--- imach/src/imach.c	2015/04/23 12:01:52	1.186
+++ imach/src/imach.c	2015/09/30 17:45:14	1.203
@@ -1,6 +1,73 @@
-/* $Id: imach.c,v 1.186 2015/04/23 12:01:52 brouard Exp $
+/* $Id: imach.c,v 1.203 2015/09/30 17:45:14 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.203  2015/09/30 17:45:14  brouard
+  Summary: looking at better estimation of the hessian
+
+  Also a better criteria for convergence to the period prevalence And
+  therefore adding the number of years needed to converge. (The
+  prevalence in any alive state shold sum to one
+
+  Revision 1.202  2015/09/22 19:45:16  brouard
+  Summary: Adding some overall graph on contribution to likelihood. Might change
+
+  Revision 1.201  2015/09/15 17:34:58  brouard
+  Summary: 0.98r0
+
+  - Some new graphs like suvival functions
+  - Some bugs fixed like model=1+age+V2.
+
+  Revision 1.200  2015/09/09 16:53:55  brouard
+  Summary: Big bug thanks to Flavia
+
+  Even model=1+age+V2. did not work anymore
+
+  Revision 1.199  2015/09/07 14:09:23  brouard
+  Summary: 0.98q6 changing default small png format for graph to vectorized svg.
+
+  Revision 1.198  2015/09/03 07:14:39  brouard
+  Summary: 0.98q5 Flavia
+
+  Revision 1.197  2015/09/01 18:24:39  brouard
+  *** empty log message ***
+
+  Revision 1.196  2015/08/18 23:17:52  brouard
+  Summary: 0.98q5
+
+  Revision 1.195  2015/08/18 16:28:39  brouard
+  Summary: Adding a hack for testing purpose
+
+  After reading the title, ftol and model lines, if the comment line has
+  a q, starting with #q, the answer at the end of the run is quit. It
+  permits to run test files in batch with ctest. The former workaround was
+  $ echo q | imach foo.imach
+
+  Revision 1.194  2015/08/18 13:32:00  brouard
+  Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+
+  Revision 1.193  2015/08/04 07:17:42  brouard
+  Summary: 0.98q4
+
+  Revision 1.192  2015/07/16 16:49:02  brouard
+  Summary: Fixing some outputs
+
+  Revision 1.191  2015/07/14 10:00:33  brouard
+  Summary: Some fixes
+
+  Revision 1.190  2015/05/05 08:51:13  brouard
+  Summary: Adding digits in output parameters (7 digits instead of 6)
+
+  Fix 1+age+.
+
+  Revision 1.189  2015/04/30 14:45:16  brouard
+  Summary: 0.98q2
+
+  Revision 1.188  2015/04/30 08:27:53  brouard
+  *** empty log message ***
+
+  Revision 1.187  2015/04/29 09:11:15  brouard
+  *** empty log message ***
+
   Revision 1.186  2015/04/23 12:01:52  brouard
   Summary: V1*age is working now, version 0.98q1
 
@@ -585,7 +652,14 @@
  end
 */
 
+/* #define DEBUG */
+/* #define DEBUGBRENT */
+/* #define DEBUGLINMIN */
+/* #define DEBUGHESS */
+#define DEBUGHESSIJ
+/* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
 #define POWELL /* Instead of NLOPT */
+#define POWELLF1F3 /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
 
@@ -654,11 +728,12 @@ typedef struct {
 #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 codtabm(h,k)  (1 & (h-1) >> (k-1))+1
 #define MAXN 20000
 #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
+#define AGEOVERFLOW 1.e20
 #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef _WIN32
 #define DIRSEPARATOR '\\'
@@ -670,15 +745,16 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.186 2015/04/23 12:01:52 brouard Exp $ */
+/* $Id: imach.c,v 1.203 2015/09/30 17:45:14 brouard Exp $ */
 /* $State: Exp $ */
-
-char version[]="Imach version 0.98q1, April 2015,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: 1.186 $ $Date: 2015/04/23 12:01:52 $"; 
+#include "version.h"
+char version[]=__IMACH_VERSION__;
+char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+char fullversion[]="$Revision: 1.203 $ $Date: 2015/09/30 17:45:14 $"; 
 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 nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
 /* 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) */
@@ -740,7 +816,7 @@ char command[FILENAMELENGTH];
 int  outcmd=0;
 
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-
+char fileresu[FILENAMELENGTH]; /* fileres without r in front */
 char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];
@@ -808,7 +884,13 @@ int estepm;
 
 int m,nb;
 long *num;
-int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+int firstpass=0, lastpass=4,*cod, *cens;
+int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
+		   covariate for which somebody answered excluding 
+		   undefined. Usually 2: 0 and 1. */
+int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
+			     covariate for which somebody answered including 
+			     undefined. Usually 3: -1, 0 and 1. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;
 double *ageexmed,*agecens;
@@ -819,11 +901,12 @@ int **s; /* Status */
 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]; */
+		  * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
 double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+int *Tage;
 int *Ndum; /** Freq of modality (tricode */
-int **codtab; /**< codtab=imatrix(1,100,1,10); */
+/* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double *lsurv, *lpop, *tpop;
 
@@ -915,11 +998,54 @@ char *trimbb(char *out, char *in)
   return s;
 }
 
+/* char *substrchaine(char *out, char *in, char *chain) */
+/* { */
+/*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
+/*   char *s, *t; */
+/*   t=in;s=out; */
+/*   while ((*in != *chain) && (*in != '\0')){ */
+/*     *out++ = *in++; */
+/*   } */
+
+/*   /\* *in matches *chain *\/ */
+/*   while ((*in++ == *chain++) && (*in != '\0')){ */
+/*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+/*   } */
+/*   in--; chain--; */
+/*   while ( (*in != '\0')){ */
+/*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+/*     *out++ = *in++; */
+/*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+/*   } */
+/*   *out='\0'; */
+/*   out=s; */
+/*   return out; */
+/* } */
+char *substrchaine(char *out, char *in, char *chain)
+{
+  /* Substract chain 'chain' from 'in', return and output 'out' */
+  /* in="V1+V1*age+age*age+V2", chain="age*age" */
+
+  char *strloc;
+
+  strcpy (out, in); 
+  strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
+  printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
+  if(strloc != NULL){ 
+    /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
+    memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
+    /* strcpy (strloc, strloc +strlen(chain));*/
+  }
+  printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
+  return out;
+}
+
+
 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' 
+  /* 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".
+     gives blocc="abcdef" and alocc="ghi2j".
      If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */
   char *s, *t;
@@ -945,7 +1071,7 @@ char *cutl(char *blocc, char *alocc, cha
 }
 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' 
+  /* 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
@@ -1256,7 +1382,13 @@ double f1dim(double x)
 
 /*****************brent *************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol, 	double *xmin) 
-{ 
+{
+  /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
+   * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
+   * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
+   * the minimum is returned as xmin, and the minimum function value is returned as brent , the
+   * returned function value. 
+  */
   int iter; 
   double a,b,d,etemp;
   double fu=0,fv,fw,fx;
@@ -1339,9 +1471,20 @@ values at the three points, fa, fb , and
    */
   double ulim,u,r,q, dum;
   double fu; 
- 
-  *fa=(*func)(*ax); 
-  *fb=(*func)(*bx); 
+
+  double scale=10.;
+  int iterscale=0;
+
+  *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
+  *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
+
+
+  /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
+  /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
+  /*   *bx = *ax - (*ax - *bx)/scale; */
+  /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
+  /* } */
+
   if (*fb > *fa) { 
     SHFT(dum,*ax,*bx,dum) 
     SHFT(dum,*fb,*fa,dum) 
@@ -1374,31 +1517,41 @@ values at the three points, fa, fb , and
 #endif 
 #ifdef MNBRAKORIGINAL
 #else
-      if (fu > *fc) {
-#ifdef DEBUG
-      printf("mnbrak4  fu > fc \n");
-      fprintf(ficlog, "mnbrak4 fu > fc\n");
-#endif
-	/* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */
-	/* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
-	dum=u; /* Shifting c and u */
-	u = *cx;
-	*cx = dum;
-	dum = fu;
-	fu = *fc;
-	*fc =dum;
-      } else { /* end */
+/*       if (fu > *fc) { */
+/* #ifdef DEBUG */
+/*       printf("mnbrak4  fu > fc \n"); */
+/*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
+/* #endif */
+/* 	/\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
+/* 	/\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
+/* 	dum=u; /\* Shifting c and u *\/ */
+/* 	u = *cx; */
+/* 	*cx = dum; */
+/* 	dum = fu; */
+/* 	fu = *fc; */
+/* 	*fc =dum; */
+/*       } else { /\* end *\/ */
+/* #ifdef DEBUG */
+/*       printf("mnbrak3  fu < fc \n"); */
+/*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
+/* #endif */
+/* 	dum=u; /\* Shifting c and u *\/ */
+/* 	u = *cx; */
+/* 	*cx = dum; */
+/* 	dum = fu; */
+/* 	fu = *fc; */
+/* 	*fc =dum; */
+/*       } */
 #ifdef DEBUG
-      printf("mnbrak3  fu < fc \n");
-      fprintf(ficlog, "mnbrak3 fu < fc\n");
+      printf("mnbrak34  fu < or >= fc \n");
+      fprintf(ficlog, "mnbrak34 fu < fc\n");
 #endif
-	dum=u; /* Shifting c and u */
-	u = *cx;
-	*cx = dum;
-	dum = fu;
-	fu = *fc;
-	*fc =dum;
-      }
+      dum=u; /* Shifting c and u */
+      u = *cx;
+      *cx = dum;
+      dum = fu;
+      fu = *fc;
+      *fc =dum;
 #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 #ifdef DEBUG
@@ -1458,27 +1611,97 @@ void linmin(double p[], double xi[], int
   int j; 
   double xx,xmin,bx,ax; 
   double fx,fb,fa;
- 
+
+#ifdef LINMINORIGINAL
+#else
+  double scale=10., axs, xxs; /* Scale added for infinity */
+#endif
+  
   ncom=n; 
   pcom=vector(1,n); 
   xicom=vector(1,n); 
   nrfunc=func; 
   for (j=1;j<=n;j++) { 
     pcom[j]=p[j]; 
-    xicom[j]=xi[j]; 
+    xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
   } 
-  ax=0.0; 
-  xx=1.0; 
-  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 LINMINORIGINAL
+  xx=1.;
+#else
+  axs=0.0;
+  xxs=1.;
+  do{
+    xx= xxs;
+#endif
+    ax=0.;
+    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
+    /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
+    /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
+    /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
+    /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
+    /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
+    /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
+#ifdef LINMINORIGINAL
+#else
+    if (fx != fx){
+  	xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
+	printf("|");
+	fprintf(ficlog,"|");
+#ifdef DEBUGLINMIN
+  	printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
+#endif
+    }
+  }while(fx != fx);
+#endif
+  
+#ifdef DEBUGLINMIN
+  printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+  fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+#endif
+  *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
+  /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
+  /* fmin = f(p[j] + xmin * xi[j]) */
+  /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
+  /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
 #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #endif
+#ifdef DEBUGLINMIN
+  printf("linmin end ");
+  fprintf(ficlog,"linmin end ");
+#endif
   for (j=1;j<=n;j++) { 
+#ifdef LINMINORIGINAL
     xi[j] *= xmin; 
-    p[j] += xi[j]; 
+#else
+#ifdef DEBUGLINMIN
+    if(xxs <1.0)
+      printf(" before xi[%d]=%12.8f", j,xi[j]);
+#endif
+    xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
+#ifdef DEBUGLINMIN
+    if(xxs <1.0)
+      printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
+#endif
+#endif
+    p[j] += xi[j]; /* Parameters values are updated accordingly */
   } 
+#ifdef DEBUGLINMIN
+  printf("\n");
+  printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+  fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+  for (j=1;j<=n;j++) { 
+    printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+    fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+    if(j % ncovmodel == 0){
+      printf("\n");
+      fprintf(ficlog,"\n");
+    }
+  }
+#else
+#endif
   free_vector(xicom,1,n); 
   free_vector(pcom,1,n); 
 } 
@@ -1511,9 +1734,9 @@ 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);  
+  rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) { 
-    fp=(*fret); 
+    fp=(*fret); /* From former iteration or initial value */
     ibig=0; 
     del=0.0; 
     rlast_time=rcurr_time;
@@ -1523,7 +1746,7 @@ void powell(double p[], double **xi, int
     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++) {
+    for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);
@@ -1551,22 +1774,22 @@ void powell(double p[], double **xi, int
 	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]; 
+    for (i=1;i<=n;i++) { /* For each direction i */
+      for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       fptt=(*fret); 
 #ifdef DEBUG
-	  printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-	  fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *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);
+      printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);
-      linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
-      if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
-				       because that direction will be replaced unless the gain del is small
-				      in comparison with the 'probable' gain, mu^2, with the last average direction.
-				      Unless the n directions are conjugate some gain in the determinant may be obtained
-				      with the new direction.
-				      */
+      linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
+				    /* Outputs are fret(new point p) p is updated and xit rescaled */
+      if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
+	/* because that direction will be replaced unless the gain del is small */
+	/* in comparison with the 'probable' gain, mu^2, with the last average direction. */
+	/* Unless the n directions are conjugate some gain in the determinant may be obtained */
+	/* with the new direction. */
 	del=fabs(fptt-(*fret)); 
 	ibig=i; 
       } 
@@ -1585,8 +1808,23 @@ void powell(double p[], double **xi, int
       printf("\n");
       fprintf(ficlog,"\n");
 #endif
-    } /* end i */
+    } /* end loop on each direction i */
+    /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
+    /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
+    /* New value of last point Pn is not computed, P(n-1) */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
+      /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
+      /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
+      /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
+      /* decreased of more than 3.84  */
+      /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
+      /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
+      /* By adding 10 parameters more the gain should be 18.31 */
+
+      /* Starting the program with initial values given by a former maximization will simply change */
+      /* the scales of the directions and the directions, because the are reset to canonical directions */
+      /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
+      /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
 #ifdef DEBUG
       int k[2],l;
       k[0]=1;
@@ -1616,7 +1854,7 @@ void powell(double p[], double **xi, int
       free_vector(ptt,1,n); 
       free_vector(pt,1,n); 
       return; 
-    } 
+    } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
       ptt[j]=2.0*p[j]-pt[j]; 
@@ -1624,7 +1862,10 @@ void powell(double p[], double **xi, int
       pt[j]=p[j]; 
     } 
     fptt=(*func)(ptt); /* f_3 */
+#ifdef POWELLF1F3
+#else
     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
+#endif
       /* (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.  */
@@ -1638,7 +1879,7 @@ void powell(double p[], double **xi, int
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       t= t- del*SQR(fp-fptt);
 #endif
-      directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
+      directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
 #ifdef DEBUG
       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
@@ -1653,14 +1894,35 @@ void powell(double p[], double **xi, int
       if (t < 0.0) { /* Then we use it for new direction */
 #else
       if (directest*t < 0.0) { /* Contradiction between both tests */
-      printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
-      printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-      fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
-      fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-    } 
+	printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
+        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+        fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
+        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+      } 
       if (directest < 0.0) { /* Then we use it for new direction */
 #endif
-	linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
+#ifdef DEBUGLINMIN
+	printf("Before linmin in direction P%d-P0\n",n);
+	for (j=1;j<=n;j++) { 
+	  printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+	  fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+	  if(j % ncovmodel == 0){
+	    printf("\n");
+	    fprintf(ficlog,"\n");
+	  }
+	}
+#endif
+	linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+#ifdef DEBUGLINMIN
+	for (j=1;j<=n;j++) { 
+	  printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+	  fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+	  if(j % ncovmodel == 0){
+	    printf("\n");
+	    fprintf(ficlog,"\n");
+	  }
+	}
+#endif
 	for (j=1;j<=n;j++) { 
 	  xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
 	  xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
@@ -1678,24 +1940,28 @@ void powell(double p[], double **xi, int
 	printf("\n");
 	fprintf(ficlog,"\n");
 #endif
-      } /* end of t negative */
+      } /* end of t or directest negative */
+#ifdef POWELLF1F3
+#else
     } /* end if (fptt < fp)  */
-  } 
+#endif
+  } /* loop iteration */ 
 } 
 
 /**** Prevalence limit (stable or period prevalence)  ****************/
 
-double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
 {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-     matrix by transitions matrix until convergence is reached */
+     matrix by transitions matrix until convergence is reached with precision ftolpl */
   
   int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();
   double **newm;
-  double agefin, delaymax=50 ; /* Max number of years to converge */
+  double agefin, delaymax=100 ; /* Max number of years to converge */
+  int ncvloop=0;
   
   for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=nlstate+ndeath;j++){
@@ -1705,19 +1971,25 @@ double **prevalim(double **prlim, int nl
   cov[1]=1.;
   
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+  /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+    ncvloop++;
     newm=savm;
     /* Covariates have to be included here again */
     cov[2]=agefin;
-    
+    if(nagesqr==1)
+      cov[3]= agefin*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]]);*/
+      /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+      cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+      /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
     }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-    for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
+    /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
+    for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,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]]];
+      /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+      cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
     
     /*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]);*/
@@ -1736,17 +2008,23 @@ 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]);
+        /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */
       }
-      maxmin=max-min;
+      maxmin=(max-min)/(max+min)*2;
       maxmax=FMAX(maxmax,maxmin);
     } /* j loop */
+    *ncvyear= (int)age- (int)agefin;
+    /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){
+      /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
       return prlim;
     }
   } /* age loop */
+  printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\
+Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   return prlim; /* should not reach here */
 }
 
@@ -1871,6 +2149,7 @@ double ***hpxij(double ***po, int nhstep
   int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];
   double **newm;
+  double agexact;
 
   /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)
@@ -1884,14 +2163,20 @@ double ***hpxij(double ***po, int nhstep
       newm=savm;
       /* Covariates have to be included here again */
       cov[1]=1.;
-      cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+      agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+      cov[2]=agexact;
+      if(nagesqr==1)
+	cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++) 
-	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
 	/* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-	cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
+	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       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]]];
+	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
 
 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
@@ -1943,6 +2228,7 @@ double func( double *x)
   int s1, s2;
   double bbh, survp;
   long ipmx;
+  double agexact;
   /*extern weight */
   /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
@@ -1964,7 +2250,7 @@ double func( double *x)
 	 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];
+	  cov[2+nagesqr+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] 
@@ -1977,9 +2263,12 @@ double func( double *x)
 	  }
 	for(d=0; d<dh[mi][i]; d++){
 	  newm=savm;
-	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  cov[2]=agexact;
+	  if(nagesqr==1)
+	    cov[3]= agexact*agexact;
 	  for (kk=1; kk<=cptcovage;kk++) {
-	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
+	    cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* 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));
@@ -2090,7 +2379,7 @@ double func( double *x)
     } /* end of individual */
   }  else if(mle==2){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 	for (ii=1;ii<=nlstate+ndeath;ii++)
 	  for (j=1;j<=nlstate+ndeath;j++){
@@ -2099,9 +2388,12 @@ double func( double *x)
 	  }
 	for(d=0; d<=dh[mi][i]; d++){
 	  newm=savm;
-	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  cov[2]=agexact;
+	  if(nagesqr==1)
+	    cov[3]= agexact*agexact;
 	  for (kk=1; kk<=cptcovage;kk++) {
-	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	    cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 	  }
 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
@@ -2120,7 +2412,7 @@ double func( double *x)
     } /* end of individual */
   }  else if(mle==3){  /* exponential inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 	for (ii=1;ii<=nlstate+ndeath;ii++)
 	  for (j=1;j<=nlstate+ndeath;j++){
@@ -2129,9 +2421,12 @@ double func( double *x)
 	  }
 	for(d=0; d<dh[mi][i]; d++){
 	  newm=savm;
-	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  cov[2]=agexact;
+	  if(nagesqr==1)
+	    cov[3]= agexact*agexact;
 	  for (kk=1; kk<=cptcovage;kk++) {
-	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	    cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 	  }
 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
@@ -2150,7 +2445,7 @@ double func( double *x)
     } /* end of individual */
   }else if (mle==4){  /* ml=4 no inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 	for (ii=1;ii<=nlstate+ndeath;ii++)
 	  for (j=1;j<=nlstate+ndeath;j++){
@@ -2159,9 +2454,12 @@ double func( double *x)
 	  }
 	for(d=0; d<dh[mi][i]; d++){
 	  newm=savm;
-	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  cov[2]=agexact;
+	  if(nagesqr==1)
+	    cov[3]= agexact*agexact;
 	  for (kk=1; kk<=cptcovage;kk++) {
-	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	    cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 	  }
 	
 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
@@ -2185,7 +2483,7 @@ double func( double *x)
     } /* end of individual */
   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 	for (ii=1;ii<=nlstate+ndeath;ii++)
 	  for (j=1;j<=nlstate+ndeath;j++){
@@ -2194,9 +2492,12 @@ double func( double *x)
 	  }
 	for(d=0; d<dh[mi][i]; d++){
 	  newm=savm;
-	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	  cov[2]=agexact;
+	  if(nagesqr==1)
+	    cov[3]= agexact*agexact;
 	  for (kk=1; kk<=cptcovage;kk++) {
-	    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	    cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 	  }
 	
 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
@@ -2232,6 +2533,7 @@ double funcone( double *x)
   double llt;
   int s1, s2;
   double bbh, survp;
+  double agexact;
   /*extern weight */
   /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
@@ -2243,7 +2545,7 @@ double funcone( double *x)
   for(k=1; k<=nlstate; k++) ll[k]=0.;
 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-    for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+    for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     for(mi=1; mi<= wav[i]-1; mi++){
       for (ii=1;ii<=nlstate+ndeath;ii++)
 	for (j=1;j<=nlstate+ndeath;j++){
@@ -2252,10 +2554,14 @@ double funcone( double *x)
 	}
       for(d=0; d<dh[mi][i]; d++){
 	newm=savm;
-	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	cov[2]=agexact;
+	if(nagesqr==1)
+	  cov[3]= agexact*agexact;
 	for (kk=1; kk<=cptcovage;kk++) {
-	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+	  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
 	}
+
 	/* 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));
@@ -2294,9 +2600,9 @@ double funcone( double *x)
       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,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+	fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %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],
+		num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 		2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 	  llt +=ll[k]*gipmx/gsw;
@@ -2328,14 +2634,14 @@ void likelione(FILE *ficres,double p[],
   int k;
 
   if(*globpri !=0){ /* Just counts and sums, no printings */
-    strcpy(fileresilk,"ilk"); 
-    strcat(fileresilk,fileres);
+    strcpy(fileresilk,"ILK_"); 
+    strcat(fileresilk,fileresu);
     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     }
     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-    fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+    fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     /* 	i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(k=1; k<=nlstate; k++) 
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
@@ -2345,8 +2651,10 @@ void likelione(FILE *ficres,double p[],
   *fretone=(*funcone)(p);
   if(*globpri !=0){
     fclose(ficresilk);
-    fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-    fflush(fichtm); 
+    fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+    fprintf(fichtm,"<br>- The first 3 individuals are drawn with lines. The function drawn is -2Log(L) in log scale: <a href=\"%s.png\">%s.png</a><br> \
+<img src=\"%s.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+    fflush(fichtm);
   } 
   return;
 }
@@ -2378,7 +2686,7 @@ void mlikeli(FILE *ficres,double p[], in
     for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-  strcpy(filerespow,"pow"); 
+  strcpy(filerespow,"POW_"); 
   strcat(filerespow,fileres);
   if((ficrespow=fopen(filerespow,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", filerespow);
@@ -2421,32 +2729,32 @@ void mlikeli(FILE *ficres,double p[], in
 #endif
   free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);
-  printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-  fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,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,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 
 }
 
 /**** Computes Hessian and covariance matrix ***/
-void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 {
   double  **a,**y,*x,pd;
-  double **hess;
+  /* double **hess; */
   int i, j;
   int *indx;
 
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-  double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+  double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
   void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;
   double gompertz(double p[]);
-  hess=matrix(1,npar,1,npar);
+  /* hess=matrix(1,npar,1,npar); */
 
   printf("\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (i=1;i<=npar;i++){
-    printf("%d",i);fflush(stdout);
-    fprintf(ficlog,"%d",i);fflush(ficlog);
+    printf("%d-",i);fflush(stdout);
+    fprintf(ficlog,"%d-",i);fflush(ficlog);
    
      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     
@@ -2457,9 +2765,9 @@ void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++) {
     for (j=1;j<=npar;j++)  {
       if (j>i) { 
-	printf(".%d%d",i,j);fflush(stdout);
-	fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-	hess[i][j]=hessij(p,delti,i,j,func,npar);
+	printf(".%d-%d",i,j);fflush(stdout);
+	fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
+	hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
 	
 	hess[j][i]=hess[i][j];    
 	/*printf(" %lf ",hess[i][j]);*/
@@ -2493,53 +2801,78 @@ void hesscov(double **matcov, double p[]
   fprintf(ficlog,"\n#Hessian matrix#\n");
   for (i=1;i<=npar;i++) { 
     for (j=1;j<=npar;j++) { 
-      printf("%.3e ",hess[i][j]);
-      fprintf(ficlog,"%.3e ",hess[i][j]);
+      printf("%.6e ",hess[i][j]);
+      fprintf(ficlog,"%.6e ",hess[i][j]);
     }
     printf("\n");
     fprintf(ficlog,"\n");
   }
 
+  /* printf("\n#Covariance matrix#\n"); */
+  /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
+  /* for (i=1;i<=npar;i++) {  */
+  /*   for (j=1;j<=npar;j++) {  */
+  /*     printf("%.6e ",matcov[i][j]); */
+  /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
+  /*   } */
+  /*   printf("\n"); */
+  /*   fprintf(ficlog,"\n"); */
+  /* } */
+
   /* Recompute Inverse */
-  for (i=1;i<=npar;i++)
-    for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-  ludcmp(a,npar,indx,&pd);
+  /* for (i=1;i<=npar;i++) */
+  /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
+  /* ludcmp(a,npar,indx,&pd); */
+
+  /*  printf("\n#Hessian matrix recomputed#\n"); */
+
+  /* for (j=1;j<=npar;j++) { */
+  /*   for (i=1;i<=npar;i++) x[i]=0; */
+  /*   x[j]=1; */
+  /*   lubksb(a,npar,indx,x); */
+  /*   for (i=1;i<=npar;i++){  */
+  /*     y[i][j]=x[i]; */
+  /*     printf("%.3e ",y[i][j]); */
+  /*     fprintf(ficlog,"%.3e ",y[i][j]); */
+  /*   } */
+  /*   printf("\n"); */
+  /*   fprintf(ficlog,"\n"); */
+  /* } */
 
-  /*  printf("\n#Hessian matrix recomputed#\n");
+  /* Verifying the inverse matrix */
+#ifdef DEBUGHESS
+  y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
+
+   printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
+   fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
 
   for (j=1;j<=npar;j++) {
-    for (i=1;i<=npar;i++) x[i]=0;
-    x[j]=1;
-    lubksb(a,npar,indx,x);
     for (i=1;i<=npar;i++){ 
-      y[i][j]=x[i];
-      printf("%.3e ",y[i][j]);
-      fprintf(ficlog,"%.3e ",y[i][j]);
+      printf("%.2f ",y[i][j]);
+      fprintf(ficlog,"%.2f ",y[i][j]);
     }
     printf("\n");
     fprintf(ficlog,"\n");
   }
-  */
+#endif
 
   free_matrix(a,1,npar,1,npar);
   free_matrix(y,1,npar,1,npar);
   free_vector(x,1,npar);
   free_ivector(indx,1,npar);
-  free_matrix(hess,1,npar,1,npar);
+  /* free_matrix(hess,1,npar,1,npar); */
 
 
 }
 
 /*************** hessian matrix ****************/
 double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-{
+{ /* Around values of x, computes the function func and returns the scales delti and hessian */
   int i;
   int l=1, lmax=20;
-  double k1,k2;
+  double k1,k2, res, fx;
   double p2[MAXPARM+1]; /* identical to x */
-  double res;
   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-  double fx;
   int k=0,kmax=10;
   double l1;
 
@@ -2555,9 +2888,9 @@ double hessii(double x[], double delta,
       p2[theta]=x[theta]-delt;
       k2=func(p2)-fx;
       /*res= (k1-2.0*fx+k2)/delt/delt; */
-      res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+      res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
       
-#ifdef DEBUGHESS
+#ifdef DEBUGHESSII
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 #endif
@@ -2571,48 +2904,122 @@ double hessii(double x[], double delta,
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 	delts=delt;
       }
-    }
+    } /* End loop k */
   }
   delti[theta]=delts;
   return res; 
   
 }
 
-double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {
   int i;
   int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];
-  int k;
-
+  int k, kmax=1;
+  double v1, v2, cv12, lc1, lc2;
+  
   fx=func(x);
-  for (k=1; k<=2; k++) {
+  for (k=1; k<=kmax; k=k+10) {
     for (i=1;i<=npar;i++) p2[i]=x[i];
-    p2[thetai]=x[thetai]+delti[thetai]/k;
-    p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+    p2[thetai]=x[thetai]+delti[thetai]*k;
+    p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k1=func(p2)-fx;
   
-    p2[thetai]=x[thetai]+delti[thetai]/k;
-    p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+    p2[thetai]=x[thetai]+delti[thetai]*k;
+    p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k2=func(p2)-fx;
   
-    p2[thetai]=x[thetai]-delti[thetai]/k;
-    p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+    p2[thetai]=x[thetai]-delti[thetai]*k;
+    p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k3=func(p2)-fx;
   
-    p2[thetai]=x[thetai]-delti[thetai]/k;
-    p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+    p2[thetai]=x[thetai]-delti[thetai]*k;
+    p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k4=func(p2)-fx;
-    res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-#ifdef DEBUG
-    printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-    fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+    res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
+    if(k1*k2*k3*k4 <0.){
+      kmax=kmax+10;
+      if(kmax >=10){
+      printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
+      fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
+      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+      }
+    }
+#ifdef DEBUGHESSIJ
+    v1=hess[thetai][thetai];
+    v2=hess[thetaj][thetaj];
+    cv12=res;
+    /* Computing eigen value of Hessian matrix */
+    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) ){
+      printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+      fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+    }
 #endif
   }
   return res;
 }
 
+    /* Not done yet: Was supposed to fix if not exactly at the maximum */
+/* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
+/* { */
+/*   int i; */
+/*   int l=1, lmax=20; */
+/*   double k1,k2,k3,k4,res,fx; */
+/*   double p2[MAXPARM+1]; */
+/*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
+/*   int k=0,kmax=10; */
+/*   double l1; */
+  
+/*   fx=func(x); */
+/*   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 = delti*(l1*k); */
+/*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
+/*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+/*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+/*       k1=func(p2)-fx; */
+      
+/*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+/*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+/*       k2=func(p2)-fx; */
+      
+/*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+/*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+/*       k3=func(p2)-fx; */
+      
+/*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+/*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+/*       k4=func(p2)-fx; */
+/*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
+/* #ifdef DEBUGHESSIJ */
+/*       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
+/*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
+/* #endif */
+/*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
+/* 	k=kmax; */
+/*       } */
+/*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
+/* 	k=kmax; l=lmax*10; */
+/*       } */
+/*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
+/* 	delts=delt; */
+/*       } */
+/*     } /\* End loop k *\/ */
+/*   } */
+/*   delti[theta]=delts; */
+/*   return res;  */
+/* } */
+
+
 /************** Inverse of matrix **************/
 void ludcmp(double **a, int n, int *indx, double *d) 
 { 
@@ -2689,7 +3096,7 @@ void lubksb(double **a, int n, int *indx
 
 void pstamp(FILE *fichier)
 {
-  fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+  fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }
 
 /************ Frequencies ********************/
@@ -2705,8 +3112,8 @@ void  freqsummary(char fileres[], int ia
   
   pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin,iagemax+3);
-  strcpy(fileresp,"p");
-  strcat(fileresp,fileres);
+  strcpy(fileresp,"P_");
+  strcat(fileresp,fileresu);
   if((ficresp=fopen(fileresp,"w"))==NULL) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
@@ -2741,13 +3148,13 @@ void  freqsummary(char fileres[], int ia
 	bool=1;
 	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]]){
+            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(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*/
+              /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
+                bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
+                j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+              /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
             } 
 	}
  
@@ -2776,10 +3183,10 @@ void  freqsummary(char fileres[], int ia
       pstamp(ficresp);
       if  (cptcovn>0) {
 	fprintf(ficresp, "\n#********** Variable "); 
-	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(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]]);
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 	fprintf(ficlog, "**********\n#");
       }
       for(i=1; i<=nlstate;i++) 
@@ -2907,7 +3314,7 @@ void prevalence(double ***probs, double
 	bool=1;
 	if  (cptcovn>0) {
 	  for (z1=1; z1<=cptcoveff; z1++) 
-	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
+	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
 	      bool=0;
 	} 
 	if (bool==1) { 
@@ -3112,11 +3519,11 @@ void tricode(int *Tvar, int **nbcode, in
 
   cptcoveff=0; 
  
-  for (k=-1; k < maxncov; k++) Ndum[k]=0;
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
 
   /* Loop on covariates without age and products */
   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
+    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     for (i=1; i<=imx; i++) { /* Loop 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
@@ -3139,15 +3546,24 @@ void tricode(int *Tvar, int **nbcode, in
       /* 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.*/
-    }
+    } /* end for loop on individuals i */
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+    fprintf(ficlog," 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. */
+    for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
+      printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+      fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+      if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
+	if( k != -1){
+	  ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
+			     covariate for which somebody answered excluding 
+			     undefined. Usually 2: 0 and 1. */
+	}
+	ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
+			     covariate for which somebody answered including 
+			     undefined. Usually 3: -1, 0 and 1. */
       }
       /* 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 */
@@ -3164,41 +3580,53 @@ void tricode(int *Tvar, int **nbcode, in
        nbcode[Tvar[j]][1]=0;
        nbcode[Tvar[j]][2]=1;
        nbcode[Tvar[j]][3]=2;
+       To be continued (not working yet).
     */
-    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 k in an array nbcode. 
-				     k is a modality. If we have model=V1+V1*sex 
-				     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-	  ij++;
-	}
-	if (ij > ncodemax[j]) break; 
-      }  /* end of loop on */
-    } /* end of loop on modality */ 
+    ij=0; /* ij is similar to i but can jump over null modalities */
+    for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+    	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+	  break;
+	}
+	ij++;
+	nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
+	cptcode = ij; /* New max modality for covar j */
+    } /* end of loop on modality i=-1 to 1 or more */
+      
+    /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+    /* 	/\*recode from 0 *\/ */
+    /* 				     k is a modality. If we have model=V1+V1*sex  */
+    /* 				     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+    /* 				  But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+    /* 	} */
+    /* 	/\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+    /* 	if (ij > ncodemax[j]) { */
+    /* 	  printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+    /* 	  fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+    /* 	  break; */
+    /* 	} */
+    /*   }  /\* end of loop on modality k *\/ */
   } /* 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 */ 
+  for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*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]++; 
+   Ndum[ij]++; /* Might be supersed V1 + V1*age */
  } 
 
- ij=1;
+ ij=0;
  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)){
+     ij++;
      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
      Tvaraff[ij]=i; /*For printing (unclear) */
-     ij++;
-   }else
-       Tvaraff[ij]=0;
+   }else{
+       /* Tvaraff[ij]=0; */
+   }
  }
- ij--;
+ /* ij--; */
  cptcoveff=ij; /*Number of total covariates*/
 
 }
@@ -3524,7 +3952,7 @@ void cvevsij(double ***eij, double x[],
 }
 
 /************ Variance ******************/
-void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
 {
   /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
@@ -3553,11 +3981,11 @@ void varevsij(char optionfilefiname[], d
 
   if(popbased==1){
     if(mobilav!=0)
-      strcpy(digitp,"-populbased-mobilav-");
-    else strcpy(digitp,"-populbased-nomobil-");
+      strcpy(digitp,"-POPULBASED-MOBILAV_");
+    else strcpy(digitp,"-POPULBASED-NOMOBIL_");
   }
   else 
-    strcpy(digitp,"-stablbased-");
+    strcpy(digitp,"-STABLBASED_");
 
   if (mobilav!=0) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
@@ -3567,12 +3995,12 @@ void varevsij(char optionfilefiname[], d
     }
   }
 
-  strcpy(fileresprobmorprev,"prmorprev"); 
+  strcpy(fileresprobmorprev,"PRMORPREV-"); 
   sprintf(digit,"%-d",ij);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   strcat(fileresprobmorprev,digit); /* Tvar to be done */
   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-  strcat(fileresprobmorprev,fileres);
+  strcat(fileresprobmorprev,fileresu);
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobmorprev);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
@@ -3590,7 +4018,8 @@ void varevsij(char optionfilefiname[], d
   }  
   fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n# Routine varevsij");
-  /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+  fprintf(ficgp,"\nunset title \n");
+/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 /*   } */
@@ -3649,7 +4078,7 @@ void varevsij(char optionfilefiname[], d
 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
-      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
 
       if (popbased==1) {
 	if(mobilav ==0){
@@ -3680,7 +4109,7 @@ void varevsij(char optionfilefiname[], d
       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
-      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
  
       if (popbased==1) {
 	if(mobilav ==0){
@@ -3755,7 +4184,7 @@ void varevsij(char optionfilefiname[], d
     /* end ppptj */
     /*  x centered again */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
-    prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+    prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
  
     if (popbased==1) {
       if(mobilav ==0){
@@ -3802,9 +4231,11 @@ 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 size 320, 240");
+  /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
+  fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
   /* 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,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
 /*   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); */
@@ -3812,11 +4243,11 @@ void varevsij(char optionfilefiname[], d
   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);
+  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <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.svg\"> <br>\n", stepm,YEARM,digitp,digit);
 */
-/*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-  fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+/*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
+  fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
 
   free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);
@@ -3831,7 +4262,7 @@ void varevsij(char optionfilefiname[], d
 }  /* end varevsij */
 
 /************ Variance of prevlim ******************/
-void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyear, int ij, char strstart[])
 {
   /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
@@ -3870,13 +4301,13 @@ void varprevlim(char fileres[], double *
       for(i=1; i<=npar; i++){ /* Computes gradient */
 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }
-      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
       for(i=1;i<=nlstate;i++)
 	gp[i] = prlim[i][i];
     
       for(i=1; i<=npar; i++) /* Computes gradient */
 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
-      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
       for(i=1;i<=nlstate;i++)
 	gm[i] = prlim[i][i];
 
@@ -3934,20 +4365,20 @@ void varprob(char optionfilefiname[], do
   char fileresprobcor[FILENAMELENGTH];
   double ***varpij;
 
-  strcpy(fileresprob,"prob"); 
+  strcpy(fileresprob,"PROB_"); 
   strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }
-  strcpy(fileresprobcov,"probcov"); 
-  strcat(fileresprobcov,fileres);
+  strcpy(fileresprobcov,"PROBCOV_"); 
+  strcat(fileresprobcov,fileresu);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcov);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }
-  strcpy(fileresprobcor,"probcor"); 
-  strcat(fileresprobcor,fileres);
+  strcpy(fileresprobcor,"PROBCOR_"); 
+  strcat(fileresprobcor,fileresu);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
@@ -3989,10 +4420,9 @@ void varprob(char optionfilefiname[], do
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");
 
-  fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-  fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-  file %s<br>\n",optionfilehtmcov);
-  fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+  fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
+  fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
+  fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
@@ -4013,23 +4443,23 @@ To be simple, these graphs help to under
     /*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]]);
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 	fprintf(ficresprob, "**********\n#\n");
 	fprintf(ficresprobcov, "\n#********** Variable "); 
-	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 	fprintf(ficresprobcov, "**********\n#\n");
 	
 	fprintf(ficgp, "\n#********** Variable "); 
-	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 	fprintf(ficgp, "**********\n#\n");
 	
 	
 	fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
-	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 	fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 	
 	fprintf(ficresprobcor, "\n#********** Variable ");    
-	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
 	fprintf(ficresprobcor, "**********\n#");    
       }
       
@@ -4039,8 +4469,11 @@ To be simple, these graphs help to under
       gm=vector(1,(nlstate)*(nlstate+ndeath));
       for (age=bage; age<=fage; age ++){ 
 	cov[2]=age;
+	if(nagesqr==1)
+	  cov[3]= age*age;
 	for (k=1; k<=cptcovn;k++) {
-	  cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+	  cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
+	  /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
 							 * 1  1 1 1 1
 							 * 2  2 1 1 1
 							 * 3  1 2 1 1
@@ -4048,9 +4481,9 @@ To be simple, these graphs help to under
 	  /* 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<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
+	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,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]]];
+	  cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
 	
     
 	for(theta=1; theta <=npar; theta++){
@@ -4198,17 +4631,18 @@ To be simple, these graphs help to under
 		  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
 		  if(first==1){
 		    first=0;
+ 		    fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
  		    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 size 320, 240");
+		    fprintf(ficgp,"\nset ter svg size 640, 480");
 		    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
- :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-			    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-		    fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
+%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
+			    subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
+			    subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+		    fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
 		    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-		    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+		    fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
@@ -4225,7 +4659,7 @@ To be simple, these graphs help to under
 		  }/* if first */
 		} /* age mod 5 */
 	      } /* end loop age */
-	      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+	      fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
 	      first=1;
 	    } /*l12 */
 	  } /* k12 */
@@ -4247,7 +4681,7 @@ To be simple, these graphs help to under
 
 
 /******************* Printing html file ***********/
-void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
 		  int lastpass, int stepm, int weightopt, char model[],\
 		  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
 		  int popforecast, int estepm ,\
@@ -4260,20 +4694,20 @@ void printinghtml(char fileres[], char t
 </ul>");
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-	   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+	   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-	   stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+	   stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
    fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-	   subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+	   subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n",
-	   estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+	   estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
    fprintf(fichtm,"\
  - Population projections by age and states: \
-   <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+   <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
 
@@ -4282,65 +4716,90 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
 
  jj1=0;
  for(k1=1; k1<=m;k1++){
-   for(i1=1; i1<=ncodemax[k1];i1++){
+   /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;
      if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-       for (cpt=1; cpt<=cptcoveff;cpt++) 
-	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+       for (cpt=1; cpt<=cptcoveff;cpt++){ 
+	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+	 printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
+       }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
+     /* aij, bij */
+     fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
+<img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
      /* 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%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);     
+     fprintf(fichtm,"<br>\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
+<img src=\"%s_%d-2.svg\">",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%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>- 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);
-       }
+     fprintf(fichtm,"<br>\n- Iij 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,\
+ incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
+divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
+<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
+     /* Survival functions (period) in state j */
+     for(cpt=1; cpt<=nlstate;cpt++){
+       fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
+     }
+     /* State specific survival functions (period) */
+     for(cpt=1; cpt<=nlstate;cpt++){
+       fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
+ Or probability to survive in various states (1 to %d) being in state %d at different ages.\
+ <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
+     }
+     /* Period (stable) prevalence in each health state */
+     for(cpt=1; cpt<=nlstate;cpt++){
+       fprintf(fichtm,"<br>\n- 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.svg\">%s%d_%d.svg</a><br> \
+<img src=\"%s_%d-%d.svg\">", 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 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);
+       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) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
+<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
      }
-   } /* end i1 */
+   /* } /\* end i1 *\/ */
  }/* End k1 */
  fprintf(fichtm,"</ul>");
 
-
  fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+ - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
+But because parameters are usually highly correlated (a higher incidence of disability \
+and a higher incidence of recovery can give very close observed transition) it might \
+be very useful to look not only at linear confidence intervals estimated from the \
+variances but at the covariance matrix. And instead of looking at the estimated coefficients \
+(parameters) of the logistic regression, it might be more meaningful to visualize the \
+covariance matrix of the one-step probabilities. \
+See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
 
- fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-	 subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+ fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+	 subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
  fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-	 subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+	 subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
 
  fprintf(fichtm,"\
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-	 subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+	 subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
  fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",
-	   estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+	   estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
  fprintf(fichtm,"\
  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",
-	   estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+	   estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
  fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
-	 estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+	 estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
  fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
-	 estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+	 estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
  fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-	 subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+	 subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
 
 /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
@@ -4356,37 +4815,38 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
 
  jj1=0;
  for(k1=1; k1<=m;k1++){
-   for(i1=1; i1<=ncodemax[k1];i1++){
+   /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;
      if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++) 
-	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      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.svg <br>\
+<img src=\"%s_%d-%d.svg\">",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) \
 true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\
- observed and cahotic prevalences: %s%d.png<br>\
-<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   } /* end i1 */
+ observed and cahotic prevalences: %s_%d.svg<br>\
+<img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
+   /* } /\* end i1 *\/ */
  }/* End k1 */
  fprintf(fichtm,"</ul>");
  fflush(fichtm);
 }
 
 /******************* Gnuplot file **************/
-void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 
   char dirfileres[132],optfileres[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng=0;
+  int vpopbased;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
@@ -4397,76 +4857,97 @@ void printinggnuplot(char fileres[], cha
     /*#endif */
   m=pow(2,cptcoveff);
 
+  /* Contribution to likelihood */
+  /* Plot the probability implied in the likelihood */
+    fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
+    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
+    /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
+    fprintf(ficgp,"\nset ter png size 640, 480");
+/* good for mle=4 plot by number of matrix products.
+   replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
+/* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
+    /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
+    fprintf(ficgp,"\nset out \"%s.png\";",subdirf2(optionfilefiname,"ILK_"));
+    fprintf(ficgp,"\nplot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk));
+    fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk));
+    fprintf(ficgp,"\nset out;unset log\n");
+    /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
+
   strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");
  /* 1eme*/
-  fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
+  fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {
     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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+     fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
      fprintf(ficgp,"set xlabel \"Age\" \n\
 set ylabel \"Probability\" \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);
+set ter svg size 640, 480\n\
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"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 lt 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(fileresu,"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 lt 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*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," %%*lf (%%*lf)");
      }  
-     fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-   }
-  }
+     fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
+     fprintf(ficgp,"\nset out \n");
+    } /* k1 */
+  } /* cpt */
   /*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 size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-    
-    for (i=1; i<= nlstate+1 ; i ++) {
-      k=2*i;
-      fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%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== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-      else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-      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)");
-      }   
-      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 lt 0");
-      else fprintf(ficgp,"\" t\"\" w l lt 0,");
-    }
-  }
-  
+    fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
+    for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+      if(vpopbased==0)
+	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
+      else
+	fprintf(ficgp,"\nreplot ");
+      for (i=1; i<= nlstate+1 ; i ++) {
+	k=2*i;
+	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
+	for (j=1; j<= nlstate+1 ; j ++) {
+	  if (j==i) fprintf(ficgp," %%lf (%%lf)");
+	  else fprintf(ficgp," %%*lf (%%*lf)");
+	}   
+	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
+	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+	for (j=1; j<= nlstate+1 ; j ++) {
+	  if (j==i) fprintf(ficgp," %%lf (%%lf)");
+	  else fprintf(ficgp," %%*lf (%%*lf)");
+	}   
+	fprintf(ficgp,"\" t\"\" w l lt 0,");
+	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+	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 lt 0");
+	else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+      } /* state */
+    } /* vpopbased */
+    fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
+  } /* k1 */
   /*3eme*/
   
   for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       /*       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 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,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
+      fprintf(ficgp,"set ter svg size 640, 480\n\
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"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) ");
 	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
@@ -4476,99 +4957,224 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
 	
       */
       for (i=1; i< nlstate ; i ++) {
-	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
 	/*	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
 	
       } 
-      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
     }
   }
   
-  /* CV preval stable (period) */
+  /* Survival functions (period) from state i in state j by initial state i */
   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,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
+      fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+set ter svg size 640, 480\n\
+unset log y\n\
+plot [%.f:%.f]  ", ageminpar, agemaxpar);
+      for (i=1; i<= nlstate ; i ++){
+	if(i==1)
+	  fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+	else
+	  fprintf(ficgp,", '' ");
+	l=(nlstate+ndeath)*(i-1)+1;
+	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+	for (j=2; j<= nlstate+ndeath ; j ++)
+	  fprintf(ficgp,"+$%d",k+l+j-1);
+	fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+      } /* nlstate */
+      fprintf(ficgp,"\nset out\n");
+    } /* end cpt state*/ 
+  } /* end covariate */  
+
+  /* Survival functions (period) from state i in state j by final state j */
+  for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
+    for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+      k=3;
+      fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
+      fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+set ter svg size 640, 480\n\
+unset log y\n\
+plot [%.f:%.f]  ", ageminpar, agemaxpar);
+      for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+	if(j==1)
+	  fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+	else
+	  fprintf(ficgp,", '' ");
+	l=(nlstate+ndeath)*(cpt-1) +j;
+	fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+	/* for (i=2; i<= nlstate+ndeath ; i ++) */
+	/*   fprintf(ficgp,"+$%d",k+l+i-1); */
+	fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+      } /* nlstate */
+      fprintf(ficgp,", '' ");
+      fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+      for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+	l=(nlstate+ndeath)*(cpt-1) +j;
+	if(j < nlstate)
+	  fprintf(ficgp,"$%d +",k+l);
+	else
+	  fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+      }
+      fprintf(ficgp,"\nset out\n");
+    } /* end cpt state*/ 
+  } /* end covariate */  
+
+  /* CV preval stable (period) for each covariate */
+  for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
+    for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+      k=3;
       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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-set ter png small size 320, 240\n\
+set ter svg size 640, 480\n\
 unset log y\n\
 plot [%.f:%.f]  ", ageminpar, agemaxpar);
       for (i=1; i<= nlstate ; i ++){
 	if(i==1)
-	  fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+	  fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"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);
+	for (j=2; j<= nlstate ; j ++)
+	  fprintf(ficgp,"+$%d",k+l+j-1);
 	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */
-      fprintf(ficgp,"\n");
+      fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/ 
   } /* end covariate */  
-  
+
   /* proba elementaires */
+  fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){
+    fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {
+	fprintf(ficgp,"#   current state %d\n",k);
 	for(j=1; j <=ncovmodel; j++){
-	  fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+	  fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
 	  jk++; 
-	  fprintf(ficgp,"\n");
 	}
+	fprintf(ficgp,"\n");
       }
     }
    }
+  fprintf(ficgp,"##############\n#\n");
+
   /*goto avoid;*/
-   for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+  fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
+  fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
+  fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
+  fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
+  fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
+  fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+  fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
+  fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+  fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
+  fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
+  fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+  fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
+  fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
+  fprintf(ficgp,"#\n");
+   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
+     fprintf(ficgp,"# ng=%d\n",ng);
+     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
      for(jk=1; jk <=m; jk++) {
-       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
-       if (ng==2)
+       fprintf(ficgp,"#    jk=%d\n",jk);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
+       fprintf(ficgp,"\nset ter svg size 640, 480 ");
+       if (ng==1){
+	 fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
+	 fprintf(ficgp,"\nunset log y");
+       }else if (ng==2){
+	 fprintf(ficgp,"\nset ylabel \"Probability\"\n");
+	 fprintf(ficgp,"\nset log y");
+       }else if (ng==3){
 	 fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-       else
-	 fprintf(ficgp,"\nset title \"Probability\"\n");
-       fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+	 fprintf(ficgp,"\nset log y");
+       }else
+	 fprintf(ficgp,"\nunset title ");
+       fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
        i=1;
        for(k2=1; k2<=nlstate; k2++) {
 	 k3=i;
 	 for(k=1; k<=(nlstate+ndeath); k++) {
 	   if (k != k2){
-	     if(ng==2)
-	       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);
+	     switch( ng) {
+	     case 1:
+	       if(nagesqr==0)
+		 fprintf(ficgp," p%d+p%d*x",i,i+1);
+	       else /* nagesqr =1 */
+		 fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+	       break;
+	     case 2: /* ng=2 */
+	       if(nagesqr==0)
+		 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+	       else /* nagesqr =1 */
+		   fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+	       break;
+	     case 3:
+	       if(nagesqr==0)
+		 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+	       else /* nagesqr =1 */
+		 fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
+	       break;
+	     }
 	     ij=1;/* To be checked else nbcode[0][0] wrong */
-	     for(j=3; j <=ncovmodel; j++) {
-	       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++;
+	     for(j=3; j <=ncovmodel-nagesqr; j++) {
+	       /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
+	       if(ij <=cptcovage) { /* Bug valgrind */
+		 if((j-2)==Tage[ij]) { /* Bug valgrind */
+		   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+		   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+		   ij++;
+		 }
 	       }
 	       else
-		 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+		 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
 	     }
-	     fprintf(ficgp,")/(1");
+	     if(ng != 1){
+	       fprintf(ficgp,")/(1");
 	     
-	     for(k1=1; k1 <=nlstate; k1++){   
-	       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++;
+	       for(k1=1; k1 <=nlstate; k1++){ 
+		 if(nagesqr==0)
+		   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+		 else /* nagesqr =1 */
+		   fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
+		 
+		 ij=1;
+		 for(j=3; j <=ncovmodel-nagesqr; j++){
+		   if(ij <=cptcovage) { /* Bug valgrind */
+		     if((j-2)==Tage[ij]) { /* Bug valgrind */
+		       fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+		       /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+		       ij++;
+		     }
+		   }
+		   else
+		     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
 		 }
-		 else
-		   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+		 fprintf(ficgp,")");
 	       }
 	       fprintf(ficgp,")");
+	       if(ng ==2)
+		 fprintf(ficgp," t \"p%d%d\" ", k2,k);
+	       else /* ng= 3 */
+		 fprintf(ficgp," t \"i%d%d\" ", k2,k);
+	     }else{ /* end ng <> 1 */
+	       fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
 	     }
-	     fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 	     if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 	     i=i+ncovmodel;
 	   }
 	 } /* end k */
        } /* end k2 */
+       fprintf(ficgp,"\n set out\n");
      } /* end jk */
    } /* end ng */
  /* avoid: */
@@ -4636,8 +5242,8 @@ void prevforecast(char fileres[], double
   agelim=AGESUP;
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
  
-  strcpy(fileresf,"f"); 
-  strcat(fileresf,fileres);
+  strcpy(fileresf,"F_"); 
+  strcat(fileresf,fileresu);
   if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
@@ -4686,7 +5292,7 @@ void prevforecast(char fileres[], double
       k=k+1;
       fprintf(ficresf,"\n#******");
       for(j=1;j<=cptcoveff;j++) {
-	fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       fprintf(ficresf,"******\n");
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
@@ -4710,7 +5316,7 @@ void prevforecast(char fileres[], double
 	    if (h*hstepm/YEARM*stepm ==yearp) {
               fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++) 
-                fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	      fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
 	    } 
 	    for(j=1; j<=nlstate+ndeath;j++) {
@@ -4760,8 +5366,8 @@ void populforecast(char fileres[], doubl
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   
   
-  strcpy(filerespop,"pop"); 
-  strcat(filerespop,fileres);
+  strcpy(filerespop,"POP_"); 
+  strcat(filerespop,fileresu);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", filerespop);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
@@ -4808,7 +5414,7 @@ void populforecast(char fileres[], doubl
       k=k+1;
       fprintf(ficrespop,"\n#******");
       for(j=1;j<=cptcoveff;j++) {
-	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       fprintf(ficrespop,"******\n");
       fprintf(ficrespop,"# Age");
@@ -5114,7 +5720,7 @@ double gompertz_f(const gsl_vector *v, v
 #endif
 
 /******************* Printing html file ***********/
-void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+void printinghtmlmort(char fileresu[], 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;
@@ -5123,7 +5729,7 @@ void printinghtmlmort(char fileres[], ch
   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,"<br><br><img src=\"graphmort.svg\">");
   fprintf(fichtm,"</ul>");
 
 fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
@@ -5138,7 +5744,7 @@ fprintf(fichtm,"<ul><li><h4>Life table</
 }
 
 /******************* Gnuplot file **************/
-void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 
   char dirfileres[132],optfileres[132];
 
@@ -5152,9 +5758,9 @@ void printinggnuplotmort(char fileres[],
 
   strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");
-  fprintf(ficgp,"set out \"graphmort.png\"\n "); 
+  fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
-  fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
+  fprintf(ficgp, "set ter svg size 640, 480\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);
 
@@ -5175,8 +5781,8 @@ int readdata(char datafile[], int firsto
 
 
   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;
+    printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
+    fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
   }
 
   i=1;
@@ -5353,9 +5959,10 @@ void removespace(char *str) {
 }
 
 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
+   * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
+   * - nagesqr = 1 if age*age in the model, otherwise 0.
+   * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
+   * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
    * - 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
@@ -5370,22 +5977,14 @@ int decodemodel ( char model[], int last
   int  j1, k1, k2;
   char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];
+  char *strpt;
 
   /*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);
+      printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
+      fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
       return 1;
     }
     if (strstr(model,"v") !=0){
@@ -5393,117 +5992,153 @@ int decodemodel ( char model[], int last
       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 []
-     */
+    strcpy(modelsav,model); 
+    if ((strpt=strstr(model,"age*age")) !=0){
+      printf(" strpt=%s, model=%s\n",strpt, model);
+      if(strpt != model){
+      printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+ 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
+ corresponding column of parameters.\n",model);
+      fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+ 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
+ corresponding column of parameters.\n",model); fflush(ficlog);
+      return 1;
+    }
 
-    /* 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]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[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 */
+      nagesqr=1;
+      if (strstr(model,"+age*age") !=0)
+	substrchaine(modelsav, model, "+age*age");
+      else if (strstr(model,"age*age+") !=0)
+	substrchaine(modelsav, model, "age*age+");
+      else 
+	substrchaine(modelsav, model, "age*age");
+    }else
+      nagesqr=0;
+    if (strlen(modelsav) >1){
+      j=nbocc(modelsav,'+'); /**< j=Number of '+' */
+      j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
+      cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
+      cptcovt= j+1; /* Number of total covariates in the model, not including
+		   * cst, age and age*age 
+		   * V1+V1*age+ V3 + V3*V4+age*age=> 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  */
+
+    
+      /*   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]][codtabm(ij,Tvar[k])]; */
+      /* 	} */
+      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[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;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
-	  /*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 */
+      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; V1+V1*age Tvar[2]=1 */
+	    cptcovage++; /* Sums the number of covariates which include age as a product */
+	    Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+	    /*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++;
-	  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 */
+	  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 + on total covariates */
+    } /* end if strlen(modelsave == 0) age*age might exist */
+  } /* end if strlen(model == 0) */
   
   /*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*/
@@ -5656,7 +6291,7 @@ BOOL IsWow64()
 }
 #endif
 
-void syscompilerinfo()
+void syscompilerinfo(int logged)
  {
    /* #include "syscompilerinfo.h"*/
    /* command line Intel compiler 32bit windows, XP compatible:*/
@@ -5705,52 +6340,52 @@ void syscompilerinfo()
    int cross = CROSS;
    if (cross){
 	   printf("Cross-");
-	   fprintf(ficlog, "Cross-");
+	   if(logged) fprintf(ficlog, "Cross-");
    }
 #endif
 
 #include <stdint.h>
 
-   printf("Compiled with:");fprintf(ficlog,"Compiled with:");
+   printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)
-   printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM");	/* Clang/LLVM. ---------------------------------------------- */
+   printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");	/* Clang/LLVM. ---------------------------------------------- */
 #endif
 #if defined(__ICC) || defined(__INTEL_COMPILER)
-   printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+   printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
 #endif
 #if defined(__GNUC__) || defined(__GNUG__)
-   printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+   printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
 #endif
 #if defined(__HP_cc) || defined(__HP_aCC)
-   printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+   printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
 #endif
 #if defined(__IBMC__) || defined(__IBMCPP__)
-   printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
+   printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
 #endif
 #if defined(_MSC_VER)
-   printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+   printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
 #endif
 #if defined(__PGI)
-   printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
+   printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
 #endif
 #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
-   printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+   printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
 #endif
-   printf(" for ");fprintf(ficlog," for ");
+   printf(" for "); if (logged) fprintf(ficlog, " for ");
    
 // 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)
-   printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
+   printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
 #elif __unix__ // all unices, not all compilers
     // Unix
-   printf("Unix ");fprintf(ficlog,"Unix ");
+   printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
 #elif __linux__
     // linux
-   printf("linux ");fprintf(ficlog,"linux ");
+   printf("linux ");if(logged) fprintf(ficlog,"linux ");
 #elif __APPLE__
     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
-   printf("Mac OS ");fprintf(ficlog,"Mac OS ");
+   printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
 #endif
 
 /*  __MINGW32__	  */
@@ -5764,11 +6399,11 @@ void syscompilerinfo()
 /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
 
 #if UINTPTR_MAX == 0xffffffff
-   printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
+   printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
 #elif UINTPTR_MAX == 0xffffffffffffffff
-   printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
+   printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
 #else
-   printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
+   printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
 #endif
 
 #if defined(__GNUC__)
@@ -5781,18 +6416,18 @@ void syscompilerinfo()
                             + __GNUC_MINOR__ * 100)
 # endif
    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
-   fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
+   if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
 
    if (uname(&sysInfo) != -1) {
      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-     fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+	 if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
    }
    else
       perror("uname() error");
    //#ifndef __INTEL_COMPILER 
 #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
    printf("GNU libc version: %s\n", gnu_get_libc_version()); 
-   fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+   if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
 #endif
 #endif
 
@@ -5800,12 +6435,12 @@ void syscompilerinfo()
    //   {
 #if defined(_MSC_VER)
    if (IsWow64()){
-	   printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
-	   fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+	   printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+	   if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
    }
    else{
-	   printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
-	   fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+	   printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+	   if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
    }
    //	   printf("\nPress Enter to continue...");
    //	   getchar();
@@ -5816,25 +6451,26 @@ void syscompilerinfo()
 
  }
 
-int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
+ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   int i, j, k, i1 ;
-  double ftolpl = 1.e-10;
+  /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;
+  double tot;
 
-    strcpy(filerespl,"pl");
-    strcat(filerespl,fileres);
-    if((ficrespl=fopen(filerespl,"w"))==NULL) {
-      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-    }
-    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");
+  strcpy(filerespl,"PL_");
+  strcat(filerespl,fileresu);
+  if((ficrespl=fopen(filerespl,"w"))==NULL) {
+    printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+    fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+  }
+  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. Precision given by ftolpl=%g \n", ftolpl);
+  fprintf(ficrespl,"#Age ");
+  for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+  fprintf(ficrespl,"\n");
   
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
 
@@ -5849,14 +6485,14 @@ int prevalence_limit(double *p, double *
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 	k=k+1;
 	/* to clean */
-	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
-	fprintf(ficrespl,"\n#******");
-	printf("\n#******");
-	fprintf(ficlog,"\n#******");
+	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+	fprintf(ficrespl,"#******");
+	printf("#******");
+	fprintf(ficlog,"#******");
 	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," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+	  printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+	  fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	}
 	fprintf(ficrespl,"******\n");
 	printf("******\n");
@@ -5864,20 +6500,23 @@ int prevalence_limit(double *p, double *
 
 	fprintf(ficrespl,"#Age ");
 	for(j=1;j<=cptcoveff;j++) {
-	  fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	}
-	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-	fprintf(ficrespl,"\n");
+	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+	fprintf(ficrespl,"Total Years_to_converge\n");
 	
 	for (age=agebase; age<=agelim; age++){
 	/* for (age=agebase; age<=agebase; age++){ */
-	  prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+	  prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, 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,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+	  tot=0.;
+	  for(i=1; i<=nlstate;i++){
+	    tot +=  prlim[i][i];
 	    fprintf(ficrespl," %.5f", prlim[i][i]);
-	  fprintf(ficrespl,"\n");
+	  }
+	  fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
 	} /* Age */
 	/* was end of cptcod */
     } /* cptcov */
@@ -5896,7 +6535,7 @@ int hPijx(double *p, int bage, int fage)
   double agedeb;
   double ***p3mat;
 
-    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+    strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
@@ -5921,7 +6560,7 @@ int hPijx(double *p, int bage, int fage)
     for (k=1; k <= (int) pow(2,cptcoveff); k++){
       fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) 
-	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespij,"******\n");
       
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
@@ -5970,9 +6609,11 @@ int main(int argc, char *argv[])
 #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-
+  int ncvyearnp=0;
+  int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
   int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */
+  int num_filled;
   int itimes;
   int NDIM=2;
   int vpopbased=0;
@@ -5981,37 +6622,43 @@ int main(int argc, char *argv[])
   /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;
-  double agedeb;
-  double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+  double agedeb=0.;
+
+  double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
 
   double fret;
-  double dum; /* Dummy variable */
+  double dum=0.; /* Dummy variable */
   double ***p3mat;
   double ***mobaverage;
 
   char line[MAXLINE];
-  char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+  char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
+
+  char model[MAXLINE], modeltemp[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;
-  int c,  h , cpt;
-  int jl;
-  int i1, j1, jk, stepsize;
+  int c,  h , cpt, c2;
+  int jl=0;
+  int i1, j1, jk, stepsize=0;
+  int count=0;
+
   int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;
-  int hstepm, nhstepm;
+  int hstepm=0, nhstepm=0;
   int agemortsup;
   float  sumlpop=0.;
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
 
-  double bage=0, fage=110, age, agelim, agebase;
+  double bage=0, fage=110., age, agelim=0., agebase=0.;
   double ftolpl=FTOL;
   double **prlim;
   double ***param; /* Matrix of parameters */
   double  *p;
   double **matcov; /* Matrix of covariance */
+  double **hess; /* Hessian matrix */
   double ***delti3; /* Scale */
   double *delti; /* Scale */
   double ***eij, ***vareij;
@@ -6067,8 +6714,8 @@ int main(int argc, char *argv[])
 #else
   getcwd(pathcd, size);
 #endif
-
-  printf("\n%s\n%s",version,fullversion);
+  syscompilerinfo(0);
+  printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
   if(argc <=1){
     printf("\nEnter the parameter file name: ");
     fgets(pathr,FILENAMELENGTH,stdin);
@@ -6132,7 +6779,7 @@ int main(int argc, char *argv[])
     goto end;
   }
   fprintf(ficlog,"Log filename:%s\n",filelog);
-  fprintf(ficlog,"\n%s\n%s",version,fullversion);
+  fprintf(ficlog,"Version %s %s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: \n");
   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
  path=%s \n\
@@ -6140,7 +6787,7 @@ int main(int argc, char *argv[])
  optionfilext=%s\n\
  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
 
-  syscompilerinfo();
+  syscompilerinfo(1);
 
   printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);
@@ -6151,7 +6798,9 @@ int main(int argc, char *argv[])
   /* */
   strcpy(fileres,"r");
   strcat(fileres, optionfilefiname);
+  strcat(fileresu, optionfilefiname); /* Without r in front */
   strcat(fileres,".txt");    /* Other files have txt extension */
+  strcat(fileresu,".txt");    /* Other files have txt extension */
 
   /* Main ---------arguments file --------*/
 
@@ -6166,7 +6815,7 @@ int main(int argc, char *argv[])
 
 
   strcpy(filereso,"o");
-  strcat(filereso,fileres);
+  strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
@@ -6176,37 +6825,103 @@ int main(int argc, char *argv[])
 
   /* Reads comments: lines beginning with '#' */
   numlinepar=0;
-  while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
+
+    /* First parameter line */
+  while(fgets(line, MAXLINE, ficpar)) {
+    /* If line starts with a # it is a comment */
+    if (line[0] == '#') {
+      numlinepar++;
+      fputs(line,stdout);
+      fputs(line,ficparo);
+      fputs(line,ficlog);
+      continue;
+    }else
+      break;
+  }
+  if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
+			title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
+    if (num_filled != 5) {
+      printf("Should be 5 parameters\n");
+    }
     numlinepar++;
-    fputs(line,stdout);
-    fputs(line,ficparo);
-    fputs(line,ficlog);
+    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
   }
-  ungetc(c,ficpar);
-
-  fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-  numlinepar++;
-  /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
-  printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n",title, datafile, lastobs, firstpass,lastpass);
-  /*
-
-
-
-   */
-  printf("\nftol=%e \n", ftol);
-  printf("stepm=%d \n", stepm);
-  printf("ncovcol=%d nlstate=%d \n", ncovcol, nlstate);
-  printf("ndeath=%d maxwav=%d mle=%d weight=%d\n", ndeath, maxwav, mle, weightopt);
-  printf("model=%s\n",model);
-  fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-  fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+  /* Second parameter line */
+  while(fgets(line, MAXLINE, ficpar)) {
+    /* If line starts with a # it is a comment */
+    if (line[0] == '#') {
+      numlinepar++;
+      fputs(line,stdout);
+      fputs(line,ficparo);
+      fputs(line,ficlog);
+      continue;
+    }else
+      break;
+  }
+  if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+			&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+    if (num_filled != 8) {
+      printf("Not 8\n");
+    }
+    printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
+  }
+  /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+  ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+  /* Third parameter line */
+  while(fgets(line, MAXLINE, ficpar)) {
+    /* If line starts with a # it is a comment */
+    if (line[0] == '#') {
+      numlinepar++;
+      fputs(line,stdout);
+      fputs(line,ficparo);
+      fputs(line,ficlog);
+      continue;
+    }else
+      break;
+  }
+  if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+    if (num_filled == 0)
+            model[0]='\0';
+    else if (num_filled != 1){
+      printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+      fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+      model[0]='\0';
+      goto end;
+    }
+    else{
+      if (model[0]=='+'){
+	for(i=1; i<=strlen(model);i++)
+	  modeltemp[i-1]=model[i];
+	strcpy(model,modeltemp); 
+      }
+    }
+    /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+    printf("model=1+age+%s\n",model);fflush(stdout);
+  }
+  /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
+  /* numlinepar=numlinepar+3; /\* In general *\/ */
+  /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
+  fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+  fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   fflush(ficlog);
+  /* if(model[0]=='#'|| model[0]== '\0'){ */
+  if(model[0]=='#'){
+    printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+ 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
+ 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");		\
+    if(mle != -1){
+      printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+      exit(1);
+    }
+  }
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
     numlinepar++;
+    if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+      z[0]=line[1];
+    }
+    /* printf("****line [1] = %c \n",line[1]); */
     fputs(line, stdout);
     //puts(line);
     fputs(line,ficparo);
@@ -6221,10 +6936,9 @@ int main(int argc, char *argv[])
      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*/
+    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,age*age makes 3*/
   else
-    ncovmodel=2;
-  nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+    ncovmodel=2; /* Constant and age */
   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
   npar= nforce*ncovmodel; /* Number of parameters like aij*/
   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
@@ -6239,8 +6953,8 @@ int main(int argc, char *argv[])
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-    printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-    fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+    printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+    fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     fclose (ficparo);
     fclose (ficlog);
@@ -6249,10 +6963,11 @@ int main(int argc, char *argv[])
   }
   else if(mle==-3) { /* Main Wizard */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-    printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-    fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+    printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+    fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     matcov=matrix(1,npar,1,npar);
+    hess=matrix(1,npar,1,npar);
   }
   else{
     /* Read guessed parameters */
@@ -6274,7 +6989,7 @@ int main(int argc, char *argv[])
 	if(jj==i) continue;
 	j++;
 	fscanf(ficpar,"%1d%1d",&i1,&j1);
-	if ((i1 != i) && (j1 != j)){
+	if ((i1 != i) || (j1 != jj)){
 	  printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
 It might be a problem of design; if ncovcol and the model are correct\n \
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
@@ -6282,8 +6997,8 @@ run imach with mle=-1 to get a correct t
 	}
 	fprintf(ficparo,"%1d%1d",i1,j1);
 	if(mle==1)
-	  printf("%1d%1d",i,j);
-	fprintf(ficlog,"%1d%1d",i,j);
+	  printf("%1d%1d",i,jj);
+	fprintf(ficlog,"%1d%1d",i,jj);
 	for(k=1; k<=ncovmodel;k++){
 	  fscanf(ficpar," %lf",&param[i][j][k]);
 	  if(mle==1){
@@ -6361,15 +7076,26 @@ run imach with mle=-1 to get a correct t
     ungetc(c,ficpar);
   
     matcov=matrix(1,npar,1,npar);
+    hess=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++)
       for(j=1; j <=npar; j++) matcov[i][j]=0.;
       
+    /* Scans npar lines */
     for(i=1; i <=npar; i++){
-      fscanf(ficpar,"%s",str);
+      count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
+      if(count != 3){
+	printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+	fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+	exit(1);
+      }else
       if(mle==1)
-	printf("%s",str);
-      fprintf(ficlog,"%s",str);
-      fprintf(ficparo,"%s",str);
+	printf("%1d%1d%1d",i1,j1,jk);
+      fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
+      fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
       for(j=1; j <=i; j++){
 	fscanf(ficpar," %le",&matcov[i][j]);
 	if(mle==1){
@@ -6385,6 +7111,7 @@ run imach with mle=-1 to get a correct t
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
+    /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
 	matcov[i][j]=matcov[j][i];
@@ -6401,8 +7128,8 @@ run imach with mle=-1 to get a correct t
     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;
+      printf("Problem writing new parameter file: %s\n", rfileres);goto end;
+      fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */
@@ -6424,6 +7151,7 @@ run imach with mle=-1 to get a correct t
   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 */
+  ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
 
   /* Reads data from file datafile */
   if (readdata(datafile, firstobs, lastobs, &imx)==1)
@@ -6461,6 +7189,7 @@ run imach with mle=-1 to get a correct t
 
 /* Main decodemodel */
 
+
   if(decodemodel(model, lastobs) == 1)
     goto end;
 
@@ -6504,14 +7233,14 @@ run imach with mle=-1 to get a correct t
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;
   Ndum =ivector(-1,NCOVMAX);  
-  if (ncovmodel > 2)
+  if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   /* Nbcode gives the value of the lth modality of jth covariate, in
      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /* 1 to ncodemax[j] is the maximum value of this jth covariate */
 
-  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]);*/
+  /*  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],codtabm(100,10));*/
   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;
 
@@ -6521,13 +7250,6 @@ run imach with mle=-1 to get a correct t
  
   m=pow(2,cptcoveff);
  
-  for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-    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)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
 	   * For k=4 covariates, h goes from 1 to 2**k
 	   * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
@@ -6541,32 +7263,47 @@ run imach with mle=-1 to get a correct t
 	   *     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
+	   *     9 i=5 1 i=3 1 i=2 1     2
+	   *    10     2     1     1     2
+	   *    11 i=6 1     2     1     2
+	   *    12     2     2     1     2
+	   *    13 i=7 1 i=4 1     2     2    
+	   *    14     2     1     2     2
+	   *    15 i=8 1     2     2     2
+	   *    16     2     2     2     2
 	   */
-	  codtab[h][k]=j;
-	  /* codtab[12][3]=1; */
-	  /*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]]);
-	} 
-      }
-    }
-  } 
+  /* /\* for(h=1; h <=100 ;h++){  *\/ */
+  /*   /\* printf("h=%2d ", h); *\/ */
+  /*    /\* for(k=1; k <=10; k++){ *\/ */
+  /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
+  /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */
+  /*    /\* } *\/ */
+  /*    /\* printf("\n"); *\/ */
+  /* } */
+  /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
+  /*   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[12][3]=1; *\/ */
+  /* 	  /\*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]]); *\/ */
+  /* 	}  */
+  /*     } */
+  /*   } */
+  /* }  */
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
      codtab[1][2]=1;codtab[2][2]=2; */
-  /* for(i=1; i <=m ;i++){ 
-     for(k=1; k <=cptcovn; k++){
-       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-     }
-     printf("\n");
-     }
-     scanf("%d",i);*/
+  /* for(i=1; i <=m ;i++){  */
+  /*    for(k=1; k <=cptcovn; k++){ */
+  /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
+  /*    } */
+  /*    printf("\n"); */
+  /* } */
+  /*   scanf("%d",i);*/
 
  free_ivector(Ndum,-1,NCOVMAX);
 
@@ -6575,7 +7312,7 @@ run imach with mle=-1 to get a correct t
   /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)
-    strcat(optionfilegnuplot,"-mort");
+    strcat(optionfilegnuplot,"-MORT_");
   strcat(optionfilegnuplot,".gp");
 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
@@ -6594,7 +7331,7 @@ run imach with mle=-1 to get a correct t
 
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   if(mle==-3)
-    strcat(optionfilehtm,"-mort");
+    strcat(optionfilehtm,"-MORT_");
   strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm);
@@ -6710,8 +7447,8 @@ Interval (in months) between two waves:
 #else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
 #endif
-    strcpy(filerespow,"pow-mort"); 
-    strcat(filerespow,fileres);
+    strcpy(filerespow,"POW-MORT_"); 
+    strcat(filerespow,fileresu);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
@@ -6807,24 +7544,27 @@ Interval (in months) between two waves:
 #endif  
     fclose(ficrespow);
     
-    hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
+    hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
 
     for(i=1; i <=NDIM; i++)
       for(j=i+1;j<=NDIM;j++)
 	matcov[i][j]=matcov[j][i];
     
     printf("\nCovariance matrix\n ");
+    fprintf(ficlog,"\nCovariance matrix\n ");
     for(i=1; i <=NDIM; i++) {
       for(j=1;j<=NDIM;j++){ 
 	printf("%f ",matcov[i][j]);
+	fprintf(ficlog,"%f ",matcov[i][j]);
       }
-      printf("\n ");
+      printf("\n ");  fprintf(ficlog,"\n ");
     }
     
     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-    for (i=1;i<=NDIM;i++) 
+    for (i=1;i<=NDIM;i++) {
       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-
+      fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+    }
     lsurv=vector(1,AGESUP);
     lpop=vector(1,AGESUP);
     tpop=vector(1,AGESUP);
@@ -6856,9 +7596,16 @@ Interval (in months) between two waves:
     
     
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-    printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-    
-    printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+    if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
+      	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+      	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+    }else
+      printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+    printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
 		     stepm, weightopt,\
 		     model,imx,p,matcov,agemortsup);
     
@@ -6873,7 +7620,7 @@ Interval (in months) between two waves:
 #endif
   } /* Endof if mle==-3 mortality only */
   /* Standard maximisation */
-  else{ /* For mle >=1 */
+  else{ /* For mle !=- 3 */
     globpr=0;/* debug */
     /* Computes likelihood for initial parameters */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
@@ -6892,7 +7639,7 @@ Interval (in months) between two waves:
     }
     
     /*--------- results files --------------*/
-    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
     
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
@@ -6905,9 +7652,9 @@ Interval (in months) between two waves:
 	  fprintf(ficlog,"%d%d ",i,k);
 	  fprintf(ficres,"%1d%1d ",i,k);
 	  for(j=1; j <=ncovmodel; j++){
-	    printf("%lf ",p[jk]);
-	    fprintf(ficlog,"%lf ",p[jk]);
-	    fprintf(ficres,"%lf ",p[jk]);
+	    printf("%12.7f ",p[jk]);
+	    fprintf(ficlog,"%12.7f ",p[jk]);
+	    fprintf(ficres,"%12.7f ",p[jk]);
 	    jk++; 
 	  }
 	  printf("\n");
@@ -6916,11 +7663,30 @@ Interval (in months) between two waves:
 	}
       }
     }
-    if(mle!=0){
-      /* Computing hessian and covariance matrix */
+    if(mle != 0){
+      /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
       ftolhess=ftol; /* Usually correct */
-      hesscov(matcov, p, npar, delti, ftolhess, func);
-    }
+      hesscov(matcov, hess, p, npar, delti, ftolhess, func);
+      printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+      fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+      for(i=1,jk=1; i <=nlstate; i++){
+	for(k=1; k <=(nlstate+ndeath); k++){
+	  if (k != i) {
+	    printf("%d%d ",i,k);
+	    fprintf(ficlog,"%d%d ",i,k);
+	    for(j=1; j <=ncovmodel; j++){
+	      printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+	      fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+	      jk++; 
+	    }
+	    printf("\n");
+	    fprintf(ficlog,"\n");
+	  }
+	}
+      }
+    } /* end of hesscov and Wald tests */
+
+    /*  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
@@ -6944,7 +7710,7 @@ Interval (in months) between two waves:
     }
     
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-    if(mle>=1)
+    if(mle >= 1) /* To big for the screen */
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     /* # 121 Var(a12)\n\ */
@@ -7007,9 +7773,9 @@ Interval (in months) between two waves:
 			fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
 		      }else{
 			if(mle>=1)
-			  printf(" %.5e",matcov[jj][ll]); 
-			fprintf(ficlog," %.5e",matcov[jj][ll]); 
-			fprintf(ficres," %.5e",matcov[jj][ll]); 
+			  printf(" %.7e",matcov[jj][ll]); 
+			fprintf(ficlog," %.7e",matcov[jj][ll]); 
+			fprintf(ficres," %.7e",matcov[jj][ll]); 
 		      }
 		    }
 		  }
@@ -7077,6 +7843,7 @@ Interval (in months) between two waves:
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
     
     fscanf(ficpar,"pop_based=%d\n",&popbased);
+    fprintf(ficlog,"pop_based=%d\n",popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
@@ -7101,9 +7868,17 @@ Interval (in months) between two waves:
     /* ,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);
+    if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
+      	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+      	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+    }else
+      printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
     
-    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+    printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
 		 model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
 		 jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
       
@@ -7128,7 +7903,7 @@ Interval (in months) between two waves:
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);
-    prevalence_limit(p, prlim,  ageminpar, agemaxpar);
+    prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, ncvyear);
     fclose(ficrespl);
 
 #ifdef FREEEXIT2
@@ -7155,7 +7930,7 @@ Interval (in months) between two waves:
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
-      prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+      prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
       /*      }  */
       /*      else{ */
@@ -7185,8 +7960,8 @@ Interval (in months) between two waves:
 
     /*---------- Health expectancies, no variances ------------*/
 
-    strcpy(filerese,"e");
-    strcat(filerese,fileres);
+    strcpy(filerese,"E_");
+    strcat(filerese,fileresu);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
@@ -7199,7 +7974,7 @@ Interval (in months) between two waves:
     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]]);
+	  fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	}
 	fprintf(ficreseij,"******\n");
 
@@ -7216,8 +7991,8 @@ Interval (in months) between two waves:
     /*---------- Health expectancies and variances ------------*/
 
 
-    strcpy(filerest,"t");
-    strcat(filerest,fileres);
+    strcpy(filerest,"T_");
+    strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
@@ -7226,8 +8001,8 @@ Interval (in months) between two waves:
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
 
 
-    strcpy(fileresstde,"stde");
-    strcat(fileresstde,fileres);
+    strcpy(fileresstde,"STDE_");
+    strcat(fileresstde,fileresu);
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
@@ -7235,8 +8010,8 @@ Interval (in months) between two waves:
     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
 
-    strcpy(filerescve,"cve");
-    strcat(filerescve,fileres);
+    strcpy(filerescve,"CVE_");
+    strcat(filerescve,fileresu);
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
@@ -7244,8 +8019,8 @@ Interval (in months) between two waves:
     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
 
-    strcpy(fileresv,"v");
-    strcat(fileresv,fileres);
+    strcpy(fileresv,"V_");
+    strcat(fileresv,fileresu);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
@@ -7259,21 +8034,21 @@ Interval (in months) between two waves:
     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,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	fprintf(ficrest,"******\n");
 
 	fprintf(ficresstdeij,"\n#****** ");
 	fprintf(ficrescveij,"\n#****** ");
 	for(j=1;j<=cptcoveff;j++) {
-	  fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-	  fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+	  fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	}
 	fprintf(ficresstdeij,"******\n");
 	fprintf(ficrescveij,"******\n");
 
 	fprintf(ficresvij,"\n#****** ");
 	for(j=1;j<=cptcoveff;j++) 
-	  fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+	  fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	fprintf(ficresvij,"******\n");
 
 	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
@@ -7288,21 +8063,21 @@ Interval (in months) between two waves:
 
 
 	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-	  oldm=oldms;savm=savms; /* Segmentation fault */
+	  oldm=oldms;savm=savms; /* ZZ 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 */
+	  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, 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
 	    fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-	  fprintf(ficrest,"# Age e.. (std) ");
+	  fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
 	  for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
 	  fprintf(ficrest,"\n");
-
+	  /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
 	  epj=vector(1,nlstate+1);
 	  for(age=bage; age <=fage ;age++){
-	    prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+	    prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
 	    if (vpopbased==1) {
 	      if(mobilav ==0){
 		for(i=1; i<=nlstate;i++)
@@ -7313,14 +8088,17 @@ Interval (in months) between two waves:
 	      }
 	    }
 	
-	    fprintf(ficrest," %4.0f",age);
+	    fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
+	    /* printf(" age %4.0f ",age); */
 	    for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
 	      for(i=1, epj[j]=0.;i <=nlstate;i++) {
 		epj[j] += prlim[i][i]*eij[i][j][(int)age];
-		/*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+		/*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+	        /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
 	      }
 	      epj[nlstate+1] +=epj[j];
 	    }
+	    /* printf(" age %4.0f \n",age); */
 
 	    for(i=1, vepp=0.;i <=nlstate;i++)
 	      for(j=1;j <=nlstate;j++)
@@ -7352,8 +8130,8 @@ Interval (in months) between two waves:
   
     /*------- Variance of period (stable) prevalence------*/   
 
-    strcpy(fileresvpl,"vpl");
-    strcat(fileresvpl,fileres);
+    strcpy(fileresvpl,"VPL_");
+    strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
@@ -7366,12 +8144,12 @@ Interval (in months) between two waves:
     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,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 	fprintf(ficresvpl,"******\n");
       
 	varpl=matrix(1,nlstate,(int) bage, (int) fage);
 	oldm=oldms;savm=savms;
-	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
 	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       /*}*/
     }
@@ -7390,19 +8168,21 @@ Interval (in months) between two waves:
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
+    free_matrix(hess,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 
     free_ivector(ncodemax,1,NCOVMAX);
+    free_ivector(ncodemaxwundef,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);
+    /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);
   fflush(ficgp);
   
@@ -7503,7 +8283,7 @@ Interval (in months) between two waves:
   }
   end:
   while (z[0] != 'q') {
-    printf("\nType  q for exiting: ");
+    printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);
   }
 }