--- imach/src/imach.c	2003/07/15 15:38:55	1.96
+++ imach/src/imach.c	2006/01/05 20:23:19	1.105
@@ -1,6 +1,59 @@
-/* $Id: imach.c,v 1.96 2003/07/15 15:38:55 brouard Exp $
+/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $
   $State: Exp $
   $Log: imach.c,v $
+  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.
@@ -170,7 +223,7 @@
 #include <stdlib.h>
 #include <unistd.h>
 
-#include <sys/time.h>
+/* #include <sys/time.h> */
 #include <time.h>
 #include "timeval.h"
 
@@ -197,7 +250,8 @@
 #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 ODIRSEPARATOR '\\'
 #else
@@ -205,11 +259,11 @@
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.96 2003/07/15 15:38:55 brouard Exp $ */
+/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.96c, July 2003, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.96 $ $Date: 2003/07/15 15:38:55 $"; 
+char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.105 $ $Date: 2006/01/05 20:23:19 $"; 
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
@@ -238,6 +292,7 @@ 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;
@@ -300,9 +355,10 @@ 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;
@@ -310,15 +366,17 @@ 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 */
@@ -326,6 +384,9 @@ 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 */
 
@@ -357,12 +418,14 @@ static	int split( char *path, char *dirc
 #endif
   */
   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 */
 }
 
@@ -395,8 +458,8 @@ 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;
@@ -825,9 +888,10 @@ void powell(double p[], double **xi, int
     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(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++) {
+    */
+   for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);
@@ -837,11 +901,11 @@ void powell(double p[], double **xi, int
     fprintf(ficrespow,"\n");fflush(ficrespow);
     if(*iter <=3){
       tm = *localtime(&curr_time.tv_sec);
-      strcpy(strcurr,asctime(&tmf));
+      strcpy(strcurr,asctime(&tm));
 /*       asctime_r(&tm,strcurr); */
-      forecast_time=curr_time;
+      forecast_time=curr_time; 
       itmp = strlen(strcurr);
-      if(strcurr[itmp-1]=='\n')
+      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);
@@ -853,8 +917,8 @@ void powell(double p[], double **xi, int
 	itmp = strlen(strfor);
 	if(strfor[itmp-1]=='\n')
 	strfor[itmp-1]='\0';
-	printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
-	fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+	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++) { 
@@ -1019,57 +1083,57 @@ 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;
 }
 
@@ -1193,14 +1257,14 @@ 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. 
@@ -1208,15 +1272,16 @@ 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
@@ -1236,7 +1301,28 @@ 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 */
 	} 
@@ -1512,7 +1598,7 @@ 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++)
@@ -1547,11 +1633,11 @@ 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");
@@ -1559,9 +1645,11 @@ 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++) {
@@ -1569,7 +1657,8 @@ 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]);*/
       }
@@ -1640,14 +1729,14 @@ 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;
@@ -1687,7 +1776,7 @@ 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;
@@ -1797,7 +1886,7 @@ 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;
@@ -1817,7 +1906,7 @@ 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;
@@ -1830,8 +1919,8 @@ 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;
 
@@ -1870,7 +1959,7 @@ 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]]);
@@ -1956,7 +2045,7 @@ 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 */
@@ -2065,7 +2154,7 @@ 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;
@@ -2105,9 +2194,9 @@ void  concatwav(int wav[], int **dh, int
 	      nberr++;
 	      printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 	      j=1; /* Temporary Dangerous patch */
-	      printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
+	      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.\n  You MUST fix the contradiction between dates.\n",stepm);
+	      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;
@@ -2119,7 +2208,8 @@ 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;
@@ -2212,7 +2302,7 @@ 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]++;
  }
@@ -2230,7 +2320,7 @@ 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 */
@@ -2248,6 +2338,7 @@ 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++)
@@ -2402,7 +2493,7 @@ 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);*/
@@ -2453,7 +2544,9 @@ 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++){
@@ -2463,11 +2556,12 @@ 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++)
@@ -2700,7 +2794,7 @@ 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);*/
@@ -2713,7 +2807,7 @@ 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++)
@@ -2783,7 +2877,7 @@ 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;
@@ -2828,11 +2922,13 @@ 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");
 
@@ -3863,6 +3959,89 @@ void prwizard(int ncovmodel, int nlstate
   } /* 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   lx     qx    dx    Lx     Tx     e(x)<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);
+
+} 
+
+
 
 
 /***********************************************/
@@ -3876,6 +4055,7 @@ int main(int argc, char *argv[])
   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 */
@@ -3892,7 +4072,7 @@ 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;
@@ -3902,6 +4082,8 @@ 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;
 
@@ -3919,9 +4101,9 @@ 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;
 
@@ -3978,8 +4160,10 @@ int main(int argc, char *argv[])
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   /* cutv(path,optionfile,pathtot,'\\');*/
 
+  split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ /*   strcpy(pathimach,argv[0]); */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-  printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);
   strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);
@@ -4004,12 +4188,12 @@ 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("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);
@@ -4077,163 +4261,174 @@ 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);
+    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");
+	numlinepar++;
+	if(mle==1)
+	  printf("\n");
+	fprintf(ficlog,"\n");
+	fprintf(ficparo,"\n");
+      }
+    }  
+    fflush(ficlog);
 
-  npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
 
-  p=param[1][1];
-  
-  /* Reads comments: lines beginning with '#' */
-  while((c=getc(ficpar))=='#' && c!= EOF){
+    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);
-    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]);
+    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");
       }
-      fscanf(ficpar,"\n");
-      numlinepar++;
-      printf("\n");
-      fprintf(ficparo,"\n");
-      fprintf(ficlog,"\n");
     }
-  }
-  fflush(ficlog);
+    fflush(ficlog);
 
-  delti=delti3[1][1];
+    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;
@@ -4261,7 +4456,10 @@ 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);
@@ -4424,7 +4622,7 @@ 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)
@@ -4484,9 +4682,11 @@ 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);
@@ -4540,7 +4740,10 @@ 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);
   }
@@ -4553,6 +4756,8 @@ int main(int argc, char *argv[])
   /*--------- index.htm --------*/
 
   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);
@@ -4591,7 +4796,7 @@ Title=%s <br>Datafile=%s Firstpass=%d La
   
   /* 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\
@@ -4610,567 +4815,679 @@ 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);
-  }
-    
-  /*--------- 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);
-	for(j=1; j <=ncovmodel; j++){
-	  printf("%f ",p[jk]);
-	  fprintf(ficlog,"%f ",p[jk]);
-	  fprintf(ficres,"%f ",p[jk]);
-	  jk++; 
+  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;
 	}
-	printf("\n");
-	fprintf(ficlog,"\n");
-	fprintf(ficres,"\n");
+    }
+
+    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);
   }
-  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");
+  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);
+    
+    hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
+
+    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;
    
-  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" */
+     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];
+    }
 
-/* Just to have a covariance matrix which will be more understandable
-   even is we still don't want to manage dictionary of variables
-*/
-  for(itimes=1;itimes<=2;itimes++){
-    jj=0;
-    for(i=1; i <=nlstate; i++){
+ 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);
+	  for(j=1; j <=ncovmodel; j++){
+	    printf("%f ",p[jk]);
+	    fprintf(ficlog,"%f ",p[jk]);
+	    fprintf(ficres,"%f ",p[jk]);
+	    jk++; 
+	  }
+	  printf("\n");
+	  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) 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);
+	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++;
 	  }
-	  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);
+	  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");
+    /* # 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
+    */
+    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(mle>=1)
-			printf(" %.5e",matcov[jj][ll]); 
-		      fprintf(ficlog," %.5e",matcov[jj][ll]); 
-		      fprintf(ficres," %.5e",matcov[jj][ll]); 
+		      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);
-  }
-  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){
+		} /* 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);
+    }
     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;*/
+    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 */ 
-
-  /* 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);
 
-  fclose(ficrespij);
+    varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
 
-  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.;
+    fclose(ficrespij);
 
-  /*---------- 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);
@@ -5189,7 +5506,7 @@ ageminpar, agemax, s[lastpass][imx], age
   tm = *localtime(&end_time.tv_sec);
   tmg = *gmtime(&end_time.tv_sec);
   strcpy(strtend,asctime(&tm));
-  printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
+  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));
 
@@ -5206,7 +5523,10 @@ ageminpar, agemax, s[lastpass][imx], age
   /*------ End -----------*/
 
   chdir(path);
-  strcpy(plotcmd,GNUPLOTPROGRAM);
+  strcpy(plotcmd,"\"");
+  strcat(plotcmd,pathimach);
+  strcat(plotcmd,GNUPLOTPROGRAM);
+  strcat(plotcmd,"\"");
   strcat(plotcmd," ");
   strcat(plotcmd,optionfilegnuplot);
   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
@@ -5219,7 +5539,10 @@ ageminpar, agemax, s[lastpass][imx], age
     printf("\nType e to edit output files, g to graph again and q for exiting: ");
     scanf("%s",z);
 /*     if (z[0] == 'c') system("./imach"); */
-    if (z[0] == 'e') system(optionfilehtm);
+    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);
   }