--- imach/src/imach.c	2003/06/24 12:34:15	1.90
+++ imach/src/imach.c	2003/06/27 13:00:02	1.94
@@ -1,6 +1,25 @@
-/* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $
+/* $Id: imach.c,v 1.94 2003/06/27 13:00:02 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.94  2003/06/27 13:00:02  brouard
+  Just cleaning
+
+  Revision 1.93  2003/06/25 16:33:55  brouard
+  (Module): On windows (cygwin) function asctime_r doesn't
+  exist so I changed back to asctime which exists.
+  (Module): Version 0.96b
+
+  Revision 1.92  2003/06/25 16:30:45  brouard
+  (Module): On windows (cygwin) function asctime_r doesn't
+  exist so I changed back to asctime which exists.
+
+  Revision 1.91  2003/06/25 15:30:29  brouard
+  * imach.c (Repository): Duplicated warning errors corrected.
+  (Repository): Elapsed time after each iteration is now output. It
+  helps to forecast when convergence will be reached. Elapsed time
+  is stamped in powell.  We created a new html file for the graphs
+  concerning matrix of covariance. It has extension -cov.htm.
+
   Revision 1.90  2003/06/24 12:34:15  brouard
   (Module): Some bugs corrected for windows. Also, when
   mle=-1 a template is output in file "or"mypar.txt with the design
@@ -174,12 +193,12 @@
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.90 2003/06/24 12:34:15 brouard Exp $ */
+/* $Id: imach.c,v 1.94 2003/06/27 13:00:02 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.90 $ $Date: 2003/06/24 12:34:15 $"; 
-int erreur; /* Error number */
+char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.94 $ $Date: 2003/06/27 13:00:02 $"; 
+int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;
@@ -211,7 +230,7 @@ char fileresilk[FILENAMELENGTH]; /* File
 FILE *ficresilk;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE *ficresprobmorprev;
-FILE *fichtm; /* Html File */
+FILE *fichtm, *fichtmcov; /* Html File */
 FILE *ficreseij;
 char filerese[FILENAMELENGTH];
 FILE  *ficresvij;
@@ -226,13 +245,21 @@ char command[FILENAMELENGTH];
 int  outcmd=0;
 
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-char lfileres[FILENAMELENGTH];
+
 char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];
 char popfile[FILENAMELENGTH];
 
-char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+
+struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+struct timezone tzp;
+extern int gettimeofday();
+struct tm tmg, tm, tmf, *gmtime(), *localtime();
+long time_value;
+extern long time();
+char strcurr[80], strfor[80];
 
 #define NR_END 1
 #define FREE_ARG char*
@@ -538,6 +565,41 @@ void free_ma3x(double ***m, long nrl, lo
   free((FREE_ARG)(m+nrl-NR_END));
 }
 
+/*************** function subdirf ***********/
+char *subdirf(char fileres[])
+{
+  /* Caution optionfilefiname is hidden */
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/"); /* Add to the right */
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+
+/*************** function subdirf2 ***********/
+char *subdirf2(char fileres[], char *preop)
+{
+  
+  /* Caution optionfilefiname is hidden */
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/");
+  strcat(tmpout,preop);
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+
+/*************** function subdirf3 ***********/
+char *subdirf3(char fileres[], char *preop, char *preop2)
+{
+  
+  /* Caution optionfilefiname is hidden */
+  strcpy(tmpout,optionfilefiname);
+  strcat(tmpout,"/");
+  strcat(tmpout,preop);
+  strcat(tmpout,preop2);
+  strcat(tmpout,fileres);
+  return tmpout;
+}
+
 /***************** f1dim *************************/
 extern int ncom; 
 extern double *pcom,*xicom;
@@ -713,6 +775,19 @@ void linmin(double p[], double xi[], int
   free_vector(pcom,1,n); 
 } 
 
+char *asc_diff_time(long time_sec, char ascdiff[])
+{
+  long sec_left, days, hours, minutes;
+  days = (time_sec) / (60*60*24);
+  sec_left = (time_sec) % (60*60*24);
+  hours = (sec_left) / (60*60) ;
+  sec_left = (sec_left) %(60*60);
+  minutes = (sec_left) /60;
+  sec_left = (sec_left) % (60);
+  sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
+  return ascdiff;
+}
+
 /*************** powell ************************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 	    double (*func)(double [])) 
@@ -723,6 +798,8 @@ void powell(double p[], double **xi, int
   double del,t,*pt,*ptt,*xit;
   double fp,fptt;
   double *xits;
+  int niterf, itmp;
+
   pt=vector(1,n); 
   ptt=vector(1,n); 
   xit=vector(1,n); 
@@ -733,9 +810,11 @@ void powell(double p[], double **xi, int
     fp=(*fret); 
     ibig=0; 
     del=0.0; 
-    printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
-    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
-    fprintf(ficrespow,"%d %.12f",*iter,*fret);
+    last_time=curr_time;
+    (void) gettimeofday(&curr_time,&tzp);
+    printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+    fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);
@@ -743,7 +822,29 @@ void powell(double p[], double **xi, int
     }
     printf("\n");
     fprintf(ficlog,"\n");
-    fprintf(ficrespow,"\n");
+    fprintf(ficrespow,"\n");fflush(ficrespow);
+    if(*iter <=3){
+      tm = *localtime(&curr_time.tv_sec);
+      strcpy(strcurr,asctime(&tmf));
+/*       asctime_r(&tm,strcurr); */
+      forecast_time=curr_time;
+      itmp = strlen(strcurr);
+      if(strcurr[itmp-1]=='\n')
+	strcurr[itmp-1]='\0';
+      printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+      fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+      for(niterf=10;niterf<=30;niterf+=10){
+	forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+	tmf = *localtime(&forecast_time.tv_sec);
+/* 	asctime_r(&tmf,strfor); */
+	strcpy(strfor,asctime(&tmf));
+	itmp = strlen(strfor);
+	if(strfor[itmp-1]=='\n')
+	strfor[itmp-1]='\0';
+	printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+	fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+      }
+    }
     for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret); 
@@ -1156,31 +1257,10 @@ double func( double *x)
 	  oldm=newm;
 	} /* end mult */
       
-	/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-	/* But now since version 0.9 we anticipate for bias and large stepm.
-	 * If stepm is larger than one month (smallest stepm) and if the exact delay 
-	 * (in months) between two waves is not a multiple of stepm, we rounded to 
-	 * the nearest (and in case of equal distance, to the lowest) interval but now
-	 * we keep into memory the bias bh[mi][i] and also the previous matrix product
-	 * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-	 * probability in order to take into account the bias as a fraction of the way
-	 * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-	 * -stepm/2 to stepm/2 .
-	 * For stepm=1 the results are the same as for previous versions of Imach.
-	 * For stepm > 1 the results are less biased than in previous versions. 
-	 */
 	s1=s[mw[mi][i]][i];
 	s2=s[mw[mi+1][i]][i];
 	bbh=(double)bh[mi][i]/(double)stepm; 
-	/* bias is positive if real duration
-	 * is higher than the multiple of stepm and negative otherwise.
-	 */
 	lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-	/*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
-	/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-	/*if(lli ==000.0)*/
-	/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 	ipmx +=1;
 	sw += weight[i];
 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
@@ -1207,30 +1287,10 @@ double func( double *x)
 	  oldm=newm;
 	} /* end mult */
       
-	/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-	/* But now since version 0.9 we anticipate for bias and large stepm.
-	 * If stepm is larger than one month (smallest stepm) and if the exact delay 
-	 * (in months) between two waves is not a multiple of stepm, we rounded to 
-	 * the nearest (and in case of equal distance, to the lowest) interval but now
-	 * we keep into memory the bias bh[mi][i] and also the previous matrix product
-	 * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
-	 * probability in order to take into account the bias as a fraction of the way
-	 * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
-	 * -stepm/2 to stepm/2 .
-	 * For stepm=1 the results are the same as for previous versions of Imach.
-	 * For stepm > 1 the results are less biased than in previous versions. 
-	 */
 	s1=s[mw[mi][i]][i];
 	s2=s[mw[mi+1][i]][i];
 	bbh=(double)bh[mi][i]/(double)stepm; 
-	/* bias is positive if real duration
-	 * is higher than the multiple of stepm and negative otherwise.
-	 */
-	/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
 	lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-	/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-	/*if(lli ==000.0)*/
-	/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 	ipmx +=1;
 	sw += weight[i];
 	ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
@@ -1396,35 +1456,8 @@ double funcone( double *x)
   return -l;
 }
 
-char *subdirf(char fileres[])
-{
-  
-  strcpy(tmpout,optionfilefiname);
-  strcat(tmpout,"/"); /* Add to the right */
-  strcat(tmpout,fileres);
-  return tmpout;
-}
-
-char *subdirf2(char fileres[], char *preop)
-{
-  
-  strcpy(tmpout,optionfilefiname);
-  strcat(tmpout,"/");
-  strcat(tmpout,preop);
-  strcat(tmpout,fileres);
-  return tmpout;
-}
-char *subdirf3(char fileres[], char *preop, char *preop2)
-{
-  
-  strcpy(tmpout,optionfilefiname);
-  strcat(tmpout,"/");
-  strcat(tmpout,preop);
-  strcat(tmpout,preop2);
-  strcat(tmpout,fileres);
-  return tmpout;
-}
 
+/*************** function likelione ***********/
 void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 {
   /* This routine should help understanding what is done with 
@@ -2036,6 +2069,7 @@ void  concatwav(int wav[], int **dh, int
 
     wav[i]=mi;
     if(mi==0){
+      nbwarn++;
       if(first==0){
 	printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 	first=1;
@@ -2056,10 +2090,11 @@ void  concatwav(int wav[], int **dh, int
 	    j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 	    if(j==0) j=1;  /* Survives at least one month after exam */
 	    else if(j<0){
+	      nberr++;
 	      printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-	      j=1; /* Careful Patch */
+	      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("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,"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;
@@ -2079,6 +2114,7 @@ void  concatwav(int wav[], int **dh, int
 	  /*	    if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 	  /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
 	  if(j<0){
+	    nberr++;
 	    printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 	    fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 	  }
@@ -2809,9 +2845,19 @@ void varprob(char optionfilefiname[], do
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");
 
-  fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
-  fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-  fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
+  fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
+  fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
+  file %s<br>\n",optionfilehtmcov);
+  fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+and drawn. It helps understanding how is the covariance between two incidences.\
+ They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+  fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+standard deviations wide on each axis. <br>\
+ Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+ and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
 
   cov[1]=1;
   tj=cptcoveff;
@@ -2993,13 +3039,13 @@ void varprob(char optionfilefiname[], do
  		    fprintf(ficgp,"\nset parametric;unset label");
 		    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
 		    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+		    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
 %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
 			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
 			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-		    fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-		    fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+		    fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+		    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
 		    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
@@ -3008,7 +3054,7 @@ void varprob(char optionfilefiname[], do
 			    mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
 		  }else{
 		    first=0;
-		    fprintf(fichtm," %d (%.3f),",(int) age, c12);
+		    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 		    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
@@ -3031,7 +3077,8 @@ void varprob(char optionfilefiname[], do
   fclose(ficresprob);
   fclose(ficresprobcov);
   fclose(ficresprobcor);
-  /*  fclose(ficgp);*/
+  fflush(ficgp);
+  fflush(fichtmcov);
 }
 
 
@@ -3674,9 +3721,14 @@ int fileappend(FILE *fichier, char *opti
   fflush(fichier);
   return (1);
 }
+
+
+/**************** function prwizard **********************/
 void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
 {
 
+  /* Wizard to print covariance matrix template */
+
   char ca[32], cb[32], cc[32];
   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
   int numlinepar;
@@ -3794,6 +3846,7 @@ void prwizard(int ncovmodel, int nlstate
 
 } /* end of prwizard */
 
+
 /***********************************************/
 /**************** Main Program *****************/
 /***********************************************/
@@ -3857,15 +3910,10 @@ int main(int argc, char *argv[])
   int lstra;
 
   long total_usecs;
-  struct timeval start_time, end_time, curr_time;
-  struct timezone tzp;
-  extern int gettimeofday();
-  struct tm tmg, tm, *gmtime(), *localtime();
-  long time_value;
-  extern long time();
  
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   (void) gettimeofday(&start_time,&tzp);
+  curr_time=start_time;
   tm = *localtime(&start_time.tv_sec);
   tmg = *gmtime(&start_time.tv_sec);
   strcpy(strstart,asctime(&tm));
@@ -3886,6 +3934,8 @@ int main(int argc, char *argv[])
 *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
 */
 
+  nberr=0; /* Number of errors and warnings */
+  nbwarn=0;
   getcwd(pathcd, size);
 
   printf("\n%s\n%s",version,fullversion);
@@ -3934,9 +3984,11 @@ int main(int argc, char *argv[])
  optionfilext=%s\n\
  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
 
-  printf("Localtime (at start):%s",strstart);
-  fprintf(ficlog,"Localtime (at start): %s",strstart);
+  printf("Local time (at start):%s",strstart);
+  fprintf(ficlog,"Local time (at start): %s",strstart);
   fflush(ficlog);
+/*   (void) gettimeofday(&curr_time,&tzp); */
+/*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
 
   /* */
   strcpy(fileres,"r");
@@ -4328,11 +4380,13 @@ int main(int argc, char *argv[])
 	s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+	nberr++;
 	printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
 	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
 	s[m][i]=-1;
       }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+	nberr++;
 	printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
 	fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
 	s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
@@ -4351,6 +4405,7 @@ int main(int argc, char *argv[])
 	  /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
 	    else {
 	      if ((int)andc[i]!=9999){
+		nbwarn++;
 		printf("Warning negative age at death: %ld line:%d\n",num[i],i);
 		fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
 		agev[m][i]=-1;
@@ -4387,6 +4442,7 @@ int main(int argc, char *argv[])
   for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {
+	nberr++;
 	printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	
 	fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	
 	goto end;
@@ -4469,12 +4525,24 @@ int main(int argc, char *argv[])
   /*  fclose(ficgp);*/
   /*--------- index.htm --------*/
 
-  strcpy(optionfilehtm,optionfilefiname);
+  strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm), exit(0);
   }
 
+  strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+  strcat(optionfilehtmcov,"-cov.htm");
+  if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtmcov), exit(0);
+  }
+  else{
+  fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
+<hr size=\"2\" color=\"#EC5E5E\"> \n\
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+	  fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+  }
+
   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
@@ -4485,18 +4553,14 @@ Title=%s <br>Datafile=%s Firstpass=%d La
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
  - Date and time at start: %s</ul>\n",\
-	  fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
-	  model,fileres,fileres,\
+	  fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+	  fileres,fileres,\
 	  filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-  /*fclose(fichtm);*/
   fflush(fichtm);
 
   strcpy(pathr,path);
   strcat(pathr,optionfilefiname);
   chdir(optionfilefiname); /* Move to directory named optionfile */
-  strcpy(lfileres,fileres);
-  strcat(lfileres,"/");
-  strcat(lfileres,optionfilefiname);
   
   /* Calculates basic frequencies. Computes observed prevalence at single age
      and prints on file fileres'p'. */
@@ -5024,60 +5088,58 @@ ageminpar, agemax, s[lastpass][imx], age
   fflush(ficgp);
   
 
-  if(erreur >0){
-    printf("End of Imach with error or warning %d\n",erreur);
-    fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+  if((nberr >0) || (nbwarn>0)){
+    printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+    fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
   }else{
-   printf("End of Imach\n");
-   fprintf(ficlog,"End of Imach\n");
+    printf("End of Imach\n");
+    fprintf(ficlog,"End of Imach\n");
   }
   printf("See log file on %s\n",filelog);
-  fclose(ficlog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
   (void) gettimeofday(&end_time,&tzp);
   tm = *localtime(&end_time.tv_sec);
   tmg = *gmtime(&end_time.tv_sec);
   strcpy(strtend,asctime(&tm));
-  printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
-  fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend); 
-  /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
-
-  printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
-  fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
+  printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
+  fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
+  printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+
+  printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+  fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+  fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
   /*  printf("Total time was %d uSec.\n", total_usecs);*/
 /*   if(fileappend(fichtm,optionfilehtm)){ */
   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
   fclose(fichtm);
+  fclose(fichtmcov);
   fclose(ficgp);
+  fclose(ficlog);
   /*------ End -----------*/
 
-  end:
-#ifdef windows
-  /* chdir(pathcd);*/
-#endif 
   chdir(path);
- /*system("wgnuplot graph.plt");*/
- /*system("../gp37mgw/wgnuplot graph.plt");*/
- /*system("cd ../gp37mgw");*/
- /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
   strcpy(plotcmd,GNUPLOTPROGRAM);
   strcat(plotcmd," ");
   strcat(plotcmd,optionfilegnuplot);
   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
-  system(plotcmd);
+  if((outcmd=system(plotcmd)) != 0){
+    printf(" Problem with gnuplot\n");
+  }
   printf(" Wait...");
-
- /*#ifdef windows*/
   while (z[0] != 'q') {
     /* chdir(path); */
-    printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+    printf("\nType e to edit output files, g to graph again and q for exiting: ");
     scanf("%s",z);
-    if (z[0] == 'c') system("./imach");
-    else if (z[0] == 'e') system(optionfilehtm);
+/*     if (z[0] == 'c') system("./imach"); */
+    if (z[0] == 'e') system(optionfilehtm);
     else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);
   }
-  /*#endif */
+  end:
+  while (z[0] != 'q') {
+    printf("\nType  q for exiting: ");
+    scanf("%s",z);
+  }
 }