npar,1,npar);
 
   printf("\nCalculation of the hessian matrix. Wait...\n");
@@ -1514,9 +1663,11 @@ void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);
     fprintf(ficlog,"%d",i);fflush(ficlog);
-    hess[i][i]=hessii(p,ftolhess,i,delti);
-    /*printf(" %f ",p[i]);*/
-    /*printf(" %lf ",hess[i][i]);*/
+   
+     hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+    
+    /*  printf(" %f ",p[i]);
+	printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }
   
   for (i=1;i<=npar;i++) {
@@ -1524,7 +1675,8 @@ void hesscov(double **matcov, double p[]
       if (j>i) { 
 	printf(".%d%d",i,j);fflush(stdout);
 	fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-	hess[i][j]=hessij(p,delti,i,j);
+	hess[i][j]=hessij(p,delti,i,j,func,npar);
+	
 	hess[j][i]=hess[i][j];    
 	/*printf(" %lf ",hess[i][j]);*/
       }
@@ -1595,14 +1747,14 @@ void hesscov(double **matcov, double p[]
 }
 
 /*************** hessian matrix ****************/
-double hessii( double x[], double delta, int theta, double delti[])
+double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {
   int i;
   int l=1, lmax=20;
   double k1,k2;
   double p2[NPARMAX+1];
   double res;
-  double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+  double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;
   int k=0,kmax=10;
   double l1;
@@ -1642,7 +1794,7 @@ double hessii( double x[], double delta,
   
 }
 
-double hessij( double x[], double delti[], int thetai,int thetaj)
+double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {
   int i;
   int l=1, l1, lmax=20;
@@ -1752,7 +1904,7 @@ 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)
+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, char strstart[])
 {  /* Some frequencies */
   
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
@@ -1772,7 +1924,7 @@ void  freqsummary(char fileres[], int ia
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);
   }
-  freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
+  freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   j1=0;
   
   j=cptcoveff;
@@ -1785,8 +1937,8 @@ void  freqsummary(char fileres[], int ia
       j1++;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 	scanf("%d", i);*/
-      for (i=-1; i<=nlstate+ndeath; i++)  
-	for (jk=-1; jk<=nlstate+ndeath; jk++)  
+      for (i=-5; i<=nlstate+ndeath; i++)  
+	for (jk=-5; jk<=nlstate+ndeath; jk++)  
 	  for(m=iagemin; m <= iagemax+3; m++)
 	    freq[i][jk][m]=0;
 
@@ -1825,7 +1977,7 @@ void  freqsummary(char fileres[], int ia
       }
        
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-
+fprintf(ficresp, "#Local time at start: %s", strstart);
       if  (cptcovn>0) {
 	fprintf(ficresp, "\n#********** Variable "); 
 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
@@ -1911,7 +2063,7 @@ void  freqsummary(char fileres[], int ia
   dateintmean=dateintsum/k2cpt; 
  
   fclose(ficresp);
-  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
+  free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /* End of Freq */
@@ -2020,7 +2172,7 @@ void  concatwav(int wav[], int **dh, int
     mi=0;
     m=firstpass;
     while(s[m][i] <= nlstate){
-      if(s[m][i]>=1)
+      if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 	mw[++mi][i]=m;
       if(m >=lastpass)
 	break;
@@ -2036,6 +2188,7 @@ void  concatwav(int wav[], int **dh, int
 
     wav[i]=mi;
     if(mi==0){
+      nbwarn++;
       if(first==0){
 	printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 	first=1;
@@ -2056,11 +2209,12 @@ void  concatwav(int wav[], int **dh, int
 	    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; /* Careful 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);
-	      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]);
-	      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);
+	      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. 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. You MUST fix the contradiction between dates.\n",stepm);
 	    }
 	    k=k+1;
 	    if (j >= jmax) jmax=j;
@@ -2072,13 +2226,15 @@ void  concatwav(int wav[], int **dh, int
 	}
 	else{
 	  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-	  /*	  printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+/* 	  if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
+
 	  k=k+1;
 	  if (j >= jmax) jmax=j;
 	  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){
+	    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]);
 	  }
@@ -2164,7 +2320,7 @@ void tricode(int *Tvar, int **nbcode, in
  for (k=0; k< maxncov; k++) Ndum[k]=0;
 
  for (i=1; i<=ncovmodel-2; i++) { 
-   /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+   /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    ij=Tvar[i];
    Ndum[ij]++;
  }
@@ -2182,7 +2338,7 @@ void tricode(int *Tvar, int **nbcode, in
 
 /*********** Health Expectancies ****************/
 
-void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
 
 {
   /* Health expectancies */
@@ -2200,6 +2356,7 @@ void evsij(char fileres[], double ***eij
   dnewm=matrix(1,nlstate*nlstate,1,npar);
   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   
+  fprintf(ficreseij,"# Local time at start: %s", strstart);
   fprintf(ficreseij,"# Health expectancies\n");
   fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++)
@@ -2255,7 +2412,7 @@ void evsij(char fileres[], double ***eij
 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 
-    /* Computing Variances of health expectancies */
+    /* Computing  Variances of health expectancies */
 
      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){ 
@@ -2354,7 +2511,7 @@ void evsij(char fileres[], double ***eij
 }
 
 /************ Variance ******************/
-void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
+void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
 {
   /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
@@ -2405,7 +2562,9 @@ void varevsij(char optionfilefiname[], d
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+ 
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+  fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
@@ -2415,11 +2574,12 @@ void varevsij(char optionfilefiname[], d
   }  
   fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n# Routine varevsij");
+  /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   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, "#Local time at start: %s", strstart);
   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");
   fprintf(ficresvij,"# Age");
   for(i=1; i<=nlstate;i++)
@@ -2652,7 +2812,7 @@ void varevsij(char optionfilefiname[], d
 }  /* 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)
+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, char strstart[])
 {
   /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
@@ -2665,7 +2825,7 @@ void varprevlim(char fileres[], double *
   double **gradg, **trgradg;
   double age,agelim;
   int theta;
-   
+  fprintf(ficresvpl, "#Local time at start: %s", strstart); 
   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   fprintf(ficresvpl,"# Age");
   for(i=1; i<=nlstate;i++)
@@ -2735,7 +2895,7 @@ void varprevlim(char fileres[], double *
 }
 
 /************ Variance of one-step probabilities  ******************/
-void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
+void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {
   int i, j=0,  i1, k1, l1, t, tj;
   int k2, l2, j1,  z1;
@@ -2780,11 +2940,13 @@ void varprob(char optionfilefiname[], do
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-  
+  fprintf(ficresprob, "#Local time at start: %s", strstart);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");
+  fprintf(ficresprobcov, "#Local time at start: %s", strstart);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");
+  fprintf(ficresprobcor, "#Local time at start: %s", strstart);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcov,"# Age");
 
@@ -2809,9 +2971,19 @@ void varprob(char optionfilefiname[], do
   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(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+  fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs 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;
@@ -2833,9 +3005,9 @@ void varprob(char optionfilefiname[], do
 	fprintf(ficgp, "**********\n#\n");
 	
 	
-	fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
+	fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-	fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+	fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 	
 	fprintf(ficresprobcor, "\n#********** Variable ");    
 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
@@ -2993,13 +3165,13 @@ 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>\
+		    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(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(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);
@@ -3008,7 +3180,7 @@ 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",\
@@ -3031,7 +3203,8 @@ void varprob(char optionfilefiname[], do
   fclose(ficresprob);
   fclose(ficresprobcov);
   fclose(ficresprobcor);
-  /*  fclose(ficgp);*/
+  fflush(ficgp);
+  fflush(fichtmcov);
 }
 
 
@@ -3043,21 +3216,22 @@ void printinghtml(char fileres[], char t
 		  double jprev1, double mprev1,double anprev1, \
 		  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=\"%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 \
+   fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+   <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+</ul>");
+   fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></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 ",
+	   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   fprintf(fichtm,"\
+ - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+	   stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   fprintf(fichtm,"\
+ - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+	   subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+   fprintf(fichtm,"\
  - 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"),\
+   <a href=\"%s\">%s</a> <br>\n</li>",
 	   estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
@@ -3091,28 +3265,32 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
         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): %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=\"%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\
+ fprintf(fichtm,"\
+\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+
+ fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+	 subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+ fprintf(fichtm,"\
+ - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+	 subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+
+ fprintf(fichtm,"\
+ - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+	 subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+ fprintf(fichtm,"\
+ - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+	 estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+ fprintf(fichtm,"\
+ - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
+	 subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+ fprintf(fichtm,"\
  - 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 */
@@ -3121,7 +3299,8 @@ health expectancies in states (1) and (2
 /* 	<br>",fileres,fileres,fileres,fileres); */
 /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+ fflush(fichtm);
+ fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 
  m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
@@ -3137,10 +3316,13 @@ 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): %s%d%d.png <br>\
+       fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+prevalence (with 95%% confidence 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);  
      }
+     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>");
@@ -3674,9 +3856,14 @@ int fileappend(FILE *fichier, char *opti
   fflush(fichier);
   return (1);
 }
+
+
+/**************** function prwizard **********************/
 void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
 {
 
+  /* Wizard to print covariance matrix template */
+
   char ca[32], cb[32], cc[32];
   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
   int numlinepar;
@@ -3790,9 +3977,93 @@ void prwizard(int ncovmodel, int nlstate
 	} /* end k*/
       } /*end j */
     } /* end i */
-  }
+  } /* end itimes */
 
 } /* end of prwizard */
+/******************* Gompertz Likelihood ******************************/
+double gompertz(double x[])
+{ 
+  double A,B,L=0.0,sump=0.,num=0.;
+  int i,n=0; /* n is the size of the sample */
+  for (i=0;i<=imx-1 ; i++) {
+    sump=sump+weight[i];
+    /*    sump=sump+1;*/
+    num=num+1;
+  }
+ 
+ 
+  /* for (i=0; i<=imx; i++) 
+     if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+
+  for (i=1;i<=imx ; i++)
+    {
+      if (cens[i]==1 & wav[i]>1)
+	A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+      
+      if (cens[i]==0 & wav[i]>1)
+	A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+	     +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
+      
+      if (wav[i]>1 & agecens[i]>15) {
+	L=L+A*weight[i];
+	/* 	printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+      }
+    }
+
+ /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+ 
+  return -2*L*num/sump;
+}
+
+/******************* Printing html file ***********/
+void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+		  int lastpass, int stepm, int weightopt, char model[],\
+		  int imx,  double p[],double **matcov,double agemortsup){
+  int i,k;
+
+  fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+  fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+  for (i=1;i<=2;i++) 
+    fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+  fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+  fprintf(fichtm,"</ul>");
+
+fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+
+ fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+
+ for (k=agegomp;k<(agemortsup-2);k++) 
+   fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+
+ 
+  fflush(fichtm);
+}
+
+/******************* Gnuplot file **************/
+void printinggnuplotmort(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;
+
+
+  /*#ifdef windows */
+  fprintf(ficgp,"cd \"%s\" \n",pathc);
+    /*#endif */
+
+
+  strcpy(dirfileres,optionfilefiname);
+  strcpy(optfileres,"vpl");
+  fprintf(ficgp,"set out \"graphmort.png\"\n "); 
+  fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
+  fprintf(ficgp, "set ter png small\n set log y\n"); 
+  fprintf(ficgp, "set size 0.65,0.65\n");
+  fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+
+} 
+
+
+
 
 /***********************************************/
 /**************** Main Program *****************/
@@ -3802,10 +4073,15 @@ 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 jj, ll, li, lj, lk, imk;
   int numlinepar=0; /* Current linenumber of parameter file */
+  int itimes;
+  int NDIM=2;
+
+  char ca[32], cb[32], cc[32];
   /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */
+  struct stat info;
   double agedeb, agefin,hf;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 
@@ -3818,7 +4094,7 @@ int main(int argc, char *argv[])
   int *indx;
   char line[MAXLINE], linepar[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-  char pathr[MAXLINE]; 
+  char pathr[MAXLINE], pathimach[MAXLINE]; 
   int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;
@@ -3828,6 +4104,8 @@ int main(int argc, char *argv[])
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;
   int hstepm, nhstepm;
+  int agemortsup;
+  float  sumlpop=0.;
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
 
@@ -3845,9 +4123,9 @@ int main(int argc, char *argv[])
   double *epj, vepp;
   double kk1, kk2;
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-
+  double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4];
-
+  int *dcwave;
 
   char z[1]="c", occ;
 
@@ -3857,15 +4135,16 @@ int main(int argc, char *argv[])
   int lstra;
 
   long total_usecs;
-  struct timeval start_time, end_time, curr_time;
-  struct timezone tzp;
-  extern int gettimeofday();
-  struct tm tmg, tm, *gmtime(), *localtime();
-  long time_value;
-  extern long time();
  
+/*   setlocale (LC_ALL, ""); */
+/*   bindtextdomain (PACKAGE, LOCALEDIR); */
+/*   textdomain (PACKAGE); */
+/*   setlocale (LC_CTYPE, ""); */
+/*   setlocale (LC_MESSAGES, ""); */
+
   /*   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));
@@ -3886,6 +4165,8 @@ int main(int argc, char *argv[])
 *  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\n%s",version,fullversion);
@@ -3901,8 +4182,14 @@ int main(int argc, char *argv[])
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   /* cutv(path,optionfile,pathtot,'\\');*/
 
+  /* Split argv[0], imach program to get pathimach */
+  printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+  split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+  printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ /*   strcpy(pathimach,argv[0]); */
+  /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-  printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);
   strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);
@@ -3927,16 +4214,18 @@ 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\n\
+  fprintf(ficlog,"\nEnter the parameter file name: \n");
+  fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
  path=%s \n\
  optionfile=%s\n\
  optionfilext=%s\n\
- optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
 
-  printf("Localtime (at start):%s",strstart);
-  fprintf(ficlog,"Localtime (at start): %s",strstart);
+  printf("Local time (at start):%s",strstart);
+  fprintf(ficlog,"Local time (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");
@@ -3998,163 +4287,174 @@ int main(int argc, char *argv[])
 
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
- 
+  npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+
+  delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+  delti=delti3[1][1];
+  /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   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);
+    free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     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);
+  else if(mle==-3) {
+    prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+    printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+    fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+    matcov=matrix(1,npar,1,npar);
   }
-  ungetc(c,ficpar);
-
-  param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-  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);
-      fprintf(ficlog,"%1d%1d",i,j);
-      for(k=1; k<=ncovmodel;k++){
-	fscanf(ficpar," %lf",&param[i][j][k]);
-	if(mle==1){
-	  printf(" %lf",param[i][j][k]);
-	  fprintf(ficlog," %lf",param[i][j][k]);
-	}
-	else
-	  fprintf(ficlog," %lf",param[i][j][k]);
-	fprintf(ficparo," %lf",param[i][j][k]);
-      }
-      fscanf(ficpar,"\n");
+  else{
+    /* Read guess parameters */
+    /* Reads comments: lines beginning with '#' */
+    while((c=getc(ficpar))=='#' && c!= EOF){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
       numlinepar++;
-      if(mle==1)
-	printf("\n");
-      fprintf(ficlog,"\n");
-      fprintf(ficparo,"\n");
+      puts(line);
+      fputs(line,ficparo);
+      fputs(line,ficlog);
     }
-  }  
-  fflush(ficlog);
-
-  npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-
-  p=param[1][1];
-  
-  /* 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);
-
-  delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-  /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
-  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]);
+    
+    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+    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);
+	fprintf(ficlog,"%1d%1d",i,j);
+	for(k=1; k<=ncovmodel;k++){
+	  fscanf(ficpar," %lf",&param[i][j][k]);
+	  if(mle==1){
+	    printf(" %lf",param[i][j][k]);
+	    fprintf(ficlog," %lf",param[i][j][k]);
+	  }
+	  else
+	    fprintf(ficlog," %lf",param[i][j][k]);
+	  fprintf(ficparo," %lf",param[i][j][k]);
+	}
+	fscanf(ficpar,"\n");
+	numlinepar++;
+	if(mle==1)
+	  printf("\n");
+	fprintf(ficlog,"\n");
+	fprintf(ficparo,"\n");
       }
-      fscanf(ficpar,"\n");
+    }  
+    fflush(ficlog);
+
+
+    p=param[1][1];
+    
+    /* Reads comments: lines beginning with '#' */
+    while((c=getc(ficpar))=='#' && c!= EOF){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
       numlinepar++;
-      printf("\n");
-      fprintf(ficparo,"\n");
-      fprintf(ficlog,"\n");
+      puts(line);
+      fputs(line,ficparo);
+      fputs(line,ficlog);
     }
-  }
-  fflush(ficlog);
+    ungetc(c,ficpar);
 
-  delti=delti3[1][1];
+    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];
 
-  /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+
+    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
   
-  /* Reads comments: lines beginning with '#' */
-  while((c=getc(ficpar))=='#' && c!= EOF){
+    /* 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);
-    fgets(line, MAXLINE, ficpar);
-    numlinepar++;
-    puts(line);
-    fputs(line,ficparo);
-    fputs(line,ficlog);
-  }
-  ungetc(c,ficpar);
   
-  matcov=matrix(1,npar,1,npar);
-  for(i=1; i <=npar; i++){
-    fscanf(ficpar,"%s",&str);
-    if(mle==1)
-      printf("%s",str);
-    fprintf(ficlog,"%s",str);
-    fprintf(ficparo,"%s",str);
-    for(j=1; j <=i; j++){
-      fscanf(ficpar," %le",&matcov[i][j]);
-      if(mle==1){
-	printf(" %.5le",matcov[i][j]);
+    matcov=matrix(1,npar,1,npar);
+    for(i=1; i <=npar; i++){
+      fscanf(ficpar,"%s",&str);
+      if(mle==1)
+	printf("%s",str);
+      fprintf(ficlog,"%s",str);
+      fprintf(ficparo,"%s",str);
+      for(j=1; j <=i; j++){
+	fscanf(ficpar," %le",&matcov[i][j]);
+	if(mle==1){
+	  printf(" %.5le",matcov[i][j]);
+	}
+	fprintf(ficlog," %.5le",matcov[i][j]);
+	fprintf(ficparo," %.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");
+      fprintf(ficparo,"\n");
     }
-    fscanf(ficpar,"\n");
-    numlinepar++;
+    for(i=1; i <=npar; i++)
+      for(j=i+1;j<=npar;j++)
+	matcov[i][j]=matcov[j][i];
+    
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
-    fprintf(ficparo,"\n");
-  }
-  for(i=1; i <=npar; i++)
-    for(j=i+1;j<=npar;j++)
-      matcov[i][j]=matcov[j][i];
-   
-  if(mle==1)
-    printf("\n");
-  fprintf(ficlog,"\n");
-
-  fflush(ficlog);
-
-  /*-------- Rewriting paramater file ----------*/
-  strcpy(rfileres,"r");    /* "Rparameterfile */
-  strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-  strcat(rfileres,".");    /* */
-  strcat(rfileres,optionfilext);    /* Other files have txt extension */
-  if((ficres =fopen(rfileres,"w"))==NULL) {
-    printf("Problem writing new parameter file: %s\n", fileres);goto end;
-    fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-  }
-  fprintf(ficres,"#%s\n",version);
     
+    fflush(ficlog);
+    
+    /*-------- Rewriting parameter file ----------*/
+    strcpy(rfileres,"r");    /* "Rparameterfile */
+    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+    strcat(rfileres,".");    /* */
+    strcat(rfileres,optionfilext);    /* Other files have txt extension */
+    if((ficres =fopen(rfileres,"w"))==NULL) {
+      printf("Problem writing new parameter file: %s\n", fileres);goto end;
+      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+    }
+    fprintf(ficres,"#%s\n",version);
+  }    /* End of mle != -3 */
+
   /*-------- data file ----------*/
   if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem with datafile: %s\n", datafile);goto end;
@@ -4182,7 +4482,10 @@ int main(int argc, char *argv[])
   i=1;
   while (fgets(line, MAXLINE, fic) != NULL)    {
     if ((i >= firstobs) && (i <=lastobs)) {
-	
+      for(j=0; line[j] != '\n';j++){  /* Untabifies line */
+	if(line[j] == '\t')
+	  line[j] = ' ';
+      }
       for (j=maxwav;j>=1;j--){
 	cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
 	strcpy(line,stra);
@@ -4227,12 +4530,12 @@ int main(int argc, char *argv[])
      if (s[4][i]==9)  s[4][i]=-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]));}*/
   
- for (i=1; i<=imx; i++)
+  /* for (i=1; i<=imx; i++) */
  
    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
      else weight[i]=1;*/
 
-  /* Calculation of the number of parameter from char model*/
+  /* Calculation of the number of parameters from char model */
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
   Tprod=ivector(1,15); 
   Tvaraff=ivector(1,15); 
@@ -4328,11 +4631,13 @@ int main(int argc, char *argv[])
 	s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+	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){
+	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 */
@@ -4343,7 +4648,7 @@ int main(int argc, char *argv[])
   for (i=1; i<=imx; i++)  {
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
     for(m=firstpass; (m<= lastpass); m++){
-      if(s[m][i] >0){
+      if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
 	if (s[m][i] >= nlstate+1) {
 	  if(agedc[i]>0)
 	    if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
@@ -4351,6 +4656,7 @@ int main(int argc, char *argv[])
 	  /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
 	    else {
 	      if ((int)andc[i]!=9999){
+		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;
@@ -4387,6 +4693,7 @@ 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;
@@ -4401,9 +4708,11 @@ int main(int argc, char *argv[])
 
 }*/
 
+
   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
 
+  agegomp=(int)agemin;
   free_vector(severity,1,maxwav);
   free_imatrix(outcome,1,maxwav+1,1,n);
   free_vector(moisnais,1,n);
@@ -4457,7 +4766,10 @@ int main(int argc, char *argv[])
     
   /*------------ gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);
+  if(mle==-3)
+    strcat(optionfilegnuplot,"-mort");
   strcat(optionfilegnuplot,".gp");
+
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);
   }
@@ -4469,12 +4781,26 @@ int main(int argc, char *argv[])
   /*  fclose(ficgp);*/
   /*--------- index.htm --------*/
 
-  strcpy(optionfilehtm,optionfilefiname);
+  strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+  if(mle==-3)
+    strcat(optionfilehtm,"-mort");
   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\
@@ -4485,22 +4811,18 @@ Title=%s <br>Datafile=%s Firstpass=%d La
  - 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,\
+	  fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+	  fileres,fileres,\
 	  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);
+  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
 
   fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
@@ -4519,33 +4841,149 @@ Interval (in months) between two waves:
   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);
+  if (mle==-3){
+    ximort=matrix(1,NDIM,1,NDIM);
+    cens=ivector(1,n);
+    ageexmed=vector(1,n);
+    agecens=vector(1,n);
+    dcwave=ivector(1,n);
+ 
+    for (i=1; i<=imx; i++){
+      dcwave[i]=-1;
+      for (j=1; j<=lastpass; j++)
+	if (s[j][i]>nlstate) {
+	  dcwave[i]=j;
+	  /*	printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+	  break;
+	}
+    }
+
+    for (i=1; i<=imx; i++) {
+      if (wav[i]>0){
+	ageexmed[i]=agev[mw[1][i]][i];
+	j=wav[i];agecens[i]=1.; 
+	if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
+	cens[i]=1;
+	
+	if (ageexmed[i]<1) cens[i]=-1;
+	if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
+      }
+      else cens[i]=-1;
+    }
+    
+    for (i=1;i<=NDIM;i++) {
+      for (j=1;j<=NDIM;j++)
+	ximort[i][j]=(i == j ? 1.0 : 0.0);
+    }
+
+    p[1]=0.1; p[2]=0.1;
+    /*printf("%lf %lf", p[1], p[2]);*/
+    
+    
+  printf("Powell\n");  fprintf(ficlog,"Powell\n");
+  strcpy(filerespow,"pow-mort"); 
+  strcat(filerespow,fileres);
+  if((ficrespow=fopen(filerespow,"w"))==NULL) {
+    printf("Problem with resultfile: %s\n", filerespow);
+    fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }
+  fprintf(ficrespow,"# Powell\n# iter -2*LL");
+  /*  for (i=1;i<=nlstate;i++)
+    for(j=1;j<=nlstate+ndeath;j++)
+      if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+  */
+  fprintf(ficrespow,"\n");
+
+    powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+    fclose(ficrespow);
     
-  /*--------- results files --------------*/
-  fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
-  
+    hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
 
-  jk=1;
-  fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-  printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-  fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-  for(i=1,jk=1; i <=nlstate; i++){
-    for(k=1; k <=(nlstate+ndeath); k++){
-      if (k != i) 
-	{
+    for(i=1; i <=NDIM; i++)
+      for(j=i+1;j<=NDIM;j++)
+	matcov[i][j]=matcov[j][i];
+    
+    printf("\nCovariance matrix\n ");
+    for(i=1; i <=NDIM; i++) {
+      for(j=1;j<=NDIM;j++){ 
+	printf("%f ",matcov[i][j]);
+      }
+      printf("\n ");
+    }
+    
+    printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+    for (i=1;i<=NDIM;i++) 
+      printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+
+lsurv=vector(1,AGESUP);
+    lpop=vector(1,AGESUP);
+    tpop=vector(1,AGESUP);
+    lsurv[agegomp]=100000;
+   
+     for (k=agegomp;k<=AGESUP;k++) {
+      agemortsup=k;
+      if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+    }
+   
+      for (k=agegomp;k<agemortsup;k++)
+      lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+
+    for (k=agegomp;k<agemortsup;k++){
+      lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+      sumlpop=sumlpop+lpop[k];
+    }
+
+ tpop[agegomp]=sumlpop;
+    for (k=agegomp;k<(agemortsup-3);k++){
+      /*  tpop[k+1]=2;*/
+      tpop[k+1]=tpop[k]-lpop[k];
+       }
+   
+   
+       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+    for (k=agegomp;k<(agemortsup-2);k++) 
+      printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+
+
+    replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+    printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+    
+    printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+		     stepm, weightopt,\
+		     model,imx,p,matcov,agemortsup);
+
+    free_vector(lsurv,1,AGESUP);
+    free_vector(lpop,1,AGESUP);
+    free_vector(tpop,1,AGESUP);
+  } /* Endof if mle==-3 */
+
+  else{ /* For mle >=1 */
+  
+    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);
+    }
+    
+    /*--------- results files --------------*/
+    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+    
+    
+    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+    for(i=1,jk=1; i <=nlstate; i++){
+      for(k=1; k <=(nlstate+ndeath); k++){
+	if (k != i) {
 	  printf("%d%d ",i,k);
 	  fprintf(ficlog,"%d%d ",i,k);
 	  fprintf(ficres,"%1d%1d ",i,k);
@@ -4559,525 +4997,595 @@ Interval (in months) between two waves:
 	  fprintf(ficlog,"\n");
 	  fprintf(ficres,"\n");
 	}
+      }
     }
-  }
-  if(mle!=0){
-    /* Computing hessian and covariance matrix */
-    ftolhess=ftol; /* Usually correct */
-    hesscov(matcov, p, npar, delti, ftolhess, func);
-  }
-  fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-  printf("# Scales (for hessian or gradient estimation)\n");
-  fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-  for(i=1,jk=1; i <=nlstate; i++){
-    for(j=1; j <=nlstate+ndeath; j++){
-      if (j!=i) {
-	fprintf(ficres,"%1d%1d",i,j);
-	printf("%1d%1d",i,j);
-	fprintf(ficlog,"%1d%1d",i,j);
-	for(k=1; k<=ncovmodel;k++){
-	  printf(" %.5e",delti[jk]);
-	  fprintf(ficlog," %.5e",delti[jk]);
-	  fprintf(ficres," %.5e",delti[jk]);
-	  jk++;
+    if(mle!=0){
+      /* Computing hessian and covariance matrix */
+      ftolhess=ftol; /* Usually correct */
+      hesscov(matcov, p, npar, delti, ftolhess, func);
+    }
+    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+    printf("# Scales (for hessian or gradient estimation)\n");
+    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+    for(i=1,jk=1; i <=nlstate; i++){
+      for(j=1; j <=nlstate+ndeath; j++){
+	if (j!=i) {
+	  fprintf(ficres,"%1d%1d",i,j);
+	  printf("%1d%1d",i,j);
+	  fprintf(ficlog,"%1d%1d",i,j);
+	  for(k=1; k<=ncovmodel;k++){
+	    printf(" %.5e",delti[jk]);
+	    fprintf(ficlog," %.5e",delti[jk]);
+	    fprintf(ficres," %.5e",delti[jk]);
+	    jk++;
+	  }
+	  printf("\n");
+	  fprintf(ficlog,"\n");
+	  fprintf(ficres,"\n");
 	}
-	printf("\n");
-	fprintf(ficlog,"\n");
-	fprintf(ficres,"\n");
       }
     }
-  }
-   
-  fprintf(ficres,"# 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");
-  if(mle==1)
-    printf("# 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");
-  fprintf(ficlog,"# 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(i=1,k=1;i<=npar;i++){
-    /*  if (k>nlstate) k=1;
-	i1=(i-1)/(ncovmodel*nlstate)+1; 
-	fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
-	printf("%s%d%d",alph[k],i1,tab[i]);
+    
+    fprintf(ficres,"# 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");
+    if(mle>=1)
+      printf("# 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");
+    fprintf(ficlog,"# 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");
+    /* # 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" */
+    
+    
+    /* Just to have a covariance matrix which will be more understandable
+       even is we still don't want to manage dictionary of variables
     */
-    fprintf(ficres,"%3d",i);
-    if(mle==1)
-      printf("%3d",i);
-    fprintf(ficlog,"%3d",i);
-    for(j=1; j<=i;j++){
-      fprintf(ficres," %.5e",matcov[i][j]);
-      if(mle==1)
-	printf(" %.5e",matcov[i][j]);
-      fprintf(ficlog," %.5e",matcov[i][j]);
+    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){
+	      if(mle>=1)
+		printf("#%1d%1d%d",i,j,k);
+	      fprintf(ficlog,"#%1d%1d%d",i,j,k);
+	      fprintf(ficres,"#%1d%1d%d",i,j,k);
+	    }else{
+	      if(mle>=1)
+		printf("%1d%1d%d",i,j,k);
+	      fprintf(ficlog,"%1d%1d%d",i,j,k);
+	      fprintf(ficres,"%1d%1d%d",i,j,k);
+	    }
+	    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){
+			if(mle>=1)
+			  printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+			fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+			fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+		      }else{
+			if(mle>=1)
+			  printf(" %.5e",matcov[jj][ll]); 
+			fprintf(ficlog," %.5e",matcov[jj][ll]); 
+			fprintf(ficres," %.5e",matcov[jj][ll]); 
+		      }
+		    }else{
+		      if(itimes==1){
+			if(mle>=1)
+			  printf(" Var(%s%1d%1d)",ca,i,j);
+			fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+			fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+		      }else{
+			if(mle>=1)
+			  printf(" %.5e",matcov[jj][ll]); 
+			fprintf(ficlog," %.5e",matcov[jj][ll]); 
+			fprintf(ficres," %.5e",matcov[jj][ll]); 
+		      }
+		    }
+		  }
+		} /* end lk */
+	      } /* end lj */
+	    } /* end li */
+	    if(mle>=1)
+	      printf("\n");
+	    fprintf(ficlog,"\n");
+	    fprintf(ficres,"\n");
+	    numlinepar++;
+	  } /* end k*/
+	} /*end j */
+      } /* end i */
+    } /* end itimes */
+    
+    fflush(ficlog);
+    fflush(ficres);
+    
+    while((c=getc(ficpar))=='#' && c!= EOF){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
+      puts(line);
+      fputs(line,ficparo);
     }
-    fprintf(ficres,"\n");
-    if(mle==1)
-      printf("\n");
-    fprintf(ficlog,"\n");
-    k++;
-  }
-   
-  while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
-
-  estepm=0;
-  fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-  if (estepm==0 || estepm < stepm) estepm=stepm;
-  if (fage <= 2) {
-    bage = ageminpar;
-    fage = agemaxpar;
-  }
-   
-  fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-  fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-  fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-   
-  while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
-  
-  fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-  fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-  printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-  fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   
-  while((c=getc(ficpar))=='#' && c!= EOF){
+    
+    estepm=0;
+    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+    if (estepm==0 || estepm < stepm) estepm=stepm;
+    if (fage <= 2) {
+      bage = ageminpar;
+      fage = agemaxpar;
+    }
+    
+    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+    
+    while((c=getc(ficpar))=='#' && c!= EOF){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
+      puts(line);
+      fputs(line,ficparo);
+    }
     ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
- 
-
-  dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-  dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-
-  fscanf(ficpar,"pop_based=%d\n",&popbased);
-  fprintf(ficparo,"pop_based=%d\n",popbased);   
-  fprintf(ficres,"pop_based=%d\n",popbased);   
-  
-  while((c=getc(ficpar))=='#' && c!= EOF){
+    
+    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+    
+    while((c=getc(ficpar))=='#' && c!= EOF){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
+      puts(line);
+      fputs(line,ficparo);
+    }
     ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
-
-  fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-  fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-  printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-  fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-  fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-  /* day and month of proj2 are not used but only year anproj2.*/
-
-  while((c=getc(ficpar))=='#' && c!= EOF){
+    
+    
+    dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+    dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+    
+    fscanf(ficpar,"pop_based=%d\n",&popbased);
+    fprintf(ficparo,"pop_based=%d\n",popbased);   
+    fprintf(ficres,"pop_based=%d\n",popbased);   
+    
+    while((c=getc(ficpar))=='#' && c!= EOF){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
+      puts(line);
+      fputs(line,ficparo);
+    }
     ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
-
-  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
-  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);
-
-  /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
-  /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-
-  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); */
+    
+    fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+    fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+    printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+    fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+    fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+    /* day and month of proj2 are not used but only year anproj2.*/
+    
+    
+    
+    /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+    /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+    
+    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); */
  
-  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_lvector(num,1,n);
-  free_vector(agedc,1,n);
-  /*free_matrix(covar,0,NCOVMAX,1,n);*/
-  /*free_matrix(covar,1,NCOVMAX,1,n);*/
-  fclose(ficparo);
-  fclose(ficres);
-
-
-  /*--------------- Prevalence limit  (stable prevalence) --------------*/
-  
-  strcpy(filerespl,"pl");
-  strcat(filerespl,fileres);
-  if((ficrespl=fopen(filerespl,"w"))==NULL) {
-    printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
-    fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
-  }
-  printf("Computing stable prevalence: result on file '%s' \n", filerespl);
-  fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
-  fprintf(ficrespl,"#Stable prevalence \n");
-  fprintf(ficrespl,"#Age ");
-  for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-  fprintf(ficrespl,"\n");
-  
-  prlim=matrix(1,nlstate,1,nlstate);
-
-  agebase=ageminpar;
-  agelim=agemaxpar;
-  ftolpl=1.e-10;
-  i1=cptcoveff;
-  if (cptcovn < 1){i1=1;}
-
-  for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-      k=k+1;
-      /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-      fprintf(ficrespl,"\n#******");
-      printf("\n#******");
-      fprintf(ficlog,"\n#******");
-      for(j=1;j<=cptcoveff;j++) {
-	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      }
-      fprintf(ficrespl,"******\n");
-      printf("******\n");
-      fprintf(ficlog,"******\n");
+    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_lvector(num,1,n);
+    free_vector(agedc,1,n);
+    /*free_matrix(covar,0,NCOVMAX,1,n);*/
+    /*free_matrix(covar,1,NCOVMAX,1,n);*/
+    fclose(ficparo);
+    fclose(ficres);
+
+
+    /*--------------- Prevalence limit  (stable prevalence) --------------*/
+  
+    strcpy(filerespl,"pl");
+    strcat(filerespl,fileres);
+    if((ficrespl=fopen(filerespl,"w"))==NULL) {
+      printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+      fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+    }
+    printf("Computing stable prevalence: result on file '%s' \n", filerespl);
+    fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
+    fprintf(ficrespl, "#Local time at start: %s", strstart);
+    fprintf(ficrespl,"#Stable prevalence \n");
+    fprintf(ficrespl,"#Age ");
+    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+    fprintf(ficrespl,"\n");
+  
+    prlim=matrix(1,nlstate,1,nlstate);
+
+    agebase=ageminpar;
+    agelim=agemaxpar;
+    ftolpl=1.e-10;
+    i1=cptcoveff;
+    if (cptcovn < 1){i1=1;}
+
+    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+	k=k+1;
+	/*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+	fprintf(ficrespl,"\n#******");
+	printf("\n#******");
+	fprintf(ficlog,"\n#******");
+	for(j=1;j<=cptcoveff;j++) {
+	  fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	}
+	fprintf(ficrespl,"******\n");
+	printf("******\n");
+	fprintf(ficlog,"******\n");
 	
-      for (age=agebase; age<=agelim; age++){
-	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-	fprintf(ficrespl,"%.0f ",age );
-        for(j=1;j<=cptcoveff;j++)
- 	  fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-	for(i=1; i<=nlstate;i++)
-	  fprintf(ficrespl," %.5f", prlim[i][i]);
-	fprintf(ficrespl,"\n");
+	for (age=agebase; age<=agelim; age++){
+	  prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+	  fprintf(ficrespl,"%.0f ",age );
+	  for(j=1;j<=cptcoveff;j++)
+	    fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  for(i=1; i<=nlstate;i++)
+	    fprintf(ficrespl," %.5f", prlim[i][i]);
+	  fprintf(ficrespl,"\n");
+	}
       }
     }
-  }
-  fclose(ficrespl);
+    fclose(ficrespl);
 
-  /*------------- h Pij x at various ages ------------*/
+    /*------------- h Pij x at various ages ------------*/
   
-  strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-  if((ficrespij=fopen(filerespij,"w"))==NULL) {
-    printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-    fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-  }
-  printf("Computing pij: result on file '%s' \n", filerespij);
-  fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+    if((ficrespij=fopen(filerespij,"w"))==NULL) {
+      printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+      fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+    }
+    printf("Computing pij: result on file '%s' \n", filerespij);
+    fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
   
-  stepsize=(int) (stepm+YEARM-1)/YEARM;
-  /*if (stepm<=24) stepsize=2;*/
-
-  agelim=AGESUP;
-  hstepm=stepsize*YEARM; /* Every year of age */
-  hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
+    stepsize=(int) (stepm+YEARM-1)/YEARM;
+    /*if (stepm<=24) stepsize=2;*/
 
-  /* hstepm=1;   aff par mois*/
+    agelim=AGESUP;
+    hstepm=stepsize*YEARM; /* Every year of age */
+    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
 
-  fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-  for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-      k=k+1;
-      fprintf(ficrespij,"\n#****** ");
-      for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      fprintf(ficrespij,"******\n");
+    /* hstepm=1;   aff par mois*/
+    fprintf(ficrespij, "#Local time at start: %s", strstart);
+    fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+	k=k+1;
+	fprintf(ficrespij,"\n#****** ");
+	for(j=1;j<=cptcoveff;j++) 
+	  fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficrespij,"******\n");
 	
-      for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
-	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
+	  nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 
-	/*	  nhstepm=nhstepm*YEARM; aff par mois*/
+	  /*	  nhstepm=nhstepm*YEARM; aff par mois*/
 
-	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-	oldm=oldms;savm=savms;
-	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
-	fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-	for(i=1; i<=nlstate;i++)
-	  for(j=1; j<=nlstate+ndeath;j++)
-	    fprintf(ficrespij," %1d-%1d",i,j);
-	fprintf(ficrespij,"\n");
-	for (h=0; h<=nhstepm; h++){
-	  fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	  oldm=oldms;savm=savms;
+	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
+	  fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
 	  for(i=1; i<=nlstate;i++)
 	    for(j=1; j<=nlstate+ndeath;j++)
-	      fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+	      fprintf(ficrespij," %1d-%1d",i,j);
+	  fprintf(ficrespij,"\n");
+	  for (h=0; h<=nhstepm; h++){
+	    fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+	    for(i=1; i<=nlstate;i++)
+	      for(j=1; j<=nlstate+ndeath;j++)
+		fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+	    fprintf(ficrespij,"\n");
+	  }
+	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 	  fprintf(ficrespij,"\n");
 	}
-	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-	fprintf(ficrespij,"\n");
       }
     }
-  }
 
-  varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
+    varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
 
-  fclose(ficrespij);
+    fclose(ficrespij);
 
-  probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-
-  /*---------- Forecasting ------------------*/
-  /*if((stepm == 1) && (strcmp(model,".")==0)){*/
-  if(prevfcast==1){
-    /*    if(stepm ==1){*/
+    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    for(i=1;i<=AGESUP;i++)
+      for(j=1;j<=NCOVMAX;j++)
+	for(k=1;k<=NCOVMAX;k++)
+	  probs[i][j][k]=0.;
+
+    /*---------- Forecasting ------------------*/
+    /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+    if(prevfcast==1){
+      /*    if(stepm ==1){*/
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
-/*      }  */
-/*      else{ */
-/*        erreur=108; */
-/*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-/*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-/*      } */
-  }
+      /*      }  */
+      /*      else{ */
+      /*        erreur=108; */
+      /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+      /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+      /*      } */
+    }
   
 
-  /*---------- Health expectancies and variances ------------*/
+    /*---------- Health expectancies and variances ------------*/
 
-  strcpy(filerest,"t");
-  strcat(filerest,fileres);
-  if((ficrest=fopen(filerest,"w"))==NULL) {
-    printf("Problem with total LE resultfile: %s\n", filerest);goto end;
-    fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
-  }
-  printf("Computing Total LEs with variances: file '%s' \n", filerest); 
-  fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
+    strcpy(filerest,"t");
+    strcat(filerest,fileres);
+    if((ficrest=fopen(filerest,"w"))==NULL) {
+      printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+      fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+    }
+    printf("Computing Total LEs with variances: file '%s' \n", filerest); 
+    fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
 
 
-  strcpy(filerese,"e");
-  strcat(filerese,fileres);
-  if((ficreseij=fopen(filerese,"w"))==NULL) {
-    printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-    fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-  }
-  printf("Computing Health Expectancies: result on file '%s' \n", filerese);
-  fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+    strcpy(filerese,"e");
+    strcat(filerese,fileres);
+    if((ficreseij=fopen(filerese,"w"))==NULL) {
+      printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+      fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+    }
+    printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+    fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
 
-  strcpy(fileresv,"v");
-  strcat(fileresv,fileres);
-  if((ficresvij=fopen(fileresv,"w"))==NULL) {
-    printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-    fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-  }
-  printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-  fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+    strcpy(fileresv,"v");
+    strcat(fileresv,fileres);
+    if((ficresvij=fopen(fileresv,"w"))==NULL) {
+      printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+      fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+    }
+    printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+    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(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);
-  */
+    /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+    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);
+    */
 
-  if (mobilav!=0) {
-    mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-    if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-      fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-      printf(" Error in movingaverage mobilav=%d\n",mobilav);
+    if (mobilav!=0) {
+      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+	printf(" Error in movingaverage mobilav=%d\n",mobilav);
+      }
     }
-  }
 
-  for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-      k=k+1; 
-      fprintf(ficrest,"\n#****** ");
-      for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      fprintf(ficrest,"******\n");
-
-      fprintf(ficreseij,"\n#****** ");
-      for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      fprintf(ficreseij,"******\n");
-
-      fprintf(ficresvij,"\n#****** ");
-      for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      fprintf(ficresvij,"******\n");
-
-      eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-      oldm=oldms;savm=savms;
-      evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
- 
-      vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-      oldm=oldms;savm=savms;
-      varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
-      if(popbased==1){
-	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
-      }
+    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+	k=k+1; 
+	fprintf(ficrest,"\n#****** ");
+	for(j=1;j<=cptcoveff;j++) 
+	  fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficrest,"******\n");
+
+	fprintf(ficreseij,"\n#****** ");
+	for(j=1;j<=cptcoveff;j++) 
+	  fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficreseij,"******\n");
+
+	fprintf(ficresvij,"\n#****** ");
+	for(j=1;j<=cptcoveff;j++) 
+	  fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficresvij,"******\n");
 
+	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+	oldm=oldms;savm=savms;
+	evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
  
-      fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
-      for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-      fprintf(ficrest,"\n");
-
-      epj=vector(1,nlstate+1);
-      for(age=bage; age <=fage ;age++){
-	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-	if (popbased==1) {
-	  if(mobilav ==0){
-	    for(i=1; i<=nlstate;i++)
-	      prlim[i][i]=probs[(int)age][i][k];
-	  }else{ /* mobilav */ 
-	    for(i=1; i<=nlstate;i++)
-	      prlim[i][i]=mobaverage[(int)age][i][k];
-	  }
+	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+	oldm=oldms;savm=savms;
+	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+	if(popbased==1){
+	  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
 	}
+
+	fprintf(ficrest, "#Local time at start: %s", strstart);
+	fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+	fprintf(ficrest,"\n");
+
+	epj=vector(1,nlstate+1);
+	for(age=bage; age <=fage ;age++){
+	  prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+	  if (popbased==1) {
+	    if(mobilav ==0){
+	      for(i=1; i<=nlstate;i++)
+		prlim[i][i]=probs[(int)age][i][k];
+	    }else{ /* mobilav */ 
+	      for(i=1; i<=nlstate;i++)
+		prlim[i][i]=mobaverage[(int)age][i][k];
+	    }
+	  }
 	
-	fprintf(ficrest," %4.0f",age);
-	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-	  for(i=1, epj[j]=0.;i <=nlstate;i++) {
-	    epj[j] += prlim[i][i]*eij[i][j][(int)age];
-	    /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+	  fprintf(ficrest," %4.0f",age);
+	  for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+	    for(i=1, epj[j]=0.;i <=nlstate;i++) {
+	      epj[j] += prlim[i][i]*eij[i][j][(int)age];
+	      /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+	    }
+	    epj[nlstate+1] +=epj[j];
 	  }
-	  epj[nlstate+1] +=epj[j];
-	}
 
-	for(i=1, vepp=0.;i <=nlstate;i++)
-	  for(j=1;j <=nlstate;j++)
-	    vepp += vareij[i][j][(int)age];
-	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-	for(j=1;j <=nlstate;j++){
-	  fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+	  for(i=1, vepp=0.;i <=nlstate;i++)
+	    for(j=1;j <=nlstate;j++)
+	      vepp += vareij[i][j][(int)age];
+	  fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+	  for(j=1;j <=nlstate;j++){
+	    fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+	  }
+	  fprintf(ficrest,"\n");
 	}
-	fprintf(ficrest,"\n");
-      }
-      free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-      free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-      free_vector(epj,1,nlstate+1);
-    }
-  }
-  free_vector(weight,1,n);
-  free_imatrix(Tvard,1,15,1,2);
-  free_imatrix(s,1,maxwav+1,1,n);
-  free_matrix(anint,1,maxwav,1,n); 
-  free_matrix(mint,1,maxwav,1,n);
-  free_ivector(cod,1,n);
-  free_ivector(tab,1,NCOVMAX);
-  fclose(ficreseij);
-  fclose(ficresvij);
-  fclose(ficrest);
-  fclose(ficpar);
-  
-  /*------- Variance of stable prevalence------*/   
-
-  strcpy(fileresvpl,"vpl");
-  strcat(fileresvpl,fileres);
-  if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-    printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
-    exit(0);
-  }
-  printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
-
-  for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-      k=k+1;
-      fprintf(ficresvpl,"\n#****** ");
-      for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      fprintf(ficresvpl,"******\n");
+	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+	free_vector(epj,1,nlstate+1);
+      }
+    }
+    free_vector(weight,1,n);
+    free_imatrix(Tvard,1,15,1,2);
+    free_imatrix(s,1,maxwav+1,1,n);
+    free_matrix(anint,1,maxwav,1,n); 
+    free_matrix(mint,1,maxwav,1,n);
+    free_ivector(cod,1,n);
+    free_ivector(tab,1,NCOVMAX);
+    fclose(ficreseij);
+    fclose(ficresvij);
+    fclose(ficrest);
+    fclose(ficpar);
+  
+    /*------- Variance of stable prevalence------*/   
+
+    strcpy(fileresvpl,"vpl");
+    strcat(fileresvpl,fileres);
+    if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+      printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
+      exit(0);
+    }
+    printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
+
+    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+	k=k+1;
+	fprintf(ficresvpl,"\n#****** ");
+	for(j=1;j<=cptcoveff;j++) 
+	  fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficresvpl,"******\n");
       
-      varpl=matrix(1,nlstate,(int) bage, (int) fage);
-      oldm=oldms;savm=savms;
-      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
-      free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+	varpl=matrix(1,nlstate,(int) bage, (int) fage);
+	oldm=oldms;savm=savms;
+	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+      }
     }
-  }
 
-  fclose(ficresvpl);
-
-  /*---------- End : free ----------------*/
-  free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-  free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-  free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-  free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-  
-  free_matrix(covar,0,NCOVMAX,1,n);
-  free_matrix(matcov,1,npar,1,npar);
-  /*free_vector(delti,1,npar);*/
-  free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
-  free_matrix(agev,1,maxwav,1,imx);
-  free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-  if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    fclose(ficresvpl);
+
+    /*---------- End : free ----------------*/
+    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+  }  /* mle==-3 arrives here for freeing */
+    free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+  
+    free_matrix(covar,0,NCOVMAX,1,n);
+    free_matrix(matcov,1,npar,1,npar);
+    /*free_vector(delti,1,npar);*/
+    free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
+    free_matrix(agev,1,maxwav,1,imx);
+    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+
+    free_ivector(ncodemax,1,8);
+    free_ivector(Tvar,1,15);
+    free_ivector(Tprod,1,15);
+    free_ivector(Tvaraff,1,15);
+    free_ivector(Tage,1,15);
+    free_ivector(Tcode,1,100);
 
-  free_ivector(ncodemax,1,8);
-  free_ivector(Tvar,1,15);
-  free_ivector(Tprod,1,15);
-  free_ivector(Tvaraff,1,15);
-  free_ivector(Tage,1,15);
-  free_ivector(Tcode,1,100);
 
   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 %d warnings\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 */
   (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",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("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
+  fprintf(ficlog,"Local time 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 
   chdir(path);
- /*system("wgnuplot graph.plt");*/
- /*system("../gp37mgw/wgnuplot graph.plt");*/
- /*system("cd ../gp37mgw");*/
- /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
-  strcpy(plotcmd,GNUPLOTPROGRAM);
+#ifndef UNIX
+  strcpy(plotcmd,"\"");
+#endif
+  strcat(plotcmd,pathimach);
+  /*strcat(plotcmd,CHARSEPARATOR);*/
+  strcat(plotcmd,GNUPLOTPROGRAM);
+#ifndef UNIX
+  strcat(plotcmd,"\"");
+#endif
+  if(stat(plotcmd,&info)){
+    printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+  }
   strcat(plotcmd," ");
   strcat(plotcmd,optionfilegnuplot);
   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
-  system(plotcmd);
-  printf(" Wait...");
 
- /*#ifdef windows*/
+  if((outcmd=system(plotcmd)) != 0){
+    printf(" Problem with gnuplot\n");
+  }
+  printf(" Wait...");
   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') {
+      printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+      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);
+  }
 }