From 491f271a9b2a0665c656dca006eff1db4b398c56 Mon Sep 17 00:00:00 2001
From: "N. Brouard" <brouard@ined.fr>
Date: Tue, 17 Jun 2003 13:12:43 +0000
Subject: [PATCH] * imach.c (Repository): Check when date of death was earlier
 that current date of interview. It may happen when the death was just prior
 to the death. In this case, dh was negative and likelihood was wrong
 (infinity). We still send an "Error" but patch by assuming that the date of
 death was just one stepm after the interview. (Repository): Because some
 people have very long ID (first column) we changed int to long in num[] and
 we added a new lvector for memory allocation. But we also truncated to 8
 characters (left truncation) (Repository): No more line truncation errors.

---
 src/imach.c | 434 ++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 332 insertions(+), 102 deletions(-)

diff --git a/src/imach.c b/src/imach.c
index 7a88e88..f9efc13 100644
--- a/src/imach.c
+++ b/src/imach.c
@@ -1,6 +1,13 @@
 /* $Id$
   $State$
   $Log$
+  Revision 1.84  2003/06/13 21:44:43  brouard
+  * imach.c (Repository): Replace "freqsummary" at a correct
+  place. It differs from routine "prevalence" which may be called
+  many times. Probs is memory consuming and must be used with
+  parcimony.
+  Version 0.95a2 (should output exactly the same maximization than 0.8a2)
+
   Revision 1.83  2003/06/10 13:39:11  lievre
   *** empty log message ***
 
@@ -105,9 +112,9 @@
 #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
-#define FILENAMELENGTH 80
+#define FILENAMELENGTH 132
 /*#define DEBUG*/
-#define windows
+/*#define windows*/
 #define	GLOCK_ERROR_NOPATH		-1	/* empty path */
 #define	GLOCK_ERROR_GETCWD		-2	/* cannot get cwd */
 
@@ -122,12 +129,12 @@
 #define YEARM 12. /* Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
-#ifdef windows
-#define DIRSEPARATOR '\\'
-#define ODIRSEPARATOR '/'
-#else
+#ifdef unix
 #define DIRSEPARATOR '/'
 #define ODIRSEPARATOR '\\'
+#else
+#define DIRSEPARATOR '\\'
+#define ODIRSEPARATOR '/'
 #endif
 
 /* $Id$ */
@@ -157,6 +164,12 @@ double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficlog, *ficrespow;
+int globpr; /* Global variable for printing or not */
+double fretone; /* Only one call to likelihood */
+long ipmx; /* Number of contributions */
+double sw; /* Sum of weights */
+char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+FILE *ficresilk;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE *ficresprobmorprev;
 FILE *fichtm; /* Html File */
@@ -214,7 +227,8 @@ int estepm;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 
 int m,nb;
-int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+long *num;
+int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;
 double dateintmean=0;
@@ -254,11 +268,12 @@ static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
     dirc[l1-l2] = 0;			/* add zero */
   }
   l1 = strlen( dirc );			/* length of directory */
-#ifdef windows
+  /*#ifdef windows
   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 #else
   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 #endif
+  */
   ss = strrchr( name, '.' );		/* find last / */
   ss++;
   strcpy(ext,ss);			/* save extension */
@@ -342,31 +357,31 @@ void free_vector(double*v, int nl, int nh)
 }
 
 /************************ivector *******************************/
-char *cvector(long nl,long nh)
+int *ivector(long nl,long nh)
 {
-  char *v;
-  v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
-  if (!v) nrerror("allocation failure in cvector");
+  int *v;
+  v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+  if (!v) nrerror("allocation failure in ivector");
   return v-nl+NR_END;
 }
 
 /******************free ivector **************************/
-void free_cvector(char *v, long nl, long nh)
+void free_ivector(int *v, long nl, long nh)
 {
   free((FREE_ARG)(v+nl-NR_END));
 }
 
-/************************ivector *******************************/
-int *ivector(long nl,long nh)
+/************************lvector *******************************/
+long *lvector(long nl,long nh)
 {
-  int *v;
-  v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+  long *v;
+  v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   if (!v) nrerror("allocation failure in ivector");
   return v-nl+NR_END;
 }
 
-/******************free ivector **************************/
-void free_ivector(int *v, long nl, long nh)
+/******************free lvector **************************/
+void free_lvector(long *v, long nl, long nh)
 {
   free((FREE_ARG)(v+nl-NR_END));
 }
@@ -425,7 +440,7 @@ double **matrix(long nrl, long nrh, long ncl, long nch)
 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   return m;
-  /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
+  /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
    */
 }
 
@@ -1210,7 +1225,7 @@ double func( double *x)
 	ipmx +=1;
 	sw += weight[i];
 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-	/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+/* 	printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       } /* end of wave */
     } /* end of individual */
   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
@@ -1248,10 +1263,114 @@ double func( double *x)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-  /*exit(0); */
   return -l;
 }
 
+/*************** log-likelihood *************/
+double funcone( double *x)
+{
+  int i, ii, j, k, mi, d, kk;
+  double l, ll[NLSTATEMAX], cov[NCOVMAX];
+  double **out;
+  double lli; /* Individual log likelihood */
+  int s1, s2;
+  double bbh, survp;
+  /*extern weight */
+  /* We are differentiating ll according to initial status */
+  /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+  /*for(i=1;i<imx;i++) 
+    printf(" %d\n",s[4][i]);
+  */
+  cov[1]=1.;
+
+  for(k=1; k<=nlstate; k++) ll[k]=0.;
+
+  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+    for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+    for(mi=1; mi<= wav[i]-1; mi++){
+      for (ii=1;ii<=nlstate+ndeath;ii++)
+	for (j=1;j<=nlstate+ndeath;j++){
+	  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+	  savm[ii][j]=(ii==j ? 1.0 : 0.0);
+	}
+      for(d=0; d<dh[mi][i]; d++){
+	newm=savm;
+	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	for (kk=1; kk<=cptcovage;kk++) {
+	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	}
+	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+	savm=oldm;
+	oldm=newm;
+      } /* end mult */
+      
+      s1=s[mw[mi][i]][i];
+      s2=s[mw[mi+1][i]][i];
+      bbh=(double)bh[mi][i]/(double)stepm; 
+      /* bias is positive if real duration
+       * is higher than the multiple of stepm and negative otherwise.
+       */
+      if( s2 > nlstate && (mle <5) ){  /* Jackson */
+	lli=log(out[s1][s2] - savm[s1][s2]);
+      } else if (mle==1){
+	lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+      } else if(mle==2){
+	lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+      } else if(mle==3){  /* exponential inter-extrapolation */
+	lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+      } else if (mle==4){  /* mle=4 no inter-extrapolation */
+	lli=log(out[s1][s2]); /* Original formula */
+      } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+	lli=log(out[s1][s2]); /* Original formula */
+      } /* End of if */
+      ipmx +=1;
+      sw += weight[i];
+      ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+/*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+      if(globpr){
+	fprintf(ficresilk,"%6d %1d %1d %1d %1d %3d %10.6f %6.4f %10.6f %10.6f %10.6f ", \
+		i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+	for(k=1,l=0.; k<=nlstate; k++) 
+	  fprintf(ficresilk," %10.6f",ll[k]);
+	fprintf(ficresilk,"\n");
+      }
+    } /* end of wave */
+  } /* end of individual */
+  for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+  /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+  l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+  return -l;
+}
+
+
+void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+{
+  /* This routine should help understanding what is done with the selection of individuals/waves and
+     to check the exact contribution to the likelihood.
+     Plotting could be done.
+   */
+  int k;
+  if(globpr !=0){ /* Just counts and sums no printings */
+    strcpy(fileresilk,"ilk"); 
+    strcat(fileresilk,fileres);
+    if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresilk);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+    }
+    fprintf(ficresilk, "# individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state");
+    fprintf(ficresilk, "# i s1 s2 mi mw dh likeli weight out sav ");
+    /* 	i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+    for(k=1; k<=nlstate; k++) 
+      fprintf(ficresilk," ll[%d]",k);
+    fprintf(ficresilk,"\n");
+  }
+
+  *fretone=(*funcone)(p);
+  if(globpr !=0)
+    fclose(ficresilk);
+  return;
+}
 
 /*********** Maximum Likelihood Estimation ***************/
 
@@ -1260,6 +1379,7 @@ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, doub
   int i,j, iter;
   double **xi;
   double fret;
+  double fretone; /* Only one call to likelihood */
   char filerespow[FILENAMELENGTH];
   xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)
@@ -1277,6 +1397,7 @@ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, doub
     for(j=1;j<=nlstate+ndeath;j++)
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficrespow,"\n");
+
   powell(p,xi,npar,ftol,&iter,&fret,func);
 
   fclose(ficrespow);
@@ -1829,11 +1950,11 @@ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc
     wav[i]=mi;
     if(mi==0){
       if(first==0){
-	printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
+	printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 	first=1;
       }
       if(first==1){
-	fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
+	fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       }
     } /* end mi==0 */
   } /* End individuals */
@@ -1845,15 +1966,21 @@ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc
       else{
 	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 	  if (agedc[i] < 2*AGESUP) {
-	  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
-	  if(j==0) j=1;  /* Survives at least one month after exam */
-	  k=k+1;
-	  if (j >= jmax) jmax=j;
-	  if (j <= jmin) jmin=j;
-	  sum=sum+j;
-	  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-	  /*	  printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-	  if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	    j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
+	    if(j==0) j=1;  /* Survives at least one month after exam */
+	    else if(j<0){
+	      printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	      j=1; /* Careful Patch */
+	      printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fixe the contradiction between dates.\n",stepm);
+	      printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	      fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
+	    }
+	    k=k+1;
+	    if (j >= jmax) jmax=j;
+	    if (j <= jmin) jmin=j;
+	    sum=sum+j;
+	    /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+	    /*	  printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 	  }
 	}
 	else{
@@ -1864,13 +1991,16 @@ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc
 	  else if (j <= jmin)jmin=j;
 	  /*	    if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 	  /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-	  if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	  if(j<0){
+	    printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	    fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+	  }
 	  sum=sum+j;
 	}
 	jk= j/stepm;
 	jl= j -jk*stepm;
 	ju= j -(jk+1)*stepm;
-	if(mle <=1){ 
+	if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 	  if(jl==0){
 	    dh[mi][i]=jk;
 	    bh[mi][i]=0;
@@ -1895,8 +2025,8 @@ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc
 	    bh[mi][i]=ju; /* At least one step */
 	    /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
 	  }
-	}
-      } /* end if mle */
+	} /* end if mle */
+      }
     } /* end wave */
   }
   jmean=sum/k;
@@ -2856,11 +2986,11 @@ void printinghtml(char fileres[], char title[], char datafile[], int firstpass,
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   }
 
-   fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
- - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
- - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
- - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
- - Life expectancies by age and initial health status (estepm=%2d months): 
+   fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
+ - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
+ - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
+ - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
+ - Life expectancies by age and initial health status (estepm=%2d months): \
    <a href=\"e%s\">e%s</a> <br>\n</li>", \
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
 
@@ -2880,35 +3010,36 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      /* Pij */
-     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
      /* Quasi-incidences */
-     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
        /* Stable prevalence in each health state */
        for(cpt=1; cpt<nlstate;cpt++){
-	 fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+	 fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
      }
-     fprintf(fichtm,"\n<br>- Total life expectancy by age and
-health expectancies in states (1) and (2): e%s%d.png<br>
+     fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+health expectancies in states (1) and (2): e%s%d.png<br>\
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
    } /* end i1 */
  }/* End k1 */
  fprintf(fichtm,"</ul>");
 
 
- fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
- - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
- - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
- - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
- - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
- - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
- - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+ fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
+ - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
+ - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
+ - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
+ - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
+ - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
 
 /*  if(popforecast==1) fprintf(fichtm,"\n */
@@ -2933,8 +3064,8 @@ fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      for(cpt=1; cpt<=nlstate;cpt++) {
-       fprintf(fichtm,"<br>- Observed and period prevalence (with confident
-interval) in state (%d): v%s%d%d.png <br>
+       fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
+interval) in state (%d): v%s%d%d.png <br>\
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }
    } /* end i1 */
@@ -3455,6 +3586,8 @@ int main(int argc, char *argv[])
 {
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+  int jj;
+  int numlinepar=0; /* Current linenumber of parameter file */
   double agedeb, agefin,hf;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 
@@ -3466,7 +3599,7 @@ int main(int argc, char *argv[])
   double ***mobaverage;
   int *indx;
   char line[MAXLINE], linepar[MAXLINE];
-  char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
+  char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
   int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;
@@ -3501,11 +3634,39 @@ int main(int argc, char *argv[])
 #include <sys/time.h>
 #include <time.h>
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+  char *strt, *strtend;
+  char *stratrunc;
+  int lstra;
+
+  long total_usecs;
+  struct timeval start_time, end_time, curr_time;
+  struct timezone tzp;
+  extern int gettimeofday();
+  struct tm tmg, tm, *gmtime(), *localtime();
+  long time_value;
+  extern long time();
  
-  /* long total_usecs;
-     struct timeval start_time, end_time;
-  
-     gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+  /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+  (void) gettimeofday(&start_time,&tzp);
+  tm = *localtime(&start_time.tv_sec);
+  tmg = *gmtime(&start_time.tv_sec);
+  strt=asctime(&tm);
+/*  printf("Localtime (at start)=%s",strt); */
+/*  tp.tv_sec = tp.tv_sec +86400; */
+/*  tm = *localtime(&start_time.tv_sec); */
+/*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+/*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+/*   tmg.tm_hour=tmg.tm_hour + 1; */
+/*   tp.tv_sec = mktime(&tmg); */
+/*   strt=asctime(&tmg); */
+/*   printf("Time(after) =%s",strt);  */
+/*  (void) time (&time_value);
+*  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+*  tm = *localtime(&time_value);
+*  strt=asctime(&tm);
+*  printf("tim_value=%d,asctime=%s\n",time_value,strt); 
+*/
+
   getcwd(pathcd, size);
 
   printf("\n%s\n%s",version,fullversion);
@@ -3516,13 +3677,13 @@ int main(int argc, char *argv[])
   else{
     strcpy(pathtot,argv[1]);
   }
-  /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
+  /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
   /* cutv(path,optionfile,pathtot,'\\');*/
 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-  printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);
   replace(pathc,path);
 
@@ -3536,9 +3697,11 @@ int main(int argc, char *argv[])
     goto end;
   }
   fprintf(ficlog,"Log filename:%s\n",filelog);
-  fprintf(ficlog,"\n%s",version);
+  fprintf(ficlog,"\n%s\n%s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: ");
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  printf("Localtime (at start)=%s",strt); 
+  fprintf(ficlog,"Localtime (at start)=%s",strt); 
   fflush(ficlog);
 
   /* */
@@ -3551,6 +3714,7 @@ int main(int argc, char *argv[])
   if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile %s\n",optionfile);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+    fflush(ficlog);
     goto end;
   }
 
@@ -3559,29 +3723,38 @@ int main(int argc, char *argv[])
   if((ficparo=fopen(filereso,"w"))==NULL) {
     printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+    fflush(ficlog);
     goto end;
   }
 
   /* Reads comments: lines beginning with '#' */
+  numlinepar=0;
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+  numlinepar++;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+  fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+  fflush(ficlog);
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
-  
+
    
   covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
@@ -3595,15 +3768,24 @@ int main(int argc, char *argv[])
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
-  
+
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-  for(i=1; i <=nlstate; i++)
-    for(j=1; j <=nlstate+ndeath-1; j++){
+  for(i=1; i <=nlstate; i++){
+    j=0;
+    for(jj=1; jj <=nlstate+ndeath; jj++){
+      if(jj==i) continue;
+      j++;
       fscanf(ficpar,"%1d%1d",&i1,&j1);
+      if ((i1 != i) && (j1 != j)){
+	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+	exit(1);
+      }
       fprintf(ficparo,"%1d%1d",i1,j1);
       if(mle==1)
 	printf("%1d%1d",i,j);
@@ -3619,12 +3801,15 @@ int main(int argc, char *argv[])
 	fprintf(ficparo," %lf",param[i][j][k]);
       }
       fscanf(ficpar,"\n");
+      numlinepar++;
       if(mle==1)
 	printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
-  
+  }  
+  fflush(ficlog);
+
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
 
   p=param[1][1];
@@ -3633,8 +3818,10 @@ int main(int argc, char *argv[])
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
 
@@ -3643,18 +3830,28 @@ int main(int argc, char *argv[])
   for(i=1; i <=nlstate; i++){
     for(j=1; j <=nlstate+ndeath-1; j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);
+      if ((i1-i)*(j1-j)!=0){
+	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+	exit(1);
+      }
       printf("%1d%1d",i,j);
       fprintf(ficparo,"%1d%1d",i1,j1);
+      fprintf(ficlog,"%1d%1d",i1,j1);
       for(k=1; k<=ncovmodel;k++){
 	fscanf(ficpar,"%le",&delti3[i][j][k]);
 	printf(" %le",delti3[i][j][k]);
 	fprintf(ficparo," %le",delti3[i][j][k]);
+	fprintf(ficlog," %le",delti3[i][j][k]);
       }
       fscanf(ficpar,"\n");
+      numlinepar++;
       printf("\n");
       fprintf(ficparo,"\n");
+      fprintf(ficlog,"\n");
     }
   }
+  fflush(ficlog);
+
   delti=delti3[1][1];
 
 
@@ -3664,8 +3861,10 @@ int main(int argc, char *argv[])
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
+    numlinepar++;
     puts(line);
     fputs(line,ficparo);
+    fputs(line,ficlog);
   }
   ungetc(c,ficpar);
   
@@ -3680,13 +3879,12 @@ int main(int argc, char *argv[])
       fscanf(ficpar," %le",&matcov[i][j]);
       if(mle==1){
 	printf(" %.5le",matcov[i][j]);
-	fprintf(ficlog," %.5le",matcov[i][j]);
       }
-      else
-	fprintf(ficlog," %.5le",matcov[i][j]);
+      fprintf(ficlog," %.5le",matcov[i][j]);
       fprintf(ficparo," %.5le",matcov[i][j]);
     }
     fscanf(ficpar,"\n");
+    numlinepar++;
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
@@ -3700,6 +3898,7 @@ int main(int argc, char *argv[])
     printf("\n");
   fprintf(ficlog,"\n");
 
+  fflush(ficlog);
 
   /*-------- Rewriting paramater file ----------*/
   strcpy(rfileres,"r");    /* "Rparameterfile */
@@ -3721,7 +3920,7 @@ int main(int argc, char *argv[])
   n= lastobs;
   severity = vector(1,maxwav);
   outcome=imatrix(1,maxwav+1,1,n);
-  num=ivector(1,n);
+  num=lvector(1,n);
   moisnais=vector(1,n);
   annais=vector(1,n);
   moisdc=vector(1,n);
@@ -3757,10 +3956,16 @@ int main(int argc, char *argv[])
       for (j=ncovcol;j>=1;j--){
 	cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
       } 
-      num[i]=atol(stra);
+      lstra=strlen(stra);
+      if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+	stratrunc = &(stra[lstra-9]);
+	num[i]=atol(stratrunc);
+      }
+      else
+	num[i]=atol(stra);
 	
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-	printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+	printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
 
       i=i+1;
     }
@@ -3776,7 +3981,7 @@ int main(int argc, char *argv[])
     }*/
    /*  for (i=1; i<=imx; i++){
      if (s[4][i]==9)  s[4][i]=-1; 
-     printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+     printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
   
  for (i=1; i<=imx; i++)
  
@@ -3879,13 +4084,13 @@ int main(int argc, char *argv[])
 	s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-	printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+	printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
 	s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-	printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
-	fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
+	printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
+	fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
 	s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
       }
     }
@@ -3902,8 +4107,8 @@ int main(int argc, char *argv[])
 	  /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
 	    else {
 	      if ((int)andc[i]!=9999){
-		printf("Warning negative age at death: %d line:%d\n",num[i],i);
-		fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
+		printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+		fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
 		agev[m][i]=-1;
 	      }
 	    }
@@ -3947,7 +4152,7 @@ int main(int argc, char *argv[])
 
   /*for (i=1; i<=imx; i++){
   for (m=firstpass; (m<lastpass); m++){
-     printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+     printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
 }
 
 }*/
@@ -4021,6 +4226,18 @@ int main(int argc, char *argv[])
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
 
+  globpr=0; /* To get ipmx number of contributions and 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);
   }
@@ -4207,20 +4424,25 @@ int main(int argc, char *argv[])
     printf("Problem with %s \n",optionfilehtm), exit(0);
   }
 
-  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
-Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
-\n
-Total number of observations=%d <br>\n
-Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
-Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
-<hr  size=\"2\" color=\"#EC5E5E\">
- <ul><li><h4>Parameter files</h4>\n
- - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- - Log file of the run: <a href=\"%s\">%s</a><br>\n
- - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
-   fclose(fichtm);
-
-  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n\
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+\n\
+Total number of observations=%d <br>\n\
+Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n\
+<hr  size=\"2\" color=\"#EC5E5E\">\
+ <ul><li><h4>Parameter files</h4>\n\
+ - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+ - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+ - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",\
+	  version,title,datafile,firstpass,lastpass,stepm, weightopt,\
+	  model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,\
+	  filelog,filelog,optionfilegnuplot,optionfilegnuplot);
+  fclose(fichtm);
+
+  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+	       model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+	       jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
  
   /*------------ free_vector  -------------*/
   chdir(path);
@@ -4229,7 +4451,7 @@ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
-  free_ivector(num,1,n);
+  free_lvector(num,1,n);
   free_vector(agedc,1,n);
   /*free_matrix(covar,0,NCOVMAX,1,n);*/
   /*free_matrix(covar,1,NCOVMAX,1,n);*/
@@ -4554,9 +4776,17 @@ ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[las
   printf("See log file on %s\n",filelog);
   fclose(ficlog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
-  
-  /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
-  /*printf("Total time was %d uSec.\n", total_usecs);*/
+  (void) gettimeofday(&end_time,&tzp);
+  tm = *localtime(&end_time.tv_sec);
+  tmg = *gmtime(&end_time.tv_sec);
+  strtend=asctime(&tm);
+  printf("Localtime at start %s and at end=%s",strt, strtend); 
+  fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); 
+  /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
+
+  printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
+  fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
+  /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*------ End -----------*/
 
   end:
-- 
2.43.0