--- imach/src/imach.c	2009/07/06 10:21:25	1.133
+++ imach/src/imach.c	2014/12/22 15:17:42	1.168
@@ -1,6 +1,157 @@
-/* $Id: imach.c,v 1.133 2009/07/06 10:21:25 brouard Exp $
+/* $Id: imach.c,v 1.168 2014/12/22 15:17:42 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.168  2014/12/22 15:17:42  brouard
+  Summary: udate
+
+  Revision 1.167  2014/12/22 13:50:56  brouard
+  Summary: Testing uname and compiler version and if compiled 32 or 64
+
+  Testing on Linux 64
+
+  Revision 1.166  2014/12/22 11:40:47  brouard
+  *** empty log message ***
+
+  Revision 1.165  2014/12/16 11:20:36  brouard
+  Summary: After compiling on Visual C
+
+  * imach.c (Module): Merging 1.61 to 1.162
+
+  Revision 1.164  2014/12/16 10:52:11  brouard
+  Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+
+  * imach.c (Module): Merging 1.61 to 1.162
+
+  Revision 1.163  2014/12/16 10:30:11  brouard
+  * imach.c (Module): Merging 1.61 to 1.162
+
+  Revision 1.162  2014/09/25 11:43:39  brouard
+  Summary: temporary backup 0.99!
+
+  Revision 1.1  2014/09/16 11:06:58  brouard
+  Summary: With some code (wrong) for nlopt
+
+  Author:
+
+  Revision 1.161  2014/09/15 20:41:41  brouard
+  Summary: Problem with macro SQR on Intel compiler
+
+  Revision 1.160  2014/09/02 09:24:05  brouard
+  *** empty log message ***
+
+  Revision 1.159  2014/09/01 10:34:10  brouard
+  Summary: WIN32
+  Author: Brouard
+
+  Revision 1.158  2014/08/27 17:11:51  brouard
+  *** empty log message ***
+
+  Revision 1.157  2014/08/27 16:26:55  brouard
+  Summary: Preparing windows Visual studio version
+  Author: Brouard
+
+  In order to compile on Visual studio, time.h is now correct and time_t
+  and tm struct should be used. difftime should be used but sometimes I
+  just make the differences in raw time format (time(&now).
+  Trying to suppress #ifdef LINUX
+  Add xdg-open for __linux in order to open default browser.
+
+  Revision 1.156  2014/08/25 20:10:10  brouard
+  *** empty log message ***
+
+  Revision 1.155  2014/08/25 18:32:34  brouard
+  Summary: New compile, minor changes
+  Author: Brouard
+
+  Revision 1.154  2014/06/20 17:32:08  brouard
+  Summary: Outputs now all graphs of convergence to period prevalence
+
+  Revision 1.153  2014/06/20 16:45:46  brouard
+  Summary: If 3 live state, convergence to period prevalence on same graph
+  Author: Brouard
+
+  Revision 1.152  2014/06/18 17:54:09  brouard
+  Summary: open browser, use gnuplot on same dir than imach if not found in the path
+
+  Revision 1.151  2014/06/18 16:43:30  brouard
+  *** empty log message ***
+
+  Revision 1.150  2014/06/18 16:42:35  brouard
+  Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+  Author: brouard
+
+  Revision 1.149  2014/06/18 15:51:14  brouard
+  Summary: Some fixes in parameter files errors
+  Author: Nicolas Brouard
+
+  Revision 1.148  2014/06/17 17:38:48  brouard
+  Summary: Nothing new
+  Author: Brouard
+
+  Just a new packaging for OS/X version 0.98nS
+
+  Revision 1.147  2014/06/16 10:33:11  brouard
+  *** empty log message ***
+
+  Revision 1.146  2014/06/16 10:20:28  brouard
+  Summary: Merge
+  Author: Brouard
+
+  Merge, before building revised version.
+
+  Revision 1.145  2014/06/10 21:23:15  brouard
+  Summary: Debugging with valgrind
+  Author: Nicolas Brouard
+
+  Lot of changes in order to output the results with some covariates
+  After the Edimburgh REVES conference 2014, it seems mandatory to
+  improve the code.
+  No more memory valgrind error but a lot has to be done in order to
+  continue the work of splitting the code into subroutines.
+  Also, decodemodel has been improved. Tricode is still not
+  optimal. nbcode should be improved. Documentation has been added in
+  the source code.
+
+  Revision 1.143  2014/01/26 09:45:38  brouard
+  Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+
+  * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+  (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+
+  Revision 1.142  2014/01/26 03:57:36  brouard
+  Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
+
+  * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+
+  Revision 1.141  2014/01/26 02:42:01  brouard
+  * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+
+  Revision 1.140  2011/09/02 10:37:54  brouard
+  Summary: times.h is ok with mingw32 now.
+
+  Revision 1.139  2010/06/14 07:50:17  brouard
+  After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
+  I remember having already fixed agemin agemax which are pointers now but not cvs saved.
+
+  Revision 1.138  2010/04/30 18:19:40  brouard
+  *** empty log message ***
+
+  Revision 1.137  2010/04/29 18:11:38  brouard
+  (Module): Checking covariates for more complex models
+  than V1+V2. A lot of change to be done. Unstable.
+
+  Revision 1.136  2010/04/26 20:30:53  brouard
+  (Module): merging some libgsl code. Fixing computation
+  of likelione (using inter/intrapolation if mle = 0) in order to
+  get same likelihood as if mle=1.
+  Some cleaning of code and comments added.
+
+  Revision 1.135  2009/10/29 15:33:14  brouard
+  (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+
+  Revision 1.134  2009/10/29 13:18:53  brouard
+  (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
+
   Revision 1.133  2009/07/06 10:21:25  brouard
   just nforces
 
@@ -334,10 +485,22 @@
       begin-prev-date,...
   open gnuplot file
   open html file
-  period (stable) prevalence
-   for age prevalim()
-  h Pij x
-  variance of p varprob
+  period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
+   for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
+                                  | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
+    freexexit2 possible for memory heap.
+
+  h Pij x                         | pij_nom  ficrestpij
+   # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
+       1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
+       1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
+
+       1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
+       1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
+  variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
+   Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
+   Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
+
   forecasting if prevfcast==1 prevforecast call prevalence()
   health expectancies
   Variance-covariance of DFLE
@@ -350,29 +513,52 @@
  end
 */
 
+#define POWELL /* Instead of NLOPT */
 
-
- 
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
+
+#ifdef _WIN32
+#include <io.h>
+#else
 #include <unistd.h>
+#endif
 
 #include <limits.h>
 #include <sys/types.h>
+#include <sys/utsname.h>
 #include <sys/stat.h>
 #include <errno.h>
-extern int errno;
+/* extern int errno; */
 
+/* #ifdef LINUX */
+/* #include <time.h> */
+/* #include "timeval.h" */
+/* #else */
 /* #include <sys/time.h> */
+/* #endif */
+
 #include <time.h>
-#include "timeval.h"
+
+#ifdef GSL
+#include <gsl/gsl_errno.h>
+#include <gsl/gsl_multimin.h>
+#endif
+
+
+#ifdef NLOPT
+#include <nlopt.h>
+typedef struct {
+  double (* function)(double [] );
+} myfunc_data ;
+#endif
 
 /* #include <libintl.h> */
 /* #define _(String) gettext (String) */
 
-#define MAXLINE 256
+#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 
 #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
@@ -381,38 +567,46 @@ extern int errno;
 #define	GLOCK_ERROR_NOPATH		-1	/* empty path */
 #define	GLOCK_ERROR_GETCWD		-2	/* cannot get cwd */
 
-#define MAXPARM 128 /* Maximum number of parameters for the optimization */
-#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+#define MAXPARM 128 /**< Maximum number of parameters for the optimization */
+#define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 
 #define NINTERVMAX 8
-#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
-#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
-#define NCOVMAX 20 /* Maximum number of covariates */
+#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
+#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
+#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
+#define codtabm(h,k)  1 & (h-1) >> (k-1) ;
 #define MAXN 20000
-#define YEARM 12. /* Number of months per year */
+#define YEARM 12. /**< Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
-#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
-#ifdef UNIX
-#define DIRSEPARATOR '/'
-#define CHARSEPARATOR "/"
-#define ODIRSEPARATOR '\\'
-#else
+#define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
+#ifdef _WIN32
 #define DIRSEPARATOR '\\'
 #define CHARSEPARATOR "\\"
 #define ODIRSEPARATOR '/'
+#else
+#define DIRSEPARATOR '/'
+#define CHARSEPARATOR "/"
+#define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.133 2009/07/06 10:21:25 brouard Exp $ */
+/* $Id: imach.c,v 1.168 2014/12/22 15:17:42 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite ";
-char fullversion[]="$Revision: 1.133 $ $Date: 2009/07/06 10:21:25 $"; 
+char version[]="Imach version 0.98nY, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+char fullversion[]="$Revision: 1.168 $ $Date: 2014/12/22 15:17:42 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar=0, nforce=0; /* Number of variables, number of forces */
-int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
+/* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
+int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
+int cptcovprodnoage=0; /**< Number of covariate products without age */   
+int cptcoveff=0; /* Total number of covariates to vary for printing results */
+int cptcov=0; /* Working variable */
 int npar=NPARMAX;
 int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */
@@ -430,10 +624,13 @@ int **mw; /* mw[mi][i] is number of the
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 	   * wave mi and wave mi+1 is not an exact multiple of stepm. */
+int countcallfunc=0;  /* Count the number of calls to func */
 double jmean=1; /* Mean space between 2 waves */
+double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+/*FILE *fic ; */ /* Used in readdata only */
+FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficlog, *ficrespow;
 int globpr=0; /* Global variable for printing or not */
 double fretone; /* Only one call to likelihood */
@@ -471,12 +668,17 @@ char popfile[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();
+/* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
+/* struct timezone tzp; */
+/* extern int gettimeofday(); */
+struct tm tml, *gmtime(), *localtime();
+
+extern time_t time();
+
+struct tm start_time, end_time, curr_time, last_time, forecast_time;
+time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
+struct tm tm;
+
 char strcurr[80], strfor[80];
 
 char *endptr;
@@ -506,7 +708,12 @@ static double maxarg1,maxarg2;
   
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)
-
+/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
+/* #define mytinydouble 1.0e-16 */
+/* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
+/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
+/* static double dsqrarg; */
+/* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
 static double sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
@@ -529,12 +736,19 @@ double dateintmean=0;
 
 double *weight;
 int **s; /* Status */
-double *agedc, **covar, idx;
-int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+double *agedc;
+double  **covar; /**< covar[j,i], value of jth covariate for individual i,
+		  * covar=matrix(0,NCOVMAX,1,n); 
+		  * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
+double  idx; 
+int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+int *Ndum; /** Freq of modality (tricode */
+int **codtab; /**< codtab=imatrix(1,100,1,10); */
+int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double *lsurv, *lpop, *tpop;
 
-double ftol=FTOL; /* Tolerance for computing Max Likelihood */
-double ftolhess; /* Tolerance for computing hessian */
+double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
+double ftolhess; /**< Tolerance for computing hessian */
 
 /**************** split *************************/
 static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
@@ -604,11 +818,11 @@ void replace_back_to_slash(char *s, char
 }
 
 char *trimbb(char *out, char *in)
-{ /* Trim multiple blanks in line */
+{ /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   char *s;
   s=out;
   while (*in != '\0'){
-    while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
+    while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       in++;
     }
     *out++ = *in++;
@@ -617,6 +831,63 @@ char *trimbb(char *out, char *in)
   return s;
 }
 
+char *cutl(char *blocc, char *alocc, char *in, char occ)
+{
+  /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
+     and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+     gives blocc="abcdef2ghi" and alocc="j".
+     If occ is not found blocc is null and alocc is equal to in. Returns blocc
+  */
+  char *s, *t;
+  t=in;s=in;
+  while ((*in != occ) && (*in != '\0')){
+    *alocc++ = *in++;
+  }
+  if( *in == occ){
+    *(alocc)='\0';
+    s=++in;
+  }
+ 
+  if (s == t) {/* occ not found */
+    *(alocc-(in-s))='\0';
+    in=s;
+  }
+  while ( *in != '\0'){
+    *blocc++ = *in++;
+  }
+
+  *blocc='\0';
+  return t;
+}
+char *cutv(char *blocc, char *alocc, char *in, char occ)
+{
+  /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
+     and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+     gives blocc="abcdef2ghi" and alocc="j".
+     If occ is not found blocc is null and alocc is equal to in. Returns alocc
+  */
+  char *s, *t;
+  t=in;s=in;
+  while (*in != '\0'){
+    while( *in == occ){
+      *blocc++ = *in++;
+      s=in;
+    }
+    *blocc++ = *in++;
+  }
+  if (s == t) /* occ not found */
+    *(blocc-(in-s))='\0';
+  else
+    *(blocc-(in-s)-1)='\0';
+  in=s;
+  while ( *in != '\0'){
+    *alocc++ = *in++;
+  }
+
+  *alocc='\0';
+  return s;
+}
+
 int nbocc(char *s, char occ)
 {
   int i,j=0;
@@ -629,27 +900,45 @@ int nbocc(char *s, char occ)
   return j;
 }
 
-void cutv(char *u,char *v, char*t, char occ)
-{
-  /* 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;
-  for(j=0; j<=strlen(t)-1; j++) {
-    if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
-  }
+/* void cutv(char *u,char *v, char*t, char occ) */
+/* { */
+/*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
+/*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
+/*      gives u="abcdef2ghi" and v="j" *\/ */
+/*   int i,lg,j,p=0; */
+/*   i=0; */
+/*   lg=strlen(t); */
+/*   for(j=0; j<=lg-1; j++) { */
+/*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+/*   } */
 
-  lg=strlen(t);
-  for(j=0; j<p; j++) {
-    (u[j] = t[j]);
-  }
-     u[p]='\0';
+/*   for(j=0; j<p; j++) { */
+/*     (u[j] = t[j]); */
+/*   } */
+/*      u[p]='\0'; */
+
+/*    for(j=0; j<= lg; j++) { */
+/*     if (j>=(p+1))(v[j-p-1] = t[j]); */
+/*   } */
+/* } */
 
-   for(j=0; j<= lg; j++) {
-    if (j>=(p+1))(v[j-p-1] = t[j]);
+#ifdef _WIN32
+char * strsep(char **pp, const char *delim)
+{
+  char *p, *q;
+         
+  if ((p = *pp) == NULL)
+    return 0;
+  if ((q = strpbrk (p, delim)) != NULL)
+  {
+    *pp = q + 1;
+    *q = '\0';
   }
+  else
+    *pp = 0;
+  return p;
 }
+#endif
 
 /********************** nrerror ********************/
 
@@ -758,7 +1047,9 @@ double **matrix(long nrl, long nrh, long
 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   return m;
-  /* print *(*(m+1)+70) or 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]) or &(m[1][0])
+m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
+that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
    */
 }
 
@@ -848,6 +1139,19 @@ char *subdirf3(char fileres[], char *pre
   return tmpout;
 }
 
+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,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
+  return ascdiff;
+}
+
 /***************** f1dim *************************/
 extern int ncom; 
 extern double *pcom,*xicom;
@@ -871,8 +1175,8 @@ double brent(double ax, double bx, doubl
 { 
   int iter; 
   double a,b,d,etemp;
-  double fu,fv,fw,fx;
-  double ftemp;
+  double fu=0,fv,fw,fx;
+  double ftemp=0.;
   double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double e=0.0; 
  
@@ -886,7 +1190,7 @@ double brent(double ax, double bx, doubl
     /*		if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     printf(".");fflush(stdout);
     fprintf(ficlog,".");fflush(ficlog);
-#ifdef DEBUG
+#ifdef DEBUGBRENT
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     /*		if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
@@ -956,21 +1260,29 @@ void mnbrak(double *ax, double *bx, doub
       } 
   *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx); 
-  while (*fb > *fc) { 
+  while (*fb > *fc) { /* Declining fa, fb, fc */
     r=(*bx-*ax)*(*fb-*fc); 
     q=(*bx-*cx)*(*fb-*fa); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
-      (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
-    ulim=(*bx)+GLIMIT*(*cx-*bx); 
-    if ((*bx-u)*(u-*cx) > 0.0) { 
+      (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
+    ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
+    if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
       fu=(*func)(u); 
-    } else if ((*cx-u)*(u-ulim) > 0.0) { 
+#ifdef DEBUG
+      /* f(x)=A(x-u)**2+f(u) */
+      double A, fparabu; 
+      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
+      fparabu= *fa - A*(*ax-u)*(*ax-u);
+      printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+      fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+#endif 
+    } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
       fu=(*func)(u); 
       if (fu < *fc) { 
 	SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 	  SHFT(*fb,*fc,fu,(*func)(u)) 
 	  } 
-    } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
+    } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       u=ulim; 
       fu=(*func)(u); 
     } else { 
@@ -983,7 +1295,11 @@ void mnbrak(double *ax, double *bx, doub
 } 
 
 /*************** linmin ************************/
-
+/* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
+resets p to where the function func(p) takes on a minimum along the direction xi from p ,
+and replaces xi by the actual vector displacement that p was moved. Also returns as fret
+the value of func at the returned location p . This is actually all accomplished by calling the
+routines mnbrak and brent .*/
 int ncom; 
 double *pcom,*xicom;
 double (*nrfunc)(double []); 
@@ -1009,8 +1325,8 @@ void linmin(double p[], double xi[], int
   } 
   ax=0.0; 
   xx=1.0; 
-  mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
-  *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
+  mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
+  *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
 #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
@@ -1023,20 +1339,16 @@ 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 ************************/
+/*
+Minimization of a function func of n variables. Input consists of an initial starting point
+p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
+rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
+such that failure to decrease by more than this amount on one iteration signals doneness. On
+output, p is set to the best point found, xi is the then-current direction set, fret is the returned
+function value at p , and iter is the number of iterations taken. The routine linmin is used.
+ */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 	    double (*func)(double [])) 
 { 
@@ -1054,15 +1366,18 @@ void powell(double p[], double **xi, int
   xits=vector(1,n); 
   *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j]; 
+    rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) { 
     fp=(*fret); 
     ibig=0; 
     del=0.0; 
-    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); fflush(ficlog);
-/*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+    rlast_time=rcurr_time;
+    /* (void) gettimeofday(&curr_time,&tzp); */
+    rcurr_time = time(NULL);  
+    curr_time = *localtime(&rcurr_time);
+    printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
+/*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);
@@ -1072,33 +1387,31 @@ void powell(double p[], double **xi, int
     fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");fflush(ficrespow);
     if(*iter <=3){
-      tm = *localtime(&curr_time.tv_sec);
-      strcpy(strcurr,asctime(&tm));
-/*       asctime_r(&tm,strcurr); */
-      forecast_time=curr_time; 
+      tml = *localtime(&rcurr_time);
+      strcpy(strcurr,asctime(&tml));
+      rforecast_time=rcurr_time; 
       itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 	strcurr[itmp-1]='\0';
-      printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-      fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+      printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
+      fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       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));
+	rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
+	forecast_time = *localtime(&rforecast_time);
+	strcpy(strfor,asctime(&forecast_time));
 	itmp = strlen(strfor);
 	if(strfor[itmp-1]=='\n')
 	strfor[itmp-1]='\0';
-	printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
-	fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+	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(rforecast_time-rcurr_time,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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }
     }
     for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret); 
 #ifdef DEBUG
-      printf("fret=%lf \n",*fret);
-      fprintf(ficlog,"fret=%lf \n",*fret);
+	  printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
+	  fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif
       printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
@@ -1116,13 +1429,13 @@ void powell(double p[], double **xi, int
 	fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }
       for(j=1;j<=n;j++) {
-	printf(" p=%.12e",p[j]);
-	fprintf(ficlog," p=%.12e",p[j]);
+	printf(" p(%d)=%.12e",j,p[j]);
+	fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       }
       printf("\n");
       fprintf(ficlog,"\n");
 #endif
-    } 
+    } /* end i */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 #ifdef DEBUG
       int k[2],l;
@@ -1155,20 +1468,45 @@ void powell(double p[], double **xi, int
       return; 
     } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
-    for (j=1;j<=n;j++) { 
+    for (j=1;j<=n;j++) { /* Computes an extrapolated point */
       ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j]; 
       pt[j]=p[j]; 
     } 
     fptt=(*func)(ptt); 
-    if (fptt < fp) { 
-      t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
-      if (t < 0.0) { 
-	linmin(p,xit,n,fret,func); 
+    if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
+      /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
+      /* From x1 (P0) distance of x2 is at h and x3 is 2h */
+      /* Let f"(x2) be the 2nd derivative equal everywhere.  */
+      /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
+      /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
+      /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
+      /* Thus we compare delta(2h) with observed f1-f3 */
+      /* or best gain on one ancient line 'del' with total  */
+      /* gain f1-f2 = f1 - f2 - 'del' with del  */
+      /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+
+      t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
+      t= t- del*SQR(fp-fptt);
+      printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+      fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+#ifdef DEBUG
+      printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+	     (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+      fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+	     (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+      printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+      fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+#endif
+      if (t < 0.0) { /* Then we use it for last direction */
+	linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
 	for (j=1;j<=n;j++) { 
-	  xi[j][ibig]=xi[j][n]; 
-	  xi[j][n]=xit[j]; 
+	  xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
+	  xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
 	}
+	printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+	fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
+
 #ifdef DEBUG
 	printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 	fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
@@ -1179,8 +1517,8 @@ void powell(double p[], double **xi, int
 	printf("\n");
 	fprintf(ficlog,"\n");
 #endif
-      }
-    } 
+      } /* end of t negative */
+    } /* end if (fptt < fp)  */
   } 
 } 
 
@@ -1193,7 +1531,7 @@ double **prevalim(double **prlim, int nl
 
   int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;
-  double **matprod2();
+  /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();
   double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */
@@ -1209,21 +1547,23 @@ double **prevalim(double **prlim, int nl
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     newm=savm;
     /* Covariates have to be included here again */
-     cov[2]=agefin;
-  
-      for (k=1; k<=cptcovn;k++) {
-	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-	/*	printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
-      }
-      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-      for (k=1; k<=cptcovprod;k++)
-	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-
-      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-    out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-
+    cov[2]=agefin;
+    
+    for (k=1; k<=cptcovn;k++) {
+      cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+      /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
+    }
+    /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+    /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
+    /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
+    
+    /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+    /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+    /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+    /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+    /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+    out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
+    
     savm=oldm;
     oldm=newm;
     maxmax=0.;
@@ -1234,6 +1574,7 @@ double **prevalim(double **prlim, int nl
 	sumnew=0;
 	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 	prlim[i][j]= newm[i][j]/(1-sumnew);
+        /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
 	max=FMAX(max,prlim[i][j]);
 	min=FMIN(min,prlim[i][j]);
       }
@@ -1250,41 +1591,56 @@ double **prevalim(double **prlim, int nl
 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {
-  double s1, s2;
+  /* According to parameters values stored in x and the covariate's values stored in cov,
+     computes the probability to be observed in state j being in state i by appying the
+     model to the ncovmodel covariates (including constant and age).
+     lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+     and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+     ncth covariate in the global vector x is given by the formula:
+     j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+     j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+     Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+     sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+     Outputs ps[i][j] the probability to be observed in j being in j according to
+     the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+  */
+  double s1, lnpijopii;
   /*double t34;*/
-  int i,j,j1, nc, ii, jj;
+  int i,j, 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); */
+	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+	  /*lnpijopii += param[i][j][nc]*cov[nc];*/
+	  lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+/* 	 printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
 	}
-	ps[i][j]=s2;
-/* 	printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+/* 	printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }
       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 (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+	  /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+	  lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+/* 	  printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
 	}
-	ps[i][j]=s2;
+	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }
     }
-    /*ps[3][2]=1;*/
     
     for(i=1; i<= nlstate; i++){
       s1=0;
       for(j=1; j<i; j++){
-	s1+=exp(ps[i][j]);
+	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 	/*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }
       for(j=i+1; j<=nlstate+ndeath; j++){
-	s1+=exp(ps[i][j]);
+	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 	/*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }
+      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       ps[i][i]=1./(s1+1.);
+      /* Computing other pijs */
       for(j=1; j<i; j++)
 	ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
@@ -1299,15 +1655,15 @@ double **pmij(double **ps, double *cov,
       }
     }
     
-
-/*        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(ii=1; ii<= nlstate+ndeath; ii++){ */
+    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+    /* 	printf(" pmij  ps[%d][%d]=%lf ",ii,jj,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;
@@ -1315,19 +1671,20 @@ double **pmij(double **ps, double *cov,
 
 /**************** Product of 2 matrices ******************/
 
-double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
 {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /* in, b, out are matrice of pointers which should have been initialized 
      before: only the contents of out is modified. The function returns
      a pointer to pointers identical to out */
-  long i, j, k;
+  int i, j, k;
   for(i=nrl; i<= nrh; i++)
-    for(k=ncolol; k<=ncoloh; k++)
-      for(j=ncl,out[i][k]=0.; j<=nch; j++)
-	out[i][k] +=in[i][j]*b[j][k];
-
+    for(k=ncolol; k<=ncoloh; k++){
+      out[i][k]=0.;
+      for(j=ncl; j<=nch; j++)
+  	out[i][k] +=in[i][j]*b[j][k];
+    }
   return out;
 }
 
@@ -1369,7 +1726,7 @@ double ***hpxij(double ***po, int nhstep
 	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (k=1; k<=cptcovage;k++)
 	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-      for (k=1; k<=cptcovprod;k++)
+      for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 
 
@@ -1391,6 +1748,25 @@ double ***hpxij(double ***po, int nhstep
   return po;
 }
 
+#ifdef NLOPT
+  double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
+  double fret;
+  double *xt;
+  int j;
+  myfunc_data *d2 = (myfunc_data *) pd;
+/* xt = (p1-1); */
+  xt=vector(1,n); 
+  for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
+
+  fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
+  /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
+  printf("Function = %.12lf ",fret);
+  for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
+  printf("\n");
+ free_vector(xt,1,n);
+  return fret;
+}
+#endif
 
 /*************** log-likelihood *************/
 double func( double *x)
@@ -1409,13 +1785,26 @@ double func( double *x)
   /*for(i=1;i<imx;i++) 
     printf(" %d\n",s[4][i]);
   */
+
+  ++countcallfunc;
+
   cov[1]=1.;
 
   for(k=1; k<=nlstate; k++) ll[k]=0.;
 
   if(mle==1){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      /* Computes the values of the ncovmodel covariates of the model
+	 depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+	 Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
+	 to be observed in j being in i according to the model.
+       */
+      for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
+	cov[2+k]=covar[Tvar[k]][i];
+      }
+      /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
+	 is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
+	 has been calculated etc */
       for(mi=1; mi<= wav[i]-1; mi++){
 	for (ii=1;ii<=nlstate+ndeath;ii++)
 	  for (j=1;j<=nlstate+ndeath;j++){
@@ -1426,7 +1815,7 @@ double func( double *x)
 	  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];
+	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
 	  }
 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
@@ -1680,8 +2069,11 @@ double funcone( double *x)
 	for (kk=1; kk<=cptcovage;kk++) {
 	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 	}
+	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+	/* 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 */
@@ -1706,15 +2098,16 @@ double funcone( double *x)
 	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 */
+      } else{  /* mle=0 back to 1 */
+	lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+	/*lli=log(out[s1][s2]); */ /* Original formula */
       } /* End of if */
       ipmx +=1;
       sw += weight[i];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){
-	fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+	fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
  %11.6f %11.6f %11.6f ", \
 		num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 		2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
@@ -1776,11 +2169,23 @@ void likelione(FILE *ficres,double p[],
 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {
-  int i,j, iter;
+  int i,j, iter=0;
   double **xi;
   double fret;
   double fretone; /* Only one call to likelihood */
   /*  char filerespow[FILENAMELENGTH];*/
+
+#ifdef NLOPT
+  int creturn;
+  nlopt_opt opt;
+  /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
+  double *lb;
+  double minf; /* the minimum objective value, upon return */
+  double * p1; /* Shifted parameters from 0 instead of 1 */
+  myfunc_data dinst, *d = &dinst;
+#endif
+
+
   xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++)
@@ -1797,14 +2202,41 @@ void mlikeli(FILE *ficres,double p[], in
     for(j=1;j<=nlstate+ndeath;j++)
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficrespow,"\n");
-
+#ifdef POWELL
   powell(p,xi,npar,ftol,&iter,&fret,func);
+#endif
 
+#ifdef NLOPT
+#ifdef NEWUOA
+  opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+#else
+  opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
+#endif
+  lb=vector(0,npar-1);
+  for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
+  nlopt_set_lower_bounds(opt, lb);
+  nlopt_set_initial_step1(opt, 0.1);
+  
+  p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
+  d->function = func;
+  printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
+  nlopt_set_min_objective(opt, myfunc, d);
+  nlopt_set_xtol_rel(opt, ftol);
+  if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
+    printf("nlopt failed! %d\n",creturn); 
+  }
+  else {
+    printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
+    printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
+    iter=1; /* not equal */
+  }
+  nlopt_destroy(opt);
+#endif
   free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);
-  printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-  fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-  fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+  printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
+  fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
+  fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 
 }
 
@@ -1813,7 +2245,7 @@ void hesscov(double **matcov, double p[]
 {
   double  **a,**y,*x,pd;
   double **hess;
-  int i, j,jk;
+  int i, j;
   int *indx;
 
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
@@ -1926,13 +2358,13 @@ double hessii(double x[], double delta,
 
   fx=func(x);
   for (i=1;i<=npar;i++) p2[i]=x[i];
-  for(l=0 ; l <=lmax; l++){
+  for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     l1=pow(10,l);
     delts=delt;
     for(k=1 ; k <kmax; k=k+1){
       delt = delta*(l1*k);
       p2[theta]=x[theta] +delt;
-      k1=func(p2)-fx;
+      k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
       p2[theta]=x[theta]-delt;
       k2=func(p2)-fx;
       /*res= (k1-2.0*fx+k2)/delt/delt; */
@@ -1947,7 +2379,7 @@ double hessii(double x[], double delta,
 	k=kmax;
       }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-	k=kmax; l=lmax*10.;
+	k=kmax; l=lmax*10;
       }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 	delts=delt;
@@ -1962,7 +2394,7 @@ double hessii(double x[], double delta,
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {
   int i;
-  int l=1, l1, lmax=20;
+  int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];
   int k;
@@ -2077,7 +2509,7 @@ void pstamp(FILE *fichier)
 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,j;
+  int i, m, jk, j1, bool, z1,j;
   int first;
   double ***freq; /* Frequencies */
   double *pp, **prop;
@@ -2101,29 +2533,38 @@ void  freqsummary(char fileres[], int ia
 
   first=1;
 
-  for(k1=1; k1<=j;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
-      j1++;
+  /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
+  /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
+  /*    j1++;
+*/
+  for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 	scanf("%d", i);*/
       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;
-
-    for (i=1; i<=nlstate; i++)  
-      for(m=iagemin; m <= iagemax+3; m++)
-	prop[i][m]=0;
+      
+      for (i=1; i<=nlstate; i++)  
+	for(m=iagemin; m <= iagemax+3; m++)
+	  prop[i][m]=0;
       
       dateintsum=0;
       k2cpt=0;
       for (i=1; i<=imx; i++) {
 	bool=1;
-	if  (cptcovn>0) {
-	  for (z1=1; z1<=cptcoveff; z1++) 
-	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
-	      bool=0;
+	if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+	  for (z1=1; z1<=cptcoveff; z1++)       
+            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
+                /* Tests if the value of each of the covariates of i is equal to filter j1 */
+              bool=0;
+              /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
+                bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
+                j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
+              /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
+            } 
 	}
+ 
 	if (bool==1){
 	  for(m=firstpass; m<=lastpass; m++){
 	    k2=anint[m][i]+(mint[m][i]/12.);
@@ -2143,7 +2584,7 @@ void  freqsummary(char fileres[], int ia
 	      /*}*/
 	  }
 	}
-      }
+      } /* end i */
        
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       pstamp(ficresp);
@@ -2151,6 +2592,9 @@ void  freqsummary(char fileres[], int ia
 	fprintf(ficresp, "\n#********** Variable "); 
 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 	fprintf(ficresp, "**********\n#");
+	fprintf(ficlog, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficlog, "**********\n#");
       }
       for(i=1; i<=nlstate;i++) 
 	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
@@ -2227,7 +2671,7 @@ void  freqsummary(char fileres[], int ia
 	  printf("Others in log...\n");
 	fprintf(ficlog,"\n");
       }
-    }
+      /*}*/
   }
   dateintmean=dateintsum/k2cpt; 
  
@@ -2246,12 +2690,13 @@ void prevalence(double ***probs, double
      We still use firstpass and lastpass as another selection.
   */
  
-  int i, m, jk, k1, i1, j1, bool, z1,j;
-  double ***freq; /* Frequencies */
-  double *pp, **prop;
-  double pos,posprop; 
+  int i, m, jk, j1, bool, z1,j;
+
+  double **prop;
+  double posprop; 
   double  y2; /* in fractional years */
   int iagemin, iagemax;
+  int first; /** to stop verbosity which is redirected to log file */
 
   iagemin= (int) agemin;
   iagemax= (int) agemax;
@@ -2260,12 +2705,13 @@ void prevalence(double ***probs, double
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;
   
-  j=cptcoveff;
+  /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
-  for(k1=1; k1<=j;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
-      j1++;
+  first=1;
+  for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
+    /*for(i1=1; i1<=ncodemax[k1];i1++){
+      j1++;*/
       
       for (i=1; i<=nlstate; i++)  
 	for(m=iagemin; m <= iagemax+3; m++)
@@ -2295,22 +2741,25 @@ void prevalence(double ***probs, double
 	}
       }
       for(i=iagemin; i <= iagemax+3; i++){  
-	
  	for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
  	  posprop += prop[jk][i]; 
  	} 
-
+	
  	for(jk=1; jk <=nlstate ; jk++){	    
  	  if( i <=  iagemax){ 
  	    if(posprop>=1.e-5){ 
  	      probs[i][jk][j1]= prop[jk][i]/posprop;
- 	    } else
-	      printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
+ 	    } else{
+	      if(first==1){
+		first=0;
+		printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
+	      }
+	    }
  	  } 
  	}/* end jk */ 
       }/* end i */ 
-    } /* end i1 */
-  } /* end k1 */
+    /*} *//* end i1 */
+  } /* end j1 */
   
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/
@@ -2335,7 +2784,7 @@ void  concatwav(int wav[], int **dh, int
   int j, k=0,jk, ju, jl;
   double sum=0.;
   first=0;
-  jmin=1e+5;
+  jmin=100000;
   jmax=-1;
   jmean=0.;
   for(i=1; i<=imx; i++){
@@ -2430,7 +2879,7 @@ void  concatwav(int wav[], int **dh, int
 	    dh[mi][i]=jk;
 	    bh[mi][i]=0;
 	  }else{ /* We want a negative bias in order to only have interpolation ie
-		  * at the price of an extra matrix product in likelihood */
+		  * to avoid the price of an extra matrix product in likelihood */
 	    dh[mi][i]=jk+1;
 	    bh[mi][i]=ju;
 	  }
@@ -2456,44 +2905,84 @@ void  concatwav(int wav[], int **dh, int
   }
   jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-  fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+  fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
  }
 
 /*********** Tricode ****************************/
-void tricode(int *Tvar, int **nbcode, int imx)
+void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
 {
-  
-  /*	  Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
+  /**< Uses cptcovn+2*cptcovprod as the number of covariates */
+  /*	  Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
+  /* Boring subroutine which should only output nbcode[Tvar[j]][k]
+   * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+  /* nbcode[Tvar[j]][1]= 
+  */
+
+  int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+  int modmaxcovj=0; /* Modality max of covariates j */
+  int cptcode=0; /* Modality max of covariates j */
+  int modmincovj=0; /* Modality min of covariates j */
+
 
-  int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-  int cptcode=0;
   cptcoveff=0; 
  
-  for (k=0; k<maxncov; k++) Ndum[k]=0;
-  for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
+  for (k=-1; k < maxncov; k++) Ndum[k]=0;
+  for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
 
-  for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
-    for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
-			       modality*/ 
-      ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
-      Ndum[ij]++; /*counts the occurence of this modality */
+  /* Loop on covariates without age and products */
+  for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
+    for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
+			       modality of this covariate Vj*/ 
+      ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+				    * If product of Vn*Vm, still boolean *:
+				    * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+				    * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+      /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+				      modality of the nth covariate of individual i. */
+      if (ij > modmaxcovj)
+        modmaxcovj=ij; 
+      else if (ij < modmincovj) 
+	modmincovj=ij; 
+      if ((ij < -1) && (ij > NCOVMAX)){
+	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+	exit(1);
+      }else
+      Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+      /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-      if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
-				       Tvar[j]. If V=sex and male is 0 and 
-				       female is 1, then  cptcode=1.*/
-    }
-
-    for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
-      if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
-				       th covariate. In fact
-				       ncodemax[j]=2
-				       (dichotom. variables only) but
-				       it can be more */
+      /* getting the maximum value of the modality of the covariate
+	 (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+	 female is 1, then modmaxcovj=1.*/
+    }
+    printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+    cptcode=modmaxcovj;
+    /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+   /*for (i=0; i<=cptcode; i++) {*/
+    for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
+      printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
+      if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
+	ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
+      }
+      /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
+	 historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     } /* Ndum[-1] number of undefined modalities */
 
-    ij=1; 
-    for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
-      for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
+    /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+    /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
+    /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
+       modmincovj=3; modmaxcovj = 7;
+       There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
+       which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
+       variables V1_1 and V1_2.
+       nbcode[Tvar[j]][ij]=k;
+       nbcode[Tvar[j]][1]=0;
+       nbcode[Tvar[j]][2]=1;
+       nbcode[Tvar[j]][3]=2;
+    */
+    ij=1; /* ij is similar to i but can jumps over null modalities */
+    for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
+      for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
+	/*recode from 0 */
 	if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
 	  nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
 				     k is a modality. If we have model=V1+V1*sex 
@@ -2501,36 +2990,41 @@ void tricode(int *Tvar, int **nbcode, in
 	  ij++;
 	}
 	if (ij > ncodemax[j]) break; 
-      }  
-    } 
-  }  
-
- for (k=0; k< maxncov; k++) Ndum[k]=0;
-
- for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-   /* 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]; /* Tvar might be -1 if status was unknown */
-   Ndum[ij]++;
- }
+      }  /* end of loop on */
+    } /* end of loop on modality */ 
+  } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
+  
+ for (k=-1; k< maxncov; k++) Ndum[k]=0; 
+  
+  for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
+   /* 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]; /* Tvar might be -1 if status was unknown */ 
+   Ndum[ij]++; 
+ } 
 
  ij=1;
- for (i=1; i<= maxncov; i++) {
+ for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+   /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){
-     Tvaraff[ij]=i; /*For printing */
+     /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+     Tvaraff[ij]=i; /*For printing (unclear) */
      ij++;
-   }
+   }else
+       Tvaraff[ij]=0;
  }
  ij--;
- cptcoveff=ij; /*Number of simple covariates*/
+ cptcoveff=ij; /*Number of total covariates*/
+
 }
 
+
 /*********** Health Expectancies ****************/
 
 void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
 
 {
   /* Health expectancies, no variances */
-  int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+  int i, j, nhstepm, hstepm, h, nstepm;
   int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;
   double ***p3mat;
@@ -2852,7 +3346,7 @@ void varevsij(char optionfilefiname[], d
   double **dnewm,**doldm;
   double **dnewmp,**doldmp;
   int i, j, nhstepm, hstepm, h, nstepm ;
-  int k, cptcode;
+  int k;
   double *xp;
   double **gp, **gm;  /* for var eij */
   double ***gradg, ***trgradg; /*for var eij */
@@ -3119,15 +3613,15 @@ void varevsij(char optionfilefiname[], d
   free_vector(gmp,nlstate+1,nlstate+ndeath);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-  fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
+  fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-  fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
-  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
-  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+  fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
+  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
+  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
@@ -3152,10 +3646,9 @@ void varprevlim(char fileres[], double *
 {
   /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-  double **newm;
+
   double **dnewm,**doldm;
   int i, j, nhstepm, hstepm;
-  int k, cptcode;
   double *xp;
   double *gp, *gm;
   double **gradg, **trgradg;
@@ -3234,23 +3727,22 @@ 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, char strstart[])
 {
-  int i, j=0,  i1, k1, l1, t, tj;
+  int i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;
-  int k=0,l, cptcode;
-  int first=1, first1;
+  int k=0, l;
+  int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;
   double *xp;
   double *gp, *gm;
   double **gradg, **trgradg;
   double **mu;
-  double age,agelim, cov[NCOVMAX];
+  double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;
   char fileresprob[FILENAMELENGTH];
   char fileresprobcov[FILENAMELENGTH];
   char fileresprobcor[FILENAMELENGTH];
-
   double ***varpij;
 
   strcpy(fileresprob,"prob"); 
@@ -3323,12 +3815,13 @@ standard deviations wide on each axis. <
 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;
+  /* tj=cptcoveff; */
+  tj = (int) pow(2,cptcoveff);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   j1=0;
-  for(t=1; t<=tj;t++){
-    for(i1=1; i1<=ncodemax[t];i1++){ 
-      j1++;
+  for(j1=1; j1<=tj;j1++){
+    /*for(i1=1; i1<=ncodemax[t];i1++){ */
+    /*j1++;*/
       if  (cptcovn>0) {
 	fprintf(ficresprob, "\n#********** Variable "); 
 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
@@ -3351,19 +3844,24 @@ To be simple, these graphs help to under
 	fprintf(ficresprobcor, "**********\n#");    
       }
       
+      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+      gp=vector(1,(nlstate)*(nlstate+ndeath));
+      gm=vector(1,(nlstate)*(nlstate+ndeath));
       for (age=bage; age<=fage; age ++){ 
 	cov[2]=age;
 	for (k=1; k<=cptcovn;k++) {
-	  cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+	  cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+							 * 1  1 1 1 1
+							 * 2  2 1 1 1
+							 * 3  1 2 1 1
+							 */
+	  /* nbcode[1][1]=0 nbcode[1][2]=1;*/
 	}
 	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 	for (k=1; k<=cptcovprod;k++)
 	  cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 	
-	gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-	gp=vector(1,(nlstate)*(nlstate+ndeath));
-	gm=vector(1,(nlstate)*(nlstate+ndeath));
     
 	for(theta=1; theta <=npar; theta++){
 	  for(i=1; i<=npar; i++)
@@ -3401,10 +3899,6 @@ To be simple, these graphs help to under
 	
 	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 	matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-	free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-	free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-	free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-	free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 
 	pmij(pmmij,cov,ncovmodel,x,nlstate);
 	
@@ -3438,17 +3932,22 @@ To be simple, these graphs help to under
 	i=0;
 	for (k=1; k<=(nlstate);k++){
  	  for (l=1; l<=(nlstate+ndeath);l++){ 
- 	    i=i++;
+ 	    i++;
 	    fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
 	    fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
 	    for (j=1; j<=i;j++){
+	      /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
 	      fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
 	      fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
 	    }
 	  }
 	}/* end of loop for state */
       } /* end of loop for age */
-
+      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      
       /* Confidence intervalle of pij  */
       /*
 	fprintf(ficgp,"\nunset parametric;unset label");
@@ -3461,7 +3960,7 @@ To be simple, these graphs help to under
       */
 
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-      first1=1;
+      first1=1;first2=2;
       for (k2=1; k2<=(nlstate);k2++){
 	for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 	  if(l2==k2) continue;
@@ -3482,6 +3981,16 @@ To be simple, these graphs help to under
 		  /* Computing eigen value of matrix of covariance */
 		  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 		  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+		  if ((lc2 <0) || (lc1 <0) ){
+		    if(first2==1){
+		      first1=0;
+		    printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+		    }
+		    fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+		    /* lc1=fabs(lc1); */ /* If we want to have them positive */
+		    /* lc2=fabs(lc2); */
+		  }
+
 		  /* Eigen vectors */
 		  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 		  /*v21=sqrt(1.-v11*v11); *//* error */
@@ -3501,7 +4010,7 @@ To be simple, these graphs help to under
 		    first=0;
  		    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(ficgp,"\nset ter png small size 320, 240");
 		    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,\
@@ -3532,7 +4041,7 @@ To be simple, these graphs help to under
 	  } /* k12 */
 	} /*l1 */
       }/* k1 */
-    } /* loop covariates */
+      /* } /* loop covariates */
   }
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
@@ -3578,7 +4087,7 @@ void printinghtml(char fileres[], char t
 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
 
- m=cptcoveff;
+ m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 
  jj1=0;
@@ -3592,20 +4101,20 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      /* Pij */
-     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
-<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
+     fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
+<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
      /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
-<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
+<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Period (stable) prevalence in each health state */
-       for(cpt=1; cpt<nlstate;cpt++){
-	 fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
-<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+       for(cpt=1; cpt<=nlstate;cpt++){
+	 fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
+<img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }
      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }
    } /* end i1 */
  }/* End k1 */
@@ -3652,7 +4161,7 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
  fflush(fichtm);
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 
- m=cptcoveff;
+ m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 
  jj1=0;
@@ -3667,8 +4176,8 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
      }
      for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
-<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
+prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
+<img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
@@ -3686,7 +4195,7 @@ true period expectancies (those weighted
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 
   char dirfileres[132],optfileres[132];
-  int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+  int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng=0;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */
@@ -3701,38 +4210,38 @@ void printinggnuplot(char fileres[], cha
   strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");
  /* 1eme*/
+  fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {
-   for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-     fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+    for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+     fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+     fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
      fprintf(ficgp,"set xlabel \"Age\" \n\
 set ylabel \"Probability\" \n\
-set ter png small\n\
-set size 0.65,0.65\n\
+set ter png small size 320, 240\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
 
      for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else        fprintf(ficgp," \%%*lf (\%%*lf)");
      }
-     fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+     fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");
      } 
-     fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
+     fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");
      }  
-     fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+     fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    }
   }
   /*2 eme*/
-  
+  fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
   for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-    fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+    fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
     
     for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;
@@ -3748,14 +4257,14 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 	else fprintf(ficgp," \%%*lf (\%%*lf)");
       }   
-      fprintf(ficgp,"\" t\"\" w l 0,");
+      fprintf(ficgp,"\" t\"\" w l lt 0,");
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {
 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 	else fprintf(ficgp," \%%*lf (\%%*lf)");
       }   
-      if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
-      else fprintf(ficgp,"\" t\"\" w l 0,");
+      if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+      else fprintf(ficgp,"\" t\"\" w l lt 0,");
     }
   }
   
@@ -3766,8 +4275,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
       /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-      fprintf(ficgp,"set ter png small\n\
-set size 0.65,0.65\n\
+      fprintf(ficgp,"set ter png small size 320, 240\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
@@ -3787,28 +4295,29 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
   }
   
   /* CV preval stable (period) */
-  for (k1=1; k1<= m ; k1 ++) { 
-    for (cpt=1; cpt<=nlstate ; cpt ++) {
+  for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+    for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+      fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-set ter png small\nset size 0.65,0.65\n\
+set ter png small size 320, 240\n\
 unset log y\n\
-plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-      
-      for (i=1; i< nlstate ; i ++)
-	fprintf(ficgp,"+$%d",k+i+1);
-      fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-      
-      l=3+(nlstate+ndeath)*cpt;
-      fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-      for (i=1; i< nlstate ; i ++) {
-	l=3+(nlstate+ndeath)*cpt;
-	fprintf(ficgp,"+$%d",l+i+1);
-      }
-      fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
-    } 
-  }  
+plot [%.f:%.f]  ", ageminpar, agemaxpar);
+      for (i=1; i<= nlstate ; i ++){
+	if(i==1)
+	  fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+	else
+	  fprintf(ficgp,", '' ");
+	l=(nlstate+ndeath)*(i-1)+1;
+	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+	for (j=1; j<= (nlstate-1) ; j ++)
+	  fprintf(ficgp,"+$%d",k+l+j);
+	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+      } /* nlstate */
+      fprintf(ficgp,"\n");
+    } /* end cpt state*/ 
+  } /* end covariate */  
   
   /* proba elementaires */
   for(i=1,jk=1; i <=nlstate; i++){
@@ -3822,15 +4331,15 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
       }
     }
    }
-
+  /*goto avoid;*/
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      for(jk=1; jk <=m; jk++) {
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
        if (ng==2)
 	 fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        else
 	 fprintf(ficgp,"\nset title \"Probability\"\n");
-       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+       fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
        i=1;
        for(k2=1; k2<=nlstate; k2++) {
 	 k3=i;
@@ -3840,13 +4349,13 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
 	       fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
 	     else
 	       fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-	     ij=1;
+	     ij=1;/* To be checked else nbcode[0][0] wrong */
 	     for(j=3; j <=ncovmodel; j++) {
-	       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-		 fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-		 ij++;
-	       }
-	       else
+	       /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
+	       /* 	 /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
+	       /* 	 ij++; */
+	       /* } */
+	       /* else */
 		 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 	     }
 	     fprintf(ficgp,")/(1");
@@ -3855,11 +4364,11 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
 	       fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
 	       ij=1;
 	       for(j=3; j <=ncovmodel; j++){
-		 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-		   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-		   ij++;
-		 }
-		 else
+		 /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
+		 /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
+		 /*   ij++; */
+		 /* } */
+		 /* else */
 		   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 	       }
 	       fprintf(ficgp,")");
@@ -3872,6 +4381,7 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
        } /* end k2 */
      } /* end jk */
    } /* end ng */
+ /* avoid: */
    fflush(ficgp); 
 }  /* end gnuplot */
 
@@ -3925,8 +4435,7 @@ prevforecast(char fileres[], double anpr
      dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).
   */
-  int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-  int *popage;
+  int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
   double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;
@@ -4220,8 +4729,8 @@ void prwizard(int ncovmodel, int nlstate
 
   /* 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;
+  char ca[32], cb[32];
+  int i,j, k, li, lj, lk, ll, jj, npar, itimes;
   int numlinepar;
 
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
@@ -4373,35 +4882,76 @@ double gompertz(double x[])
   return -2*L*num/sump;
 }
 
-/******************* Printing html file ***********/
-void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-		  int lastpass, int stepm, int weightopt, char model[],\
-		  int imx,  double p[],double **matcov,double agemortsup){
-  int i,k;
-
-  fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-  fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-  for (i=1;i<=2;i++) 
-    fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-  fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-  fprintf(fichtm,"</ul>");
-
-fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-
- fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
-
- for (k=agegomp;k<(agemortsup-2);k++) 
-   fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+#ifdef GSL
+/******************* Gompertz_f Likelihood ******************************/
+double gompertz_f(const gsl_vector *v, void *params)
+{ 
+  double A,B,LL=0.0,sump=0.,num=0.;
+  double *x= (double *) v->data;
+  int i,n=0; /* n is the size of the sample */
 
- 
-  fflush(fichtm);
+  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]);*/
+  printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+  for (i=1;i<=imx ; i++)
+    {
+      if (cens[i] == 1 && wav[i]>1)
+	A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+      
+      if (cens[i] == 0 && wav[i]>1)
+	A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+	     +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
+      
+      /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+      if (wav[i] > 1 ) { /* ??? */
+	LL=LL+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);*/
+  printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+ 
+  return -2*LL*num/sump;
+}
+#endif
+
+/******************* Printing html file ***********/
+void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+		  int lastpass, int stepm, int weightopt, char model[],\
+		  int imx,  double p[],double **matcov,double agemortsup){
+  int i,k;
+
+  fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+  fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+  for (i=1;i<=2;i++) 
+    fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+  fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+  fprintf(fichtm,"</ul>");
+
+fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+
+ fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+
+ for (k=agegomp;k<(agemortsup-2);k++) 
+   fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+
+ 
+  fflush(fichtm);
 }
 
 /******************* Gnuplot file **************/
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 
   char dirfileres[132],optfileres[132];
-  int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+
   int ng;
 
 
@@ -4414,15 +4964,529 @@ void printinggnuplotmort(char fileres[],
   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, "set ter png small size 320, 240\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);
 
 } 
 
+int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+{
+
+  /*-------- data file ----------*/
+  FILE *fic;
+  char dummy[]="                         ";
+  int i=0, j=0, n=0;
+  int linei, month, year,iout;
+  char line[MAXLINE], linetmp[MAXLINE];
+  char stra[MAXLINE], strb[MAXLINE];
+  char *stratrunc;
+  int lstra;
+
+
+  if((fic=fopen(datafile,"r"))==NULL)    {
+    printf("Problem while opening datafile: %s\n", datafile);return 1;
+    fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+  }
+
+  i=1;
+  linei=0;
+  while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+    linei=linei+1;
+    for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+      if(line[j] == '\t')
+	line[j] = ' ';
+    }
+    for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+      ;
+    };
+    line[j+1]=0;  /* Trims blanks at end of line */
+    if(line[0]=='#'){
+      fprintf(ficlog,"Comment line\n%s\n",line);
+      printf("Comment line\n%s\n",line);
+      continue;
+    }
+    trimbb(linetmp,line); /* Trims multiple blanks in line */
+    strcpy(line, linetmp);
+  
+
+    for (j=maxwav;j>=1;j--){
+      cutv(stra, strb, line, ' '); 
+      if(strb[0]=='.') { /* Missing status */
+	lval=-1;
+      }else{
+	errno=0;
+	lval=strtol(strb,&endptr,10); 
+      /*	if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+	if( strb[0]=='\0' || (*endptr != '\0')){
+	  printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+	  fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+	  return 1;
+	}
+      }
+      s[j][i]=lval;
+      
+      strcpy(line,stra);
+      cutv(stra, strb,line,' ');
+      if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+      }
+      else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+	month=99;
+	year=9999;
+      }else{
+	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+	return 1;
+      }
+      anint[j][i]= (double) year; 
+      mint[j][i]= (double)month; 
+      strcpy(line,stra);
+    } /* ENd Waves */
+    
+    cutv(stra, strb,line,' '); 
+    if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+    }
+    else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+      month=99;
+      year=9999;
+    }else{
+      printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+	return 1;
+    }
+    andc[i]=(double) year; 
+    moisdc[i]=(double) month; 
+    strcpy(line,stra);
+    
+    cutv(stra, strb,line,' '); 
+    if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+    }
+    else  if(iout=sscanf(strb,"%s.", dummy) != 0){
+      month=99;
+      year=9999;
+    }else{
+      printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+      fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+	return 1;
+    }
+    if (year==9999) {
+      printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+      fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+	return 1;
+
+    }
+    annais[i]=(double)(year);
+    moisnais[i]=(double)(month); 
+    strcpy(line,stra);
+    
+    cutv(stra, strb,line,' '); 
+    errno=0;
+    dval=strtod(strb,&endptr); 
+    if( strb[0]=='\0' || (*endptr != '\0')){
+      printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+      fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+      fflush(ficlog);
+      return 1;
+    }
+    weight[i]=dval; 
+    strcpy(line,stra);
+    
+    for (j=ncovcol;j>=1;j--){
+      cutv(stra, strb,line,' '); 
+      if(strb[0]=='.') { /* Missing status */
+	lval=-1;
+      }else{
+	errno=0;
+	lval=strtol(strb,&endptr,10); 
+	if( strb[0]=='\0' || (*endptr != '\0')){
+	  printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+	  fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
+	  return 1;
+	}
+      }
+      if(lval <-1 || lval >1){
+	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+ For example, for multinomial values like 1, 2 and 3,\n \
+ build V1=0 V2=0 for the reference value (1),\n \
+        V1=1 V2=0 for (2) \n \
+ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+ output of IMaCh is often meaningless.\n \
+ Exiting.\n",lval,linei, i,line,j);
+	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+ For example, for multinomial values like 1, 2 and 3,\n \
+ build V1=0 V2=0 for the reference value (1),\n \
+        V1=1 V2=0 for (2) \n \
+ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+ output of IMaCh is often meaningless.\n \
+ Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+	return 1;
+      }
+      covar[j][i]=(double)(lval);
+      strcpy(line,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("%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;
+  } /* End loop reading  data */
+
+  *imax=i-1; /* Number of individuals */
+  fclose(fic);
+ 
+  return (0);
+  /* endread: */
+    printf("Exiting readdata: ");
+    fclose(fic);
+    return (1);
+
 
 
+}
+void removespace(char *str) {
+  char *p1 = str, *p2 = str;
+  do
+    while (*p2 == ' ')
+      p2++;
+  while (*p1++ = *p2++);
+}
+
+int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
+   * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
+   * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
+   * - cptcovn or number of covariates k of the models excluding age*products =6
+   * - cptcovage number of covariates with age*products =2
+   * - cptcovs number of simple covariates
+   * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
+   *     which is a new column after the 9 (ncovcol) variables. 
+   * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+   * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+   *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+   * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+ */
+{
+  int i, j, k, ks;
+  int  j1, k1, k2;
+  char modelsav[80];
+  char stra[80], strb[80], strc[80], strd[80],stre[80];
+
+  /*removespace(model);*/
+  if (strlen(model) >1){ /* If there is at least 1 covariate */
+    j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+    j=nbocc(model,'+'); /**< j=Number of '+' */
+    j1=nbocc(model,'*'); /**< j1=Number of '*' */
+    cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
+    cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
+                  /* including age products which are counted in cptcovage.
+		  /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
+    cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+    cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
+    strcpy(modelsav,model); 
+    if (strstr(model,"AGE") !=0){
+      printf("Error. AGE must be in lower case 'age' model=%s ",model);
+      fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+      return 1;
+    }
+    if (strstr(model,"v") !=0){
+      printf("Error. 'v' must be in upper case 'V' model=%s ",model);
+      fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+      return 1;
+    }
+    
+    /*   Design
+     *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+     *  <          ncovcol=8                >
+     * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+     *   k=  1    2      3       4     5       6      7        8
+     *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+     *  covar[k,i], value of kth covariate if not including age for individual i:
+     *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+     *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+     *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
+     *  Tage[++cptcovage]=k
+     *       if products, new covar are created after ncovcol with k1
+     *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+     *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+     *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+     *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+     *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+     *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+     *  <          ncovcol=8                >
+     *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+     *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+     *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+     * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+     * p Tprod[1]@2={                         6, 5}
+     *p Tvard[1][1]@4= {7, 8, 5, 6}
+     * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
+     *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     *How to reorganize?
+     * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+     * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+     *       {2,   1,     4,      8,    5,      6,     3,       7}
+     * Struct []
+     */
 
+    /* This loop fills the array Tvar from the string 'model'.*/
+    /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+    /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+    /* 	k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+    /* 	k=3 V4 Tvar[k=3]= 4 (from V4) */
+    /* 	k=2 V1 Tvar[k=2]= 1 (from V1) */
+    /* 	k=1 Tvar[1]=2 (from V2) */
+    /* 	k=5 Tvar[5] */
+    /* for (k=1; k<=cptcovn;k++) { */
+    /* 	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+    /* 	} */
+    /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+    /*
+     * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+    for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+        Tvar[k]=0;
+    cptcovage=0;
+    for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+      cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
+				     modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
+      if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+      /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+      /*scanf("%d",i);*/
+      if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+	cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+	if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+	  /* covar is not filled and then is empty */
+	  cptcovprod--;
+	  cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+	  Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
+	  cptcovage++; /* Sums the number of covariates which include age as a product */
+	  Tage[cptcovage]=k;  /* Tage[1] = 4 */
+	  /*printf("stre=%s ", stre);*/
+	} else if (strcmp(strd,"age")==0) { /* or age*Vn */
+	  cptcovprod--;
+	  cutl(stre,strb,strc,'V');
+	  Tvar[k]=atoi(stre);
+	  cptcovage++;
+	  Tage[cptcovage]=k;
+	} else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+	  /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+	  cptcovn++;
+	  cptcovprodnoage++;k1++;
+	  cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+	  Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+				  because this model-covariate is a construction we invent a new column
+				  ncovcol + k1
+				  If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+				  Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+	  cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+	  Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+	  Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+	  Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+	  k2=k2+2;
+	  Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+	  Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+	  for (i=1; i<=lastobs;i++){
+	    /* Computes the new covariate which is a product of
+	       covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+	    covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+	  }
+	} /* End age is not in the model */
+      } /* End if model includes a product */
+      else { /* no more sum */
+	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+       /*  scanf("%d",i);*/
+	cutl(strd,strc,strb,'V');
+	ks++; /**< Number of simple covariates */
+	cptcovn++;
+	Tvar[k]=atoi(strd);
+      }
+      strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
+      /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+	scanf("%d",i);*/
+    } /* end of loop + */
+  } /* end model */
+  
+  /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+    If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+
+  /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+  printf("cptcovprod=%d ", cptcovprod);
+  fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+
+  scanf("%d ",i);*/
+
+
+  return (0); /* with covar[new additional covariate if product] and Tage if age */ 
+  /*endread:*/
+    printf("Exiting decodemodel: ");
+    return (1);
+}
+
+calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+{
+  int i, m;
+
+  for (i=1; i<=imx; i++) {
+    for(m=2; (m<= maxwav); m++) {
+      if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+	anint[m][i]=9999;
+	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 */
+      }
+    }
+  }
+
+  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 || 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)
+	      agev[m][i]=agedc[i];
+	  /*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;
+	      }
+	    }
+	}
+	else if(s[m][i] !=9){ /* Standard case, age in fractional
+				 years but with the precision of a month */
+	  agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+	  if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+	    agev[m][i]=1;
+	  else if(agev[m][i] < *agemin){ 
+	    *agemin=agev[m][i];
+	    printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+	  }
+	  else if(agev[m][i] >*agemax){
+	    *agemax=agev[m][i];
+	    /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
+	  }
+	  /*agev[m][i]=anint[m][i]-annais[i];*/
+	  /*	 agev[m][i] = age[i]+2*m;*/
+	}
+	else { /* =9 */
+	  agev[m][i]=1;
+	  s[m][i]=-1;
+	}
+      }
+      else /*= 0 Unknown */
+	agev[m][i]=1;
+    }
+    
+  }
+  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);	
+	return 1;
+      }
+    }
+  }
+
+  /*for (i=1; i<=imx; i++){
+  for (m=firstpass; (m<lastpass); m++){
+     printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+}
+
+}*/
+
+
+  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); 
+
+  return (0);
+ /* endread:*/
+    printf("Exiting calandcheckages: ");
+    return (1);
+}
+
+syscompilerinfo()
+ {
+   /* #include "syscompilerinfo.h"*/
+#include <gnu/libc-version.h>
+#if defined(__GNUC__)
+# if defined(__GNUC_PATCHLEVEL__)
+#  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                            + __GNUC_MINOR__ * 100 \
+                            + __GNUC_PATCHLEVEL__)
+# else
+#  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                            + __GNUC_MINOR__ * 100)
+# endif
+#endif
+
+// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
+#ifdef _WIN32 // note the underscore: without it, it's not msdn official!
+    // Windows (x64 and x86)
+#elif __unix__ // all unices, not all compilers
+    // Unix
+#elif __linux__
+    // linux
+#elif __APPLE__
+    // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
+#endif
+
+/*  __MINGW32__	  */
+/*  __CYGWIN__	 */
+/* __MINGW64__  */
+// http://msdn.microsoft.com/en-us/library/b0084kay.aspx
+/* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
+/* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
+/* _WIN64  // Defined for applications for Win64. */
+/* _M_X64 // Defined for compilations that target x64 processors. */
+/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
+#include <stdint.h>
+#if UINTPTR_MAX == 0xffffffff
+   printf("32-bit \n"); /* 32-bit */
+#elif UINTPTR_MAX == 0xffffffffffffffff
+  printf("64-bit \n");/* 64-bit */
+#else
+ printf("wtf-bit \n"); /* wtf */
+#endif
+
+struct utsname sysInfo;
+
+   if (uname(&sysInfo) != -1) {
+      puts(sysInfo.sysname);
+      puts(sysInfo.nodename);
+      puts(sysInfo.release);
+      puts(sysInfo.version);
+      puts(sysInfo.machine);
+   }
+   else
+      perror("uname() error");
+   printf("GNU C version %d\n", __GNUC_VERSION__);
+  printf("GNU libc version: %s\n", gnu_get_libc_version());
+
+ }
 
 /***********************************************/
 /**************** Main Program *****************/
@@ -4430,41 +5494,43 @@ void printinggnuplotmort(char fileres[],
 
 int main(int argc, char *argv[])
 {
+#ifdef GSL
+  const gsl_multimin_fminimizer_type *T;
+  size_t iteri = 0, it;
+  int rval = GSL_CONTINUE;
+  int status = GSL_SUCCESS;
+  double ssval;
+#endif
   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 linei, month, year,iout;
-  int jj, ll, li, lj, lk, imk;
+  int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
+
+  int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */
   int itimes;
   int NDIM=2;
   int vpopbased=0;
 
-  char ca[32], cb[32], cc[32];
-  char dummy[]="                         ";
+  char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;
-  double agedeb, agefin,hf;
+  double agedeb;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 
   double fret;
-  double **xi,tmp,delta;
-
   double dum; /* Dummy variable */
   double ***p3mat;
   double ***mobaverage;
-  int *indx;
-  char line[MAXLINE], linepar[MAXLINE];
-  char linetmp[MAXLINE];
-    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+
+  char line[MAXLINE];
+  char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE]; 
-  char **bp, *tok, *val; /* pathtot */
+  char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;
-  int sdeb, sfin; /* Status at beginning and end */
-  int c,  h , cpt,l;
-  int ju,jl, mi;
-  int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-  int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
+  int c,  h , cpt;
+  int jl;
+  int i1, j1, jk, stepsize;
+  int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;
   int hstepm, nhstepm;
@@ -4473,10 +5539,9 @@ int main(int argc, char *argv[])
   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;
 
-  double bage, fage, age, agelim, agebase;
+  double bage=0, fage=110, age, agelim, agebase;
   double ftolpl=FTOL;
   double **prlim;
-  double *severity;
   double ***param; /* Matrix of parameters */
   double  *p;
   double **matcov; /* Matrix of covariance */
@@ -4485,21 +5550,18 @@ int main(int argc, char *argv[])
   double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */
   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];
+  char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
   int *dcwave;
 
-  char z[1]="c", occ;
+  char z[1]="c";
+
+  /*char  *strt;*/
+  char strtend[80];
 
-  char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-  char  *strt, strtend[80];
-  char *stratrunc;
-  int lstra;
 
-  long total_usecs;
- 
 /*   setlocale (LC_ALL, ""); */
 /*   bindtextdomain (PACKAGE, LOCALEDIR); */
 /*   textdomain (PACKAGE); */
@@ -4507,19 +5569,21 @@ int main(int argc, char *argv[])
 /*   setlocale (LC_MESSAGES, ""); */
 
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-  (void) gettimeofday(&start_time,&tzp);
+  rstart_time = time(NULL);  
+  /*  (void) gettimeofday(&start_time,&tzp);*/
+  start_time = *localtime(&rstart_time);
   curr_time=start_time;
-  tm = *localtime(&start_time.tv_sec);
-  tmg = *gmtime(&start_time.tv_sec);
-  strcpy(strstart,asctime(&tm));
+  /*tml = *localtime(&start_time.tm_sec);*/
+  /* strcpy(strstart,asctime(&tml)); */
+  strcpy(strstart,asctime(&start_time));
 
 /*  printf("Localtime (at start)=%s",strstart); */
-/*  tp.tv_sec = tp.tv_sec +86400; */
-/*  tm = *localtime(&start_time.tv_sec); */
+/*  tp.tm_sec = tp.tm_sec +86400; */
+/*  tm = *localtime(&start_time.tm_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); */
+/*   tp.tm_sec = mktime(&tmg); */
 /*   strt=asctime(&tmg); */
 /*   printf("Time(after) =%s",strstart);  */
 /*  (void) time (&time_value);
@@ -4540,6 +5604,9 @@ int main(int argc, char *argv[])
     i=strlen(pathr);
     if(pathr[i-1]=='\n')
       pathr[i-1]='\0';
+    i=strlen(pathr);
+    if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+      pathr[i-1]='\0';
    for (tok = pathr; tok != NULL; ){
       printf("Pathr |%s|\n",pathr);
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
@@ -4595,13 +5662,15 @@ int main(int argc, char *argv[])
  path=%s \n\
  optionfile=%s\n\
  optionfilext=%s\n\
- optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+ optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+
+  syscompilerinfo();
 
   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)); */
+/*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
 
   /* */
   strcpy(fileres,"r");
@@ -4611,10 +5680,11 @@ int main(int argc, char *argv[])
   /*---------arguments file --------*/
 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-    printf("Problem with optionfile %s\n",optionfile);
-    fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+    printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+    fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
     fflush(ficlog);
-    goto end;
+    /* goto end; */
+    exit(70); 
   }
 
 
@@ -4634,7 +5704,7 @@ int main(int argc, char *argv[])
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
     numlinepar++;
-    puts(line);
+    fputs(line,stdout);
     fputs(line,ficparo);
     fputs(line,ficlog);
   }
@@ -4650,18 +5720,23 @@ int main(int argc, char *argv[])
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
     numlinepar++;
-    puts(line);
+    fputs(line, stdout);
+    //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*/
-  if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
-  /* where is ncovprod ?*/
-  ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+  covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+  cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+  /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+     v1+v2*age+v2*v3 makes cptcovn = 3
+  */
+  if (strlen(model)>1) 
+    ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+  else
+    ncovmodel=2;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
   npar= nforce*ncovmodel; /* Number of parameters like aij*/
@@ -4693,13 +5768,13 @@ int main(int argc, char *argv[])
     matcov=matrix(1,npar,1,npar);
   }
   else{
-    /* Read guess parameters */
+    /* Read guessed parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
-      puts(line);
+      fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
@@ -4742,6 +5817,7 @@ run imach with mle=-1 to get a correct t
     }  
     fflush(ficlog);
 
+    /* Reads scales values */
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
@@ -4749,7 +5825,7 @@ run imach with mle=-1 to get a correct t
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
-      puts(line);
+      fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
@@ -4758,7 +5834,7 @@ run imach with mle=-1 to get a correct t
     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){
+	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);
 	}
@@ -4771,459 +5847,159 @@ run imach with mle=-1 to get a correct t
 	  fprintf(ficparo," %le",delti3[i][j][k]);
 	  fprintf(ficlog," %le",delti3[i][j][k]);
 	}
-	fscanf(ficpar,"\n");
-	numlinepar++;
-	printf("\n");
-	fprintf(ficparo,"\n");
-	fprintf(ficlog,"\n");
-      }
-    }
-    fflush(ficlog);
-
-    delti=delti3[1][1];
-
-
-    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-  
-    /* 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);
-  
-    matcov=matrix(1,npar,1,npar);
-    for(i=1; i <=npar; i++)
-      for(j=1; j <=npar; j++) matcov[i][j]=0.;
-      
-    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]);
-      }
-      fscanf(ficpar,"\n");
-      numlinepar++;
-      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 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 while opening datafile: %s\n", datafile);goto end;
-    fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
-  }
-
-  n= lastobs;
-  severity = vector(1,maxwav);
-  outcome=imatrix(1,maxwav+1,1,n);
-  num=lvector(1,n);
-  moisnais=vector(1,n);
-  annais=vector(1,n);
-  moisdc=vector(1,n);
-  andc=vector(1,n);
-  agedc=vector(1,n);
-  cod=ivector(1,n);
-  weight=vector(1,n);
-  for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-  mint=matrix(1,maxwav,1,n);
-  anint=matrix(1,maxwav,1,n);
-  s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
-  tab=ivector(1,NCOVMAX);
-  ncodemax=ivector(1,8);
-
-  i=1;
-  linei=0;
-  while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-    linei=linei+1;
-    for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-      if(line[j] == '\t')
-	line[j] = ' ';
-    }
-    for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-      ;
-    };
-    line[j+1]=0;  /* Trims blanks at end of line */
-    if(line[0]=='#'){
-      fprintf(ficlog,"Comment line\n%s\n",line);
-      printf("Comment line\n%s\n",line);
-      continue;
-    }
-    trimbb(linetmp,line); /* Trims multiple blanks in line */
-    for (j=0; line[j]!='\0';j++){
-      line[j]=linetmp[j];
-    }
-  
-
-    for (j=maxwav;j>=1;j--){
-      cutv(stra, strb,line,' '); 
-      if(strb[0]=='.') { /* Missing status */
-	lval=-1;
-      }else{
-	errno=0;
-	lval=strtol(strb,&endptr,10); 
-      /*	if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-	if( strb[0]=='\0' || (*endptr != '\0')){
-	  printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-	  fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
-	  goto end;
-	}
-      }
-      s[j][i]=lval;
-      
-      strcpy(line,stra);
-      cutv(stra, strb,line,' ');
-      if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-      }
-      else  if(iout=sscanf(strb,"%s.") != 0){
-	month=99;
-	year=9999;
-      }else{
-	printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-	fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
-	goto end;
-      }
-      anint[j][i]= (double) year; 
-      mint[j][i]= (double)month; 
-      strcpy(line,stra);
-    } /* ENd Waves */
-    
-    cutv(stra, strb,line,' '); 
-    if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-    }
-    else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-      month=99;
-      year=9999;
-    }else{
-      printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-	fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-	goto end;
-    }
-    andc[i]=(double) year; 
-    moisdc[i]=(double) month; 
-    strcpy(line,stra);
-    
-    cutv(stra, strb,line,' '); 
-    if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-    }
-    else  if(iout=sscanf(strb,"%s.") != 0){
-      month=99;
-      year=9999;
-    }else{
-      printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
-      fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);fflush(ficlog);
-	goto end;
-    }
-    annais[i]=(double)(year);
-    moisnais[i]=(double)(month); 
-    strcpy(line,stra);
-    
-    cutv(stra, strb,line,' '); 
-    errno=0;
-    dval=strtod(strb,&endptr); 
-    if( strb[0]=='\0' || (*endptr != '\0')){
-      printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-      fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-      fflush(ficlog);
-      goto end;
-    }
-    weight[i]=dval; 
-    strcpy(line,stra);
-    
-    for (j=ncovcol;j>=1;j--){
-      cutv(stra, strb,line,' '); 
-      if(strb[0]=='.') { /* Missing status */
-	lval=-1;
-      }else{
-	errno=0;
-	lval=strtol(strb,&endptr,10); 
-	if( strb[0]=='\0' || (*endptr != '\0')){
-	  printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
-	  fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
-	  goto end;
-	}
-      }
-      if(lval <-1 || lval >1){
-	printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
- Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
- for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
- For example, for multinomial values like 1, 2 and 3,\n \
- build V1=0 V2=0 for the reference value (1),\n \
-        V1=1 V2=0 for (2) \n \
- and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
- output of IMaCh is often meaningless.\n \
- Exiting.\n",lval,linei, i,line,j);
-	fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
- Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
- for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
- For example, for multinomial values like 1, 2 and 3,\n \
- build V1=0 V2=0 for the reference value (1),\n \
-        V1=1 V2=0 for (2) \n \
- and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
- output of IMaCh is often meaningless.\n \
- Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-	goto end;
-      }
-      covar[j][i]=(double)(lval);
-      strcpy(line,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("%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;
-  } /* End loop reading  data */
-  fclose(fic);
-  /* printf("ii=%d", ij);
-     scanf("%d",i);*/
-  imx=i-1; /* Number of individuals */
-
-  /* for (i=1; i<=imx; i++){
-    if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
-    if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
-    if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
-    }*/
-   /*  for (i=1; i<=imx; i++){
-     if (s[4][i]==9)  s[4][i]=-1; 
-     printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
-  
-  /* for (i=1; i<=imx; i++) */
- 
-   /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-     else weight[i]=1;*/
-
-  /* Calculation of the number of parameters from char model */
-  Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
-  Tprod=ivector(1,15); 
-  Tvaraff=ivector(1,15); 
-  Tvard=imatrix(1,15,1,2);
-  Tage=ivector(1,15);      
-   
-  if (strlen(model) >1){ /* If there is at least 1 covariate */
-    j=0, j1=0, k1=1, k2=1;
-    j=nbocc(model,'+'); /* j=Number of '+' */
-    j1=nbocc(model,'*'); /* j1=Number of '*' */
-    cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
-    cptcovprod=j1; /*Number of products  V1*V2 =1 */
-    
-    strcpy(modelsav,model); 
-    if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
-      printf("Error. Non available option model=%s ",model);
-      fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
-      goto end;
-    }
-    
-    /* This loop fills the array Tvar from the string 'model'.*/
-    /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-    for(i=(j+1); i>=1;i--){
-      cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
-				     modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
-				     stra=V2
-				    */ 
-      if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-      /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-      /*scanf("%d",i);*/
-      if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
-	cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-	if (strcmp(strc,"age")==0) { /* Vn*age */
-	  cptcovprod--;
-	  cutv(strb,stre,strd,'V');
-	  Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
-	  cptcovage++; /* Sums the number of covariates including age as a product */
-	  Tage[cptcovage]=i;  /* Tage[1] =2 */
-	  /*printf("stre=%s ", stre);*/
-	}
-	else if (strcmp(strd,"age")==0) { /* or age*Vn */
-	  cptcovprod--;
-	  cutv(strb,stre,strc,'V');
-	  Tvar[i]=atoi(stre);
-	  cptcovage++;
-	  Tage[cptcovage]=i;
-	}
-	else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
-	  cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-	  Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
-				  If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
-	  cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-	  Tprod[k1]=i;  /* Tprod[1]  */
-	  Tvard[k1][1]=atoi(strc); /* m*/
-	  Tvard[k1][2]=atoi(stre); /* n */
-	  Tvar[cptcovn+k2]=Tvard[k1][1];
-	  Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
-	  for (k=1; k<=lastobs;k++) 
-	    covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
-	  k1++;
-	  k2=k2+2;
-	}
-      }
-      else { /* no more sum */
-	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-       /*  scanf("%d",i);*/
-      cutv(strd,strc,strb,'V');
-      Tvar[i]=atoi(strc);
+	fscanf(ficpar,"\n");
+	numlinepar++;
+	printf("\n");
+	fprintf(ficparo,"\n");
+	fprintf(ficlog,"\n");
       }
-      strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
-      /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-	scanf("%d",i);*/
-    } /* end of loop + */
-  } /* end model */
-  
-  /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-    If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-
-  /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-  printf("cptcovprod=%d ", cptcovprod);
-  fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+    }
+    fflush(ficlog);
 
-  scanf("%d ",i);*/
+    /* Reads covariance matrix */
+    delti=delti3[1][1];
 
-    /*  if(mle==1){*/
-  if (weightopt != 1) { /* Maximisation without weights*/
-    for(i=1;i<=n;i++) weight[i]=1.0;
-  }
-    /*-calculation of age at interview from date of interview and age at death -*/
-  agev=matrix(1,maxwav,1,imx);
 
-  for (i=1; i<=imx; i++) {
-    for(m=2; (m<= maxwav); m++) {
-      if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-	anint[m][i]=9999;
-	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 */
-      }
+    /* 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){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
+      numlinepar++;
+      fputs(line,stdout);
+      fputs(line,ficparo);
+      fputs(line,ficlog);
     }
-  }
-
-  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 || 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)
-	      agev[m][i]=agedc[i];
-	  /*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;
-	      }
-	    }
-	}
-	else if(s[m][i] !=9){ /* Standard case, age in fractional
-				 years but with the precision of a month */
-	  agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-	  if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-	    agev[m][i]=1;
-	  else if(agev[m][i] <agemin){ 
-	    agemin=agev[m][i];
-	    /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
-	  }
-	  else if(agev[m][i] >agemax){
-	    agemax=agev[m][i];
-	    /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
-	  }
-	  /*agev[m][i]=anint[m][i]-annais[i];*/
-	  /*	 agev[m][i] = age[i]+2*m;*/
-	}
-	else { /* =9 */
-	  agev[m][i]=1;
-	  s[m][i]=-1;
+    ungetc(c,ficpar);
+  
+    matcov=matrix(1,npar,1,npar);
+    for(i=1; i <=npar; i++)
+      for(j=1; j <=npar; j++) matcov[i][j]=0.;
+      
+    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]);
       }
-      else /*= 0 Unknown */
-	agev[m][i]=1;
+      fscanf(ficpar,"\n");
+      numlinepar++;
+      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];
     
-  }
-  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;
-      }
+    if(mle==1)
+      printf("\n");
+    fprintf(ficlog,"\n");
+    
+    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 */
 
-  /*for (i=1; i<=imx; i++){
-  for (m=firstpass; (m<lastpass); m++){
-     printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-}
 
-}*/
+  n= lastobs;
+  num=lvector(1,n);
+  moisnais=vector(1,n);
+  annais=vector(1,n);
+  moisdc=vector(1,n);
+  andc=vector(1,n);
+  agedc=vector(1,n);
+  cod=ivector(1,n);
+  weight=vector(1,n);
+  for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+  mint=matrix(1,maxwav,1,n);
+  anint=matrix(1,maxwav,1,n);
+  s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
+  tab=ivector(1,NCOVMAX);
+  ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+
+  /* Reads data from file datafile */
+  if (readdata(datafile, firstobs, lastobs, &imx)==1)
+    goto end;
+
+  /* Calculation of the number of parameters from char model */
+    /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
+	k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+	k=3 V4 Tvar[k=3]= 4 (from V4)
+	k=2 V1 Tvar[k=2]= 1 (from V1)
+	k=1 Tvar[1]=2 (from V2)
+    */
+  Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+  /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
+      For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
+      Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+  */
+  /* For model-covariate k tells which data-covariate to use but
+    because this model-covariate is a construction we invent a new column
+    ncovcol + k1
+    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
+    Tvar[3=V1*V4]=4+1 etc */
+  Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+  /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+     if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+  */
+  Tvaraff=ivector(1,NCOVMAX); /* Unclear */
+  Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+			    * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
+			    * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+  Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+			 4 covariates (3 plus signs)
+			 Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+		      */  
+
+  if(decodemodel(model, lastobs) == 1)
+    goto end;
+
+  if((double)(lastobs-imx)/(double)imx > 1.10){
+    nbwarn++;
+    printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
+    fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
+  }
+    /*  if(mle==1){*/
+  if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+    for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+  }
+
+    /*-calculation of age at interview from date of interview and age at death -*/
+  agev=matrix(1,maxwav,1,imx);
 
+  if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+    goto end;
 
-  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);
   free_vector(annais,1,n);
   /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/
   free_vector(moisdc,1,n);
   free_vector(andc,1,n);
-
-   
+  /* */
+  
   wav=ivector(1,imx);
   dh=imatrix(1,lastpass-firstpass+1,1,imx);
   bh=imatrix(1,lastpass-firstpass+1,1,imx);
@@ -5231,25 +6007,55 @@ run imach with mle=-1 to get a correct t
    
   /* Concatenates waves */
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-
+  /* */
+ 
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
 
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;
-  if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-      
-  codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
-				 the estimations*/
+  Ndum =ivector(-1,NCOVMAX);  
+  if (ncovmodel > 2)
+    tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+
+  codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+  /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
   h=0;
+
+
+  /*if (cptcovn > 0) */
+      
+ 
   m=pow(2,cptcoveff);
  
   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-    for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
-      for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
-	for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
+    for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
+      for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
+	for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
 	  h++;
 	  if (h>m) 
-	    h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+	    h=1;
+	  /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+	   *     h     1     2     3     4
+	   *______________________________  
+	   *     1 i=1 1 i=1 1 i=1 1 i=1 1
+	   *     2     2     1     1     1
+	   *     3 i=2 1     2     1     1
+	   *     4     2     2     1     1
+	   *     5 i=3 1 i=2 1     2     1
+	   *     6     2     1     2     1
+	   *     7 i=4 1     2     2     1
+	   *     8     2     2     2     1
+	   *     9 i=5 1 i=3 1 i=2 1     1
+	   *    10     2     1     1     1
+	   *    11 i=6 1     2     1     1
+	   *    12     2     2     1     1
+	   *    13 i=7 1 i=4 1     2     1    
+	   *    14     2     1     2     1
+	   *    15 i=8 1     2     2     1
+	   *    16     2     2     2     1
+	   */
+	  codtab[h][k]=j;
+	  /*codtab[h][Tvar[k]]=j;*/
 	  printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
 	} 
       }
@@ -5264,6 +6070,10 @@ run imach with mle=-1 to get a correct t
      printf("\n");
      }
      scanf("%d",i);*/
+
+ free_ivector(Ndum,-1,NCOVMAX);
+
+
     
   /*------------ gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);
@@ -5277,7 +6087,8 @@ run imach with mle=-1 to get a correct t
   else{
     fprintf(ficgp,"\n# %s\n", version); 
     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
-    fprintf(ficgp,"set missing 'NaNq'\n");
+    //fprintf(ficgp,"set missing 'NaNq'\n");
+    fprintf(ficgp,"set datafile missing 'NaNq'\n");
   }
   /*  fclose(ficgp);*/
   /*--------- index.htm --------*/
@@ -5347,7 +6158,8 @@ Interval (in months) between two waves:
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
 
   if (mle==-3){
-    ximort=matrix(1,NDIM,1,NDIM);
+    ximort=matrix(1,NDIM,1,NDIM); 
+/*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);
     ageexmed=vector(1,n);
     agecens=vector(1,n);
@@ -5385,25 +6197,110 @@ Interval (in months) between two waves:
 	ximort[i][j]=(i == j ? 1.0 : 0.0);
     }
     
-    p[1]=0.0268; p[NDIM]=0.083;
+    /*p[1]=0.0268; p[NDIM]=0.083;*/
     /*printf("%lf %lf", p[1], p[2]);*/
     
     
+#ifdef GSL
+    printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+#else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+#endif
     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);
     }
+#ifdef GSL
+    fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+#else
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+#endif
     /*  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");
+#ifdef GSL
+    /* gsl starts here */ 
+    T = gsl_multimin_fminimizer_nmsimplex;
+    gsl_multimin_fminimizer *sfm = NULL;
+    gsl_vector *ss, *x;
+    gsl_multimin_function minex_func;
+
+    /* Initial vertex size vector */
+    ss = gsl_vector_alloc (NDIM);
+    
+    if (ss == NULL){
+      GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+    }
+    /* Set all step sizes to 1 */
+    gsl_vector_set_all (ss, 0.001);
+
+    /* Starting point */
+    
+    x = gsl_vector_alloc (NDIM);
+    
+    if (x == NULL){
+      gsl_vector_free(ss);
+      GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+    }
+  
+    /* Initialize method and iterate */
+    /*     p[1]=0.0268; p[NDIM]=0.083; */
+/*     gsl_vector_set(x, 0, 0.0268); */
+/*     gsl_vector_set(x, 1, 0.083); */
+    gsl_vector_set(x, 0, p[1]);
+    gsl_vector_set(x, 1, p[2]);
+
+    minex_func.f = &gompertz_f;
+    minex_func.n = NDIM;
+    minex_func.params = (void *)&p; /* ??? */
+    
+    sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+    gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+    
+    printf("Iterations beginning .....\n\n");
+    printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+
+    iteri=0;
+    while (rval == GSL_CONTINUE){
+      iteri++;
+      status = gsl_multimin_fminimizer_iterate(sfm);
+      
+      if (status) printf("error: %s\n", gsl_strerror (status));
+      fflush(0);
+      
+      if (status) 
+        break;
+      
+      rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+      ssval = gsl_multimin_fminimizer_size (sfm);
+      
+      if (rval == GSL_SUCCESS)
+        printf ("converged to a local maximum at\n");
+      
+      printf("%5d ", iteri);
+      for (it = 0; it < NDIM; it++){
+	printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+      }
+      printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+    }
+    
+    printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
     
-    powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+    gsl_vector_free(x); /* initial values */
+    gsl_vector_free(ss); /* inital step size */
+    for (it=0; it<NDIM; it++){
+      p[it+1]=gsl_vector_get(sfm->x,it);
+      fprintf(ficrespow," %.12lf", p[it]);
+    }
+    gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+#endif
+#ifdef POWELL
+     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+#endif  
     fclose(ficrespow);
     
     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
@@ -5464,6 +6361,12 @@ Interval (in months) between two waves:
     free_vector(lsurv,1,AGESUP);
     free_vector(lpop,1,AGESUP);
     free_vector(tpop,1,AGESUP);
+#ifdef GSL
+    free_ivector(cens,1,n);
+    free_vector(agecens,1,n);
+    free_ivector(dcwave,1,n);
+    free_matrix(ximort,1,NDIM,1,NDIM);
+#endif
   } /* Endof if mle==-3 */
   
   else{ /* For mle >=1 */
@@ -5624,7 +6527,7 @@ Interval (in months) between two waves:
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
-      puts(line);
+      fputs(line,stdout);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
@@ -5644,7 +6547,7 @@ Interval (in months) between two waves:
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
-      puts(line);
+      fputs(line,stdout);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
@@ -5658,7 +6561,7 @@ Interval (in months) between two waves:
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
-      puts(line);
+      fputs(line,stdout);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
@@ -5674,7 +6577,7 @@ Interval (in months) between two waves:
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
-      puts(line);
+      fputs(line,stdout);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
@@ -5688,8 +6591,8 @@ Interval (in months) between two waves:
     
     
     
-    /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
-    /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+    /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
     
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
@@ -5714,117 +6617,21 @@ Interval (in months) between two waves:
 
 
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-  
-    strcpy(filerespl,"pl");
-    strcat(filerespl,fileres);
-    if((ficrespl=fopen(filerespl,"w"))==NULL) {
-      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-    }
-    printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-    fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-    pstamp(ficrespl);
-    fprintf(ficrespl,"# Period (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;
-	/* to clean */
-	printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
-	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");
-	}
-      }
-    }
+#include "prevlim.h"  /* Use ficrespl, ficlog */
     fclose(ficrespl);
 
-    /*------------- 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);
-  
-    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*/
-    pstamp(ficrespij);
-    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 */
-
-	  /*	  nhstepm=nhstepm*YEARM; aff par mois*/
+#ifdef FREEEXIT2
+#include "freeexit2.h"
+#endif
 
-	  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 );
-	    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");
-	}
-      }
-    }
+    /*------------- h Pij x at various ages ------------*/
+#include "hpijx.h"
+    fclose(ficrespij);
 
+  /*-------------- Variance of one-step probabilities---*/
+    k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
 
-    fclose(ficrespij);
 
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(i=1;i<=AGESUP;i++)
@@ -5873,9 +6680,10 @@ Interval (in months) between two waves:
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-	k=k+1; 
+    /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+          
+    for (k=1; k <= (int) pow(2,cptcoveff); k++){
 	fprintf(ficreseij,"\n#****** ");
 	for(j=1;j<=cptcoveff;j++) {
 	  fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
@@ -5887,7 +6695,7 @@ Interval (in months) between two waves:
 	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
       
 	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-      }
+      /*}*/
     }
     fclose(ficreseij);
 
@@ -5932,10 +6740,11 @@ Interval (in months) between two waves:
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
 
-    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-	k=k+1; 
-	fprintf(ficrest,"\n#****** ");
+    /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+          
+    for (k=1; k <= (int) pow(2,cptcoveff); k++){
+    	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");
@@ -5957,12 +6766,19 @@ Interval (in months) between two waves:
 	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 	oldm=oldms;savm=savms;
 	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
+	/*
+	 */
+	/* goto endfree; */
  
 	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 	pstamp(ficrest);
+
+
 	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-	  oldm=oldms;savm=savms;
-	  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);	  fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+	  oldm=oldms;savm=savms; /* Segmentation fault */
+	  cptcod= 0; /* To be deleted */
+	  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+	  fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
 	  if(vpopbased==1)
 	    fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
 	  else
@@ -6006,10 +6822,10 @@ Interval (in months) between two waves:
 	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(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
@@ -6031,10 +6847,11 @@ Interval (in months) between two waves:
     }
     printf("Computing Variance-covariance of period (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(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+          
+    for (k=1; k <= (int) pow(2,cptcoveff); k++){
+    	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");
@@ -6043,7 +6860,7 @@ Interval (in months) between two waves:
 	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);
@@ -6051,10 +6868,9 @@ Interval (in months) between two waves:
     /*---------- 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 */
- endfree:
-  free_matrix(prlim,1,nlstate,1,nlstate);
+ /* endfree:*/
+    free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     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);
@@ -6066,11 +6882,11 @@ Interval (in months) between two waves:
     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(ncodemax,1,NCOVMAX);
+    free_ivector(Tvar,1,NCOVMAX);
+    free_ivector(Tprod,1,NCOVMAX);
+    free_ivector(Tvaraff,1,NCOVMAX);
+    free_ivector(Tage,1,NCOVMAX);
 
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     free_imatrix(codtab,1,100,1,10);
@@ -6087,17 +6903,18 @@ Interval (in months) between two waves:
   }
   printf("See log file on %s\n",filelog);
   /*  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));
+  /*(void) gettimeofday(&end_time,&tzp);*/
+  rend_time = time(NULL);  
+  end_time = *localtime(&rend_time);
+  /* tml = *localtime(&end_time.tm_sec); */
+  strcpy(strtend,asctime(&end_time));
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
-  printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+  printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,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 %.0lf Sec.\n", difftime(rend_time,rstart_time));
+  fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+  fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   /*  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>\n</body></html>",strstart, strtend);
@@ -6116,19 +6933,19 @@ Interval (in months) between two waves:
     printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/
   sprintf(plotcmd,"gnuplot");
-#ifndef UNIX
+#ifdef _WIN32
   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
 #endif
   if(!stat(plotcmd,&info)){
-    printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+    printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
     if(!stat(getenv("GNUPLOTBIN"),&info)){
-      printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+      printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
     }else
       strcpy(pplotcmd,plotcmd);
-#ifdef UNIX
+#ifdef __unix
     strcpy(plotcmd,GNUPLOTPROGRAM);
     if(!stat(plotcmd,&info)){
-      printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+      printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
     }else
       strcpy(pplotcmd,plotcmd);
 #endif
@@ -6136,20 +6953,31 @@ Interval (in months) between two waves:
     strcpy(pplotcmd,plotcmd);
   
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-  printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+  printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
 
   if((outcmd=system(plotcmd)) != 0){
-    printf("\n Problem with gnuplot\n");
+    printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+    printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+    sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+    if((outcmd=system(plotcmd)) != 0)
+      printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
   }
-  printf(" Wait...");
+  printf(" Successful, please wait...");
   while (z[0] != 'q') {
     /* chdir(path); */
-    printf("\nType e to edit output files, g to graph again and q for exiting: ");
+    printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
     scanf("%s",z);
 /*     if (z[0] == 'c') system("./imach"); */
     if (z[0] == 'e') {
-      printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
-      system(optionfilehtm);
+#ifdef __APPLE__
+      sprintf(pplotcmd, "open %s", optionfilehtm);
+#elif __linux
+      sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+#else
+      sprintf(pplotcmd, "%s", optionfilehtm);
+#endif
+      printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+      system(pplotcmd);
     }
     else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);
@@ -6160,6 +6988,3 @@ Interval (in months) between two waves:
     scanf("%s",z);
   }
 }
-
-
-