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Diff for /imach/src/imach.c between versions 1.177 and 1.191

version 1.177, 2015/01/03 18:40:56	version 1.191, 2015/07/14 10:00:33
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	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

	Some codes had been disabled in order to simplify and Vn*age was
	working in the optimization phase, ie, giving correct MLE parameters,
	but, as usual, outputs were not correct and program core dumped.

	Revision 1.185 2015/03/11 13:26:42 brouard
	Summary: Inclusion of compile and links command line for Intel Compiler

	Revision 1.184 2015/03/11 11:52:39 brouard
	Summary: Back from Windows 8. Intel Compiler

	Revision 1.183 2015/03/10 20:34:32 brouard
	Summary: 0.98q0, trying with directest, mnbrak fixed

	We use directest instead of original Powell test; probably no
	incidence on the results, but better justifications;
	We fixed Numerical Recipes mnbrak routine which was wrong and gave
	wrong results.

	Revision 1.182 2015/02/12 08:19:57 brouard
	Summary: Trying to keep directest which seems simpler and more general
	Author: Nicolas Brouard

	Revision 1.181 2015/02/11 23:22:24 brouard
	Summary: Comments on Powell added

	Author:

	Revision 1.180 2015/02/11 17:33:45 brouard
	Summary: Finishing move from main to function (hpijx and prevalence_limit)

	Revision 1.179 2015/01/04 09:57:06 brouard
	Summary: back to OS/X

	Revision 1.178 2015/01/04 09:35:48 brouard
	* empty log message *

Revision 1.177 2015/01/03 18:40:56 brouard	Revision 1.177 2015/01/03 18:40:56 brouard
Summary: Still testing ilc32 on OSX	Summary: Still testing ilc32 on OSX

Line 546	Line 602
end	end
*/	*/

	/* #define DEBUG */
	/* #define DEBUGBRENT */
#define POWELL /* Instead of NLOPT */	#define POWELL /* Instead of NLOPT */
	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /

#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
Line 632 typedef struct {	Line 692 typedef struct {
/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */

char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";	char version[]="Imach version 0.98q2, 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[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	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 ageage, number of forces /
/* Number of covariates model=V2+V1+ V3age+V2V4 */	/* Number of covariates model=V2+V1+ V3age+V2V4 */
int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */	int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */
int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /	int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /
Line 748 static double maxarg1,maxarg2;	Line 808 static double maxarg1,maxarg2;
#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))	#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
#define rint(a) floor(a+0.5)	#define rint(a) floor(a+0.5)
/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */	/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
/* #define mytinydouble 1.0e-16 */	#define mytinydouble 1.0e-16
/* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */	/* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */	/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
/* static double dsqrarg; */	/* static double dsqrarg; */
Line 778 int *s; / Status */	Line 838 int *s; / Status */
double *agedc;	double *agedc;
double covar; /< covar[j,i], value of jth covariate for individual i,	double covar; /< covar[j,i], value of jth covariate for individual i,
* covar=matrix(0,NCOVMAX,1,n);	* 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;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
int Ndum; /* Freq of modality (tricode */	int Ndum; /* Freq of modality (tricode */
Line 796 static int split( char path, char dirc	Line 856 static int split( char path, char dirc
the name of the file (name), its extension only (ext) and its first part of the name (finame)	the name of the file (name), its extension only (ext) and its first part of the name (finame)
*/	*/
char ss; / pointer */	char ss; / pointer */
int l1, l2; /* length counters */	int l1=0, l2=0; /* length counters */

l1 = strlen(path ); /* length of path */	l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
Line 807 static int split( char path, char dirc	Line 867 static int split( char path, char dirc
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/	printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
/* get current working directory */	/* get current working directory */
/* extern char* getcwd ( char buf , int len);/	/* extern char* getcwd ( char buf , int len);/
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {	#ifdef WIN32
	if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
	#else
	if (getcwd(dirc, FILENAME_MAX) == NULL) {
	#endif
return( GLOCK_ERROR_GETCWD );	return( GLOCK_ERROR_GETCWD );
}	}
/* got dirc from getcwd*/	/* got dirc from getcwd*/
Line 818 static int split( char path, char dirc	Line 882 static int split( char path, char dirc
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
strcpy( name, ss ); /* save file name */	strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */	strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */	dirc[l1-l2] = '\0'; /* add zero */
printf(" DIRC2 = %s \n",dirc);	printf(" DIRC2 = %s \n",dirc);
}	}
/* We add a separator at the end of dirc if not exists */	/* We add a separator at the end of dirc if not exists */
Line 870 char trimbb(char out, char *in)	Line 934 char trimbb(char out, char *in)
return s;	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+V1age+ageage+V2", chain="ageage" /

	char *strloc;

	strcpy (out, in);
	strloc = strstr(out, chain); /* strloc points to out at ageage+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)	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')	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	If occ is not found blocc is null and alocc is equal to in. Returns blocc
*/	*/
char s, t;	char s, t;
Line 900 char cutl(char blocc, char *alocc, cha	Line 1007 char cutl(char blocc, char *alocc, cha
}	}
char cutv(char blocc, char alocc, char in, char occ)	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')	and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
gives blocc="abcdef2ghi" and alocc="j".	gives blocc="abcdef2ghi" and alocc="j".
If occ is not found blocc is null and alocc is equal to in. Returns alocc	If occ is not found blocc is null and alocc is equal to in. Returns alocc
Line 1211 double f1dim(double x)	Line 1318 double f1dim(double x)

/***************brent ***********************/	/***************brent ***********************/
double brent(double ax, double bx, double cx, double (f)(double), double tol, double xmin)	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;	int iter;
double a,b,d,etemp;	double a,b,d,etemp;
double fu=0,fv,fw,fx;	double fu=0,fv,fw,fx;
Line 1264 double brent(double ax, double bx, doubl	Line 1377 double brent(double ax, double bx, doubl
if (fu <= fx) {	if (fu <= fx) {
if (u >= x) a=x; else b=x;	if (u >= x) a=x; else b=x;
SHFT(v,w,x,u)	SHFT(v,w,x,u)
SHFT(fv,fw,fx,fu)	SHFT(fv,fw,fx,fu)
} else {	} else {
if (u < x) a=u; else b=u;	if (u < x) a=u; else b=u;
if (fu <= fw \|\| w == x) {	if (fu <= fw \|\| w == x) {
v=w;	v=w;
w=u;	w=u;
fv=fw;	fv=fw;
fw=fu;	fw=fu;
} else if (fu <= fv \|\| v == x \|\| v == w) {	} else if (fu <= fv \|\| v == x \|\| v == w) {
v=u;	v=u;
fv=fu;	fv=fu;
}	}
}	}
}	}
nrerror("Too many iterations in brent");	nrerror("Too many iterations in brent");
*xmin=x;	*xmin=x;
Line 1287 double brent(double ax, double bx, doubl	Line 1400 double brent(double ax, double bx, doubl

void mnbrak(double ax, double bx, double cx, double fa, double fb, double fc,	void mnbrak(double ax, double bx, double cx, double fa, double fb, double fc,
double (*func)(double))	double (*func)(double))
{	{ /* Given a function func , and given distinct initial points ax and bx , this routine searches in
	the downhill direction (defined by the function as evaluated at the initial points) and returns
	new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
	values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
	*/
double ulim,u,r,q, dum;	double ulim,u,r,q, dum;
double fu;	double fu;

fa=(func)(*ax);	double scale=10.;
fb=(func)(*bx);	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) {	if (fb > fa) {
SHFT(dum,ax,bx,dum)	SHFT(dum,ax,bx,dum)
SHFT(dum,fb,fa,dum)	SHFT(dum,fb,fa,dum)
}	}
cx=(bx)+GOLD(bx-*ax);	cx=(bx)+GOLD(bx-*ax);
fc=(func)(*cx);	fc=(func)(*cx);
while (fb > fc) { /* Declining fa, fb, fc */	#ifdef DEBUG
	printf("mnbrak0 fb=%.12e fc=%.12e\n",fb,fc);
	fprintf(ficlog,"mnbrak0 fb=%.12e fc=%.12e\n",fb,fc);
	#endif
	while (fb > fc) { /* Declining a,b,c with fa> fb > fc */
r=(bx-ax)(fb-*fc);	r=(bx-ax)(fb-*fc);
q=(bx-cx)(fb-*fa);	q=(bx-cx)(fb-*fa);
u=(bx)-((bx-cx)q-(bx-ax)*r)/	u=(bx)-((bx-cx)q-(bx-ax)*r)/
(2.0SIGN(FMAX(fabs(q-r),TINY),q-r)); / Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */	(2.0SIGN(FMAX(fabs(q-r),TINY),q-r)); / Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
ulim=(bx)+GLIMIT(cx-bx); /* Maximum abscisse where function can be evaluated */	ulim=(bx)+GLIMIT(cx-bx); /* Maximum abscissa where function should be evaluated */
if ((bx-u)(u-cx) > 0.0) { / if u between b and c */	if ((bx-u)(u-cx) > 0.0) { / if u_p is between b and c */
fu=(*func)(u);	fu=(*func)(u);
#ifdef DEBUG	#ifdef DEBUG
/* f(x)=A(x-u)*2+f(u) /	/* f(x)=A(x-u)*2+f(u) /
Line 1314 void mnbrak(double ax, double bx, doub	Line 1446 void mnbrak(double ax, double bx, doub
fparabu= fa - A(ax-u)(*ax-u);	fparabu= fa - A(ax-u)(*ax-u);
printf("mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);	printf("mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);
fprintf(ficlog, "mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);	fprintf(ficlog, "mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);
	/* And thus,it can be that fu > fc even if fparabu < fc */
	/* mnbrak (ax=7.666299858533, fa=299039.693133272231), (bx=8.595447774979, fb=298976.598289369489),
	(cx=10.098840694817, fc=298946.631474258087), (u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) /
	/* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
#endif	#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 \/ /
	/* #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("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;
	#endif
} else if ((cx-u)(u-ulim) > 0.0) { /* u is after c but before ulim */	} else if ((cx-u)(u-ulim) > 0.0) { /* u is after c but before ulim */
	#ifdef DEBUG
	printf("mnbrak2 u after c but before ulim\n");
	fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
	#endif
fu=(*func)(u);	fu=(*func)(u);
if (fu < *fc) {	if (fu < *fc) {
	#ifdef DEBUG
	printf("mnbrak2 u after c but before ulim AND fu < fc\n");
	fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
	#endif
SHFT(bx,cx,u,cx+GOLD(cx-bx))	SHFT(bx,cx,u,cx+GOLD(cx-bx))
SHFT(fb,fc,fu,(*func)(u))	SHFT(fb,fc,fu,(*func)(u))
}	}
} else if ((u-ulim)(ulim-cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */	} else if ((u-ulim)(ulim-cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
	#ifdef DEBUG
	printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
	fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
	#endif
u=ulim;	u=ulim;
fu=(*func)(u);	fu=(*func)(u);
} else {	} else { /* u could be left to b (if r > q parabola has a maximum) */
	#ifdef DEBUG
	printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
	fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
	#endif
u=(cx)+GOLD(cx-bx);	u=(cx)+GOLD(cx-bx);
fu=(*func)(u);	fu=(*func)(u);
}	} /* end tests */
SHFT(ax,bx,*cx,u)	SHFT(ax,bx,*cx,u)
SHFT(fa,fb,*fc,fu)	SHFT(fa,fb,*fc,fu)
}	#ifdef DEBUG
	printf("mnbrak2 (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf)\n",ax,fa,bx,fb,cx,*fc,u,fu);
	fprintf(ficlog, "mnbrak2 (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf)\n",ax,fa,bx,fb,cx,*fc,u,fu);
	#endif
	} /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
}	}

/************* linmin **********************/	/************* linmin **********************/
Line 1353 void linmin(double p[], double xi[], int	Line 1547 void linmin(double p[], double xi[], int
int j;	int j;
double xx,xmin,bx,ax;	double xx,xmin,bx,ax;
double fx,fb,fa;	double fx,fb,fa;

	double scale=10., axs, xxs, xxss; /* Scale added for infinity */

ncom=n;	ncom=n;
pcom=vector(1,n);	pcom=vector(1,n);
Line 1362 void linmin(double p[], double xi[], int	Line 1558 void linmin(double p[], double xi[], int
pcom[j]=p[j];	pcom[j]=p[j];
xicom[j]=xi[j];	xicom[j]=xi[j];
}	}
ax=0.0;
xx=1.0;	axs=0.0;
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */	xxss=1; /* 1 and using scale */
fret=brent(ax,xx,bx,f1dim,TOL,&xmin); / Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */	xxs=1;
	do{
	ax=0.;
	xx= xxs;
	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]+xxicom[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:xxsxi[j]] et non plus [0:xi[j]]/
	if (fx != fx){
	xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
	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);
	}
	}while(fx != fx);

	#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);
	#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]+xminxicom[j]; /
#ifdef DEBUG	#ifdef DEBUG
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
#endif	#endif
	#ifdef DEBUGLINMIN
	printf("linmin end ");
	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j] *= xmin;	/* printf(" before xi[%d]=%12.8f", j,xi[j]); */
p[j] += xi[j];	xi[j] = xmin; / xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
	/* 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 ); */
	p[j] += xi[j]; /* Parameters values are updated accordingly */
}	}
	/* printf("\n"); */
	#ifdef DEBUGLINMIN
	printf("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]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
free_vector(xicom,1,n);	free_vector(xicom,1,n);
free_vector(pcom,1,n);	free_vector(pcom,1,n);
}	}
Line 1395 void powell(double p[], double **xi, int	Line 1630 void powell(double p[], double **xi, int
double (*func)(double []));	double (*func)(double []));
int i,ibig,j;	int i,ibig,j;
double del,t,pt,ptt,*xit;	double del,t,pt,ptt,*xit;
	double directest;
double fp,fptt;	double fp,fptt;
double *xits;	double *xits;
int niterf, itmp;	int niterf, itmp;
Line 1407 void powell(double p[], double **xi, int	Line 1643 void powell(double p[], double **xi, int
for (j=1;j<=n;j++) pt[j]=p[j];	for (j=1;j<=n;j++) pt[j]=p[j];
rcurr_time = time(NULL);	rcurr_time = time(NULL);
for (iter=1;;++(iter)) {	for (iter=1;;++(iter)) {
fp=(*fret);	fp=(fret); / From former iteration or initial value */
ibig=0;	ibig=0;
del=0.0;	del=0.0;
rlast_time=rcurr_time;	rlast_time=rcurr_time;
Line 1445 void powell(double p[], double **xi, int	Line 1681 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);	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 (i=1;i<=n;i++) { /* For each direction i */
for (j=1;j<=n;j++) xit[j]=xi[j][i];	for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
fptt=(*fret);	fptt=(*fret);
#ifdef DEBUG	#ifdef DEBUG
printf("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);	fprintf(ficlog, "fret=%lf, %lf, %lf \n", fret, fret, *fret);
#endif	#endif
printf("%d",i);fflush(stdout);	printf("%d",i);fflush(stdout); /* print direction (parameter) i */
fprintf(ficlog,"%d",i);fflush(ficlog);	fprintf(ficlog,"%d",i);fflush(ficlog);
linmin(p,xit,n,fret,func);	linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
if (fabs(fptt-(*fret)) > del) {	/* 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));	del=fabs(fptt-(*fret));
ibig=i;	ibig=i;
}	}
Line 1474 void powell(double p[], double **xi, int	Line 1715 void powell(double p[], double **xi, int
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
} /* end i */	} /* end loop on each direction i */
if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) {	/* 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 (2.0fabs(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 ageage 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 ageage and V1age 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	#ifdef DEBUG
int k[2],l;	int k[2],l;
k[0]=1;	k[0]=1;
Line 1507 void powell(double p[], double **xi, int	Line 1763 void powell(double p[], double **xi, int
return;	return;
}	}
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");	if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
for (j=1;j<=n;j++) { /* Computes an extrapolated point */	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];	ptt[j]=2.0*p[j]-pt[j];
xit[j]=p[j]-pt[j];	xit[j]=p[j]-pt[j];
pt[j]=p[j];	pt[j]=p[j];
}	}
fptt=(*func)(ptt);	fptt=(func)(ptt); / f_3 */
if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */	if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /	/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /
/* From x1 (P0) distance of x2 is at h and x3 is 2h */	/* From x1 (P0) distance of x2 is at h and x3 is 2h */
/* Let f"(x2) be the 2nd derivative equal everywhere. */	/* Let f"(x2) be the 2nd derivative equal everywhere. */
/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */	/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h*2 /	/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h*2 /
/* f1-f3 = delta(2h) = 2 h*2 f'' = 2(f1- 2f2 +f3) /	/* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
/* Thus we compare delta(2h) with observed f1-f3 */
/* or best gain on one ancient line 'del' with total */
/* gain f1-f2 = f1 - f2 - 'del' with del */
/* t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)-delSQR(fp-fptt); */	/* t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)-delSQR(fp-fptt); */
	#ifdef NRCORIGINAL
t=2.0(fp-2.0(fret)+fptt)SQR(fp-(*fret)-del);	t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)- delSQR(fp-fptt); /* Original Numerical Recipes in C*/
	#else
	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);	t= t- del*SQR(fp-fptt);
printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t);	#endif
fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t);	directest = fp-2.0(fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
#ifdef DEBUG	#ifdef DEBUG
	printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(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),delSQR(fp-fptt),t,directest);
printf("t3= %.12lf, t4= %.12lf, t3= %.12lf, t4= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),	printf("t3= %.12lf, t4= %.12lf, t3= %.12lf, t4= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
(fp-(fret)-del)(fp-(fret)-del),(fp-fptt)(fp-fptt));	(fp-(fret)-del)(fp-(fret)-del),(fp-fptt)(fp-fptt));
fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3= %.12lf, t4= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),	fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3= %.12lf, t4= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
Line 1537 void powell(double p[], double **xi, int	Line 1794 void powell(double p[], double **xi, int
printf("tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);	printf("tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);
fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);	fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);
#endif	#endif
if (t < 0.0) { /* Then we use it for last direction */	#ifdef POWELLORIGINAL
linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/	if (t < 0.0) { /* Then we use it for new direction */
	#else
	if (directestt < 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);
	}
	if (directest < 0.0) { /* Then we use it for new direction */
	#endif
	#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]);
	if(j % ncovmodel == 0)
	printf("\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]);
	if(j % ncovmodel == 0)
	printf("\n");
	}
	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */	xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
xi[j][n]=xit[j]; /* and nth direction by the extrapolated */	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
}	}
printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);

#ifdef DEBUG	#ifdef DEBUG
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 1587 double prevalim(double prlim, int nl	Line 1869 double prevalim(double prlim, int nl
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
	if(nagesqr==1)
	cov[3]= agefin*agefin;;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+nagesqr+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]]);/	/printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);/
}	}
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
/* for (k=1; k<=cptcovprod;k++) /\* Useless \/ /	for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
/* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */	for (k=1; k<=cptcovprod;k++) /* Useless */
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
Line 1748 double *hpxij(double *po, int nhstep	Line 2032 double *hpxij(double *po, int nhstep
int i, j, d, h, k;	int i, j, d, h, k;
double **out, cov[NCOVMAX+1];	double **out, cov[NCOVMAX+1];
double **newm;	double **newm;
	double agexact;

/* Hstepm could be zero and should return the unit matrix */	/* Hstepm could be zero and should return the unit matrix */
for (i=1;i<=nlstate+ndeath;i++)	for (i=1;i<=nlstate+ndeath;i++)
Line 1761 double *hpxij(double *po, int nhstep	Line 2046 double *hpxij(double *po, int nhstep
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[1]=1.;	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++)	for (k=1; k<=cptcovn;k++)
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
for (k=1; k<=cptcovage;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]]=cov[2+Tage[k]]cov[2]; /
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */	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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
Line 1819 double func( double *x)	Line 2108 double func( double *x)
int s1, s2;	int s1, s2;
double bbh, survp;	double bbh, survp;
long ipmx;	long ipmx;
	double agexact;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 1840 double func( double *x)	Line 2130 double func( double *x)
to be observed in j being in i according to the model.	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 */	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+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]
Line 1853 double func( double *x)	Line 2143 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	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++) {	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,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 1907 double func( double *x)	Line 2200 double func( double *x)
which slows down the processing. The difference can be up to 10%	which slows down the processing. The difference can be up to 10%
lower mortality.	lower mortality.
*/	*/
lli=log(out[s1][s2] - savm[s1][s2]);	/* If, at the beginning of the maximization mostly, the
	cumulative probability or probability to be dead is
	constant (ie = 1) over time d, the difference is equal to
	0. out[s1][3] = savm[s1][3]: probability, being at state
	s1 at precedent wave, to be dead a month before current
	wave is equal to probability, being at state s1 at
	precedent wave, to be dead at mont of the current
	wave. Then the observed probability (that this person died)
	is null according to current estimated parameter. In fact,
	it should be very low but not zero otherwise the log go to
	infinity.
	*/
	/* #ifdef INFINITYORIGINAL */
	/* lli=log(out[s1][s2] - savm[s1][s2]); */
	/* #else */
	/* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
	/* lli=log(mytinydouble); */
	/* else */
	/* lli=log(out[s1][s2] - savm[s1][s2]); */
	/* #endif */
	lli=log(out[s1][s2] - savm[s1][s2]);

} else if (s2==-2) {	} else if (s2==-2) {
for (j=1,survp=0. ; j<=nlstate; j++)	for (j=1,survp=0. ; j<=nlstate; j++)
Line 1939 double func( double *x)	Line 2251 double func( double *x)
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
	/* if (lli < log(mytinydouble)){ */
	/* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
	/* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
	/* } */
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
} else if(mle==2){	} else if(mle==2){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	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(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 1952 double func( double *x)	Line 2268 double func( double *x)
}	}
for(d=0; d<=dh[mi][i]; d++){	for(d=0; d<=dh[mi][i]; d++){
newm=savm;	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++) {	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,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 1973 double func( double *x)	Line 2292 double func( double *x)
} /* end of individual */	} /* end of individual */
} else if(mle==3){ /* exponential inter-extrapolation */	} else if(mle==3){ /* exponential inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	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(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 1982 double func( double *x)	Line 2301 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	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++) {	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,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2003 double func( double *x)	Line 2325 double func( double *x)
} /* end of individual */	} /* end of individual */
}else if (mle==4){ /* ml=4 no inter-extrapolation */	}else if (mle==4){ /* ml=4 no inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	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(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2012 double func( double *x)	Line 2334 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	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++) {	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,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 2038 double func( double *x)	Line 2363 double func( double *x)
} /* end of individual */	} /* end of individual */
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */	}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	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(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2047 double func( double *x)	Line 2372 double func( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	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++) {	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,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 2085 double funcone( double *x)	Line 2413 double funcone( double *x)
double llt;	double llt;
int s1, s2;	int s1, s2;
double bbh, survp;	double bbh, survp;
	double agexact;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2096 double funcone( double *x)	Line 2425 double funcone( double *x)
for(k=1; k<=nlstate; k++) ll[k]=0.;	for(k=1; k<=nlstate; k++) ll[k]=0.;

for (i=1,ipmx=0, sw=0.; i<=imx; i++){	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(mi=1; mi<= wav[i]-1; mi++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 2105 double funcone( double *x)	Line 2434 double funcone( double *x)
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	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++) {	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); */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2274 void mlikeli(FILE *ficres,double p[], in	Line 2607 void mlikeli(FILE *ficres,double p[], in
#endif	#endif
free_matrix(xi,1,npar,1,npar);	free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);	fclose(ficrespow);
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	printf("#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(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));

}	}

Line 2969 void tricode(int Tvar, int *nbcode, in	Line 3302 void tricode(int Tvar, int *nbcode, in
for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */	for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */

/* Loop on covariates without age and products */	/* Loop on covariates without age and products */
for (j=1; j<=(cptcovs); j++) { /* model V1 + V2age+ V3 + V3V4 : V1 + V3 = 2 only */	for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only */
for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the	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*/	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	ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
* If product of VnVm, still boolean :	* If product of VnVm, still boolean :
Line 2992 void tricode(int Tvar, int *nbcode, in	Line 3325 void tricode(int Tvar, int *nbcode, in
/* getting the maximum value of the modality of the covariate	/* 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	(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
female is 1, then modmaxcovj=1.*/	female is 1, then modmaxcovj=1.*/
}	} /* end for loop on individuals */
printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);	printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
cptcode=modmaxcovj;	cptcode=modmaxcovj;
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */	/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
/for (i=0; i<=cptcode; i++) {/	/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 */	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]);	printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);
if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */	if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */	ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
}	}
Line 3007 void tricode(int Tvar, int *nbcode, in	Line 3340 void tricode(int Tvar, int *nbcode, in
} /* Ndum[-1] number of undefined modalities */	} /* Ndum[-1] number of undefined modalities */

/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */	/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
/* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */	/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
/* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;	If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
modmincovj=3; modmaxcovj = 7;	modmincovj=3; modmaxcovj = 7;
There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;	There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy	which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
variables V1_1 and V1_2.	defining two dummy variables: variables V1_1 and V1_2.
nbcode[Tvar[j]][ij]=k;	nbcode[Tvar[j]][ij]=k;
nbcode[Tvar[j]][1]=0;	nbcode[Tvar[j]][1]=0;
nbcode[Tvar[j]][2]=1;	nbcode[Tvar[j]][2]=1;
Line 3023 void tricode(int Tvar, int *nbcode, in	Line 3356 void tricode(int Tvar, int *nbcode, in
for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */	for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */
/recode from 0 /	/recode from 0 /
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */	if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.	nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode.
k is a modality. If we have model=V1+V1*sex	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; */	then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
ij++;	ij++;
Line 3035 void tricode(int Tvar, int *nbcode, in	Line 3368 void tricode(int Tvar, int *nbcode, in

for (k=-1; k< maxncov; k++) Ndum[k]=0;	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 ageage /
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./	/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./
ij=Tvar[i]; /* Tvar might be -1 if status was unknown */	ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
Ndum[ij]++;	Ndum[ij]++; /* Might be supersed V1 + V1age /
}	}

ij=1;	ij=1;
Line 3892 To be simple, these graphs help to under	Line 4225 To be simple, these graphs help to under
gm=vector(1,(nlstate)*(nlstate+ndeath));	gm=vector(1,(nlstate)*(nlstate+ndeath));
for (age=bage; age<=fage; age ++){	for (age=bage; age<=fage; age ++){
cov[2]=age;	cov[2]=age;
	if(nagesqr==1)
	cov[3]= age*age;
for (k=1; k<=cptcovn;k++) {	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]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
* 1 1 1 1 1	* 1 1 1 1 1
* 2 2 1 1 1	* 2 2 1 1 1
* 3 1 2 1 1	* 3 1 2 1 1
*/	*/
/* nbcode[1][1]=0 nbcode[1][2]=1;*/	/* nbcode[1][1]=0 nbcode[1][2]=1;*/
}	}
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	/* for (k=1; k<=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<=cptcovprod;k++)	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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];


for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
Line 4362 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4698 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* end covariate */	} /* end covariate */

/* proba elementaires */	/* proba elementaires */
	fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
	fprintf(ficgp,"# initial state %d\n",i);
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
	fprintf(ficgp,"# current state %d\n",k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
fprintf(ficgp,"p%d=%f ",jk,p[jk]);	fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
jk++;	jk++;
fprintf(ficgp,"\n");
}	}
	fprintf(ficgp,"\n");
}	}
}	}
}	}
	fprintf(ficgp,"##############\n#\n");

/goto avoid;/	/goto avoid;/
	fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
	fprintf(ficgp,"# logi(p12/p11)=a12+b12age+c12ageage+d12V1+e12V1*age\n");
	fprintf(ficgp,"# logi(p12/p11)=p1 +p2age +p3ageage+ p4V1+ p5V1age\n");
	fprintf(ficgp,"# logi(p13/p11)=a13+b13age+c13ageage+d13V1+e13V1*age\n");
	fprintf(ficgp,"# logi(p13/p11)=p6 +p7age +p8ageage+ p9V1+ p10V1age\n");
	fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12age+c12ageage+d12V1+e12V1*age)\n");
	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age)+...)\n");
	fprintf(ficgp,"# p11=1/(1+exp(a12+b12age+c12ageage+d12V1+e12V1*age)\n");
	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age)+...)\n");
	fprintf(ficgp,"# p12=exp(a12+b12age+c12ageage+d12V1+e12V1*age)/\n");
	fprintf(ficgp,"# (1+exp(a12+b12age+c12ageage+d12V1+e12V1*age)\n");
	fprintf(ficgp,"# +exp(a13+b13age+c13ageage+d13V1+e13V1*age))\n");
	fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");
	fprintf(ficgp,"#\n");
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/	for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence 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++) {	for(jk=1; jk <=m; jk++) {
	fprintf(ficgp,"# jk=%d\n",jk);
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);	fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
if (ng==2)	if (ng==2)
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
Line 4388 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4746 plot [%.f:%.f] ", ageminpar, agemaxpar)
for(k=1; k<=(nlstate+ndeath); k++) {	for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){	if (k != k2){
if(ng==2)	if(ng==2)
fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);	if(nagesqr==0)
	fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);
	else /* nagesqr =1 */
	fprintf(ficgp," %fexp(p%d+p%dx+p%dxx",YEARM/stepm,i,i+1,i+1+nagesqr);
else	else
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);	if(nagesqr==0)
	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
	else /* nagesqr =1 */
	fprintf(ficgp," exp(p%d+p%dx+p%dx*x",i,i+1,i+1+nagesqr);
ij=1;/* To be checked else nbcode[0][0] wrong */	ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel; j++) {	for(j=3; j <=ncovmodel-nagesqr; j++) {
/* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind \/ /	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
/* /\fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\/ */	fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
/* ij++; */	ij++;
/* } */	}
/* else */	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]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");

for(k1=1; k1 <=nlstate; k1++){	for(k1=1; k1 <=nlstate; k1++){
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);	if(nagesqr==0)
	fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
	else /* nagesqr =1 */
	fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(k1-1)ncovmodel,k3+(k1-1)ncovmodel+1,k3+(k1-1)ncovmodel+1+nagesqr);

ij=1;	ij=1;
for(j=3; j <=ncovmodel; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
/* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); /	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
/* ij++; */	ij++;
/* } */	}
/* else */	else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 5205 void removespace(char *str) {	Line 5573 void removespace(char *str) {
}	}

int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:	int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age	* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age
* - cptcovt total number of covariates of the model nbocc(+)+1 = 8	* - nagesqr = 1 if age*age in the model, otherwise 0.
* - cptcovn or number of covariates k of the models excluding age*products =6	* - 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 ageproducts =6 and ageage
* - cptcovage number of covariates with age*products =2	* - cptcovage number of covariates with age*products =2
* - cptcovs number of simple covariates	* - 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	* - 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
Line 5222 int decodemodel ( char model[], int last	Line 5591 int decodemodel ( char model[], int last
int j1, k1, k2;	int j1, k1, k2;
char modelsav[80];	char modelsav[80];
char stra[80], strb[80], strc[80], strd[80],stre[80];	char stra[80], strb[80], strc[80], strd[80],stre[80];
	char *strpt;

/removespace(model);/	/removespace(model);/
if (strlen(model) >1){ /* If there is at least 1 covariate */	if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;	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+V2age+V3 +V3V4=> V1 + V3 =2 /
cptcovt= j+1; /* Number of total covariates in the model V1 + V2age+ V3 + V3V4=> 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 V1V2 +v3age = 2 /
cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */
strcpy(modelsav,model);
if (strstr(model,"AGE") !=0){	if (strstr(model,"AGE") !=0){
printf("Error. AGE must be in lower case 'age' model=%s ",model);	printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);
fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);	fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);
return 1;	return 1;
}	}
if (strstr(model,"v") !=0){	if (strstr(model,"v") !=0){
Line 5245 int decodemodel ( char model[], int last	Line 5606 int decodemodel ( char model[], int last
fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);	fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
return 1;	return 1;
}	}
	strcpy(modelsav,model);
/* Design	if ((strpt=strstr(model,"age*age")) !=0){
* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight	printf(" strpt=%s, model=%s\n",strpt, model);
* < ncovcol=8 >	if(strpt != model){
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8	printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
* k= 1 2 3 4 5 6 7 8	'model=1+age+ageage+V1' or 'model=1+age+ageage+V1+V1*age', please swap as well as \n \
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8	corresponding column of parameters.\n",model);
* covar[k,i], value of kth covariate if not including age for individual i:	fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)	'model=1+age+ageage+V1' or 'model=1+age+ageage+V1+V1*age', please swap as well as \n \
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8	corresponding column of parameters.\n",model); fflush(ficlog);
* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and	return 1;
* 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 + V3age + V3 + V5V6 + V7V8 + V8age + 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 V5V6? V7V8? ? V8
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
*How to reorganize?
* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
* 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'.*/	nagesqr=1;
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */	if (strstr(model,"+age*age") !=0)
/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */	substrchaine(modelsav, model, "+age*age");
/* k=4 (ageV3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 /	else if (strstr(model,"age*age+") !=0)
/* k=3 V4 Tvar[k=3]= 4 (from V4) */	substrchaine(modelsav, model, "age*age+");
/* k=2 V1 Tvar[k=2]= 1 (from V1) */	else
/* k=1 Tvar[1]=2 (from V2) */	substrchaine(modelsav, model, "age*age");
/* k=5 Tvar[5] */	}else
/* for (k=1; k<=cptcovn;k++) { */	nagesqr=0;
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */	if (strlen(modelsav) >1){
/* } */	j=nbocc(modelsav,'+'); /*< j=Number of '+' /
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	j1=nbocc(modelsav,''); /< j1=Number of '' */
/*	cptcovs=j+1-j1; /*< Number of simple covariates V1+V1age+V3 +V3V4+ageage=> V1 + V3 =2 */
* Treating invertedly V2+V1+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */	cptcovt= j+1; /* Number of total covariates in the model, not including
for(k=cptcovt; k>=1;k--) /*< Number of covariates /	* cst, age and age*age
	* V1+V1age+ V3 + V3V4+ageage=> 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 V1V2 +v3age = 2 /
	cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */


	/* Design
	* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
	* < ncovcol=8 >
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + 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: V3age Tvar[3=V3age]=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 + V3age + V3 + V5V6 + V7V8 + V8age + 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 V5V6? V7V8? ? V8
	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	*How to reorganize?
	* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
	* 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+ageV3 strb=ageV3 stra=V2+V1+V4 */
	/* k=4 (ageV3) 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+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */
	for(k=cptcovt; k>=1;k--) /*< Number of covariates /
Tvar[k]=0;	Tvar[k]=0;
cptcovage=0;	cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */	modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /	if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /
cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /	cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /
if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
/* covar is not filled and then is empty */	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2 */	Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Sums the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tage[1] = 4 */	Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
} else if (strcmp(strd,"age")==0) { /* or ageVn /	} else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strc,'V');	cutl(stre,strb,strc,'V');
Tvar[k]=atoi(stre);	Tvar[k]=atoi(stre);
cptcovage++;	cptcovage++;
Tage[cptcovage]=k;	Tage[cptcovage]=k;
} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/	} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/
/* loops on k1=1 (V3V2) and k1=2 V4V3 */	/* loops on k1=1 (V3V2) and k1=2 V4V3 */
	cptcovn++;
	cptcovprodnoage++;k1++;
	cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 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+V1V4+ageV3+V3*V2
	Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */
	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
	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++;	cptcovn++;
cptcovprodnoage++;k1++;	Tvar[k]=atoi(strd);
cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/	}
Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but	strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
because this model-covariate is a construction we invent a new column	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
ncovcol + k1	scanf("%d",i);*/
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	} /* end of loop + on total covariates */
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	} /* end if strlen(modelsave == 0) ageage might exist /
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */	} /* end if strlen(model == 0) */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2;
Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
for (i=1; i<=lastobs;i++){
/* Computes the new covariate which is a product of
covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
}
} /* End age is not in the model */
} /* End if model includes a product */
else { /* no more sum */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');
ks++; /*< Number of simple covariates /
cptcovn++;
Tvar[k]=atoi(strd);
}
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/
} /* end of loop + */
} /* end model */

/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.	/*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+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/	If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/
Line 5508 BOOL IsWow64()	Line 5905 BOOL IsWow64()
}	}
#endif	#endif

void syscompilerinfo()	void syscompilerinfo(int logged)
{	{
/* #include "syscompilerinfo.h"*/	/* #include "syscompilerinfo.h"*/
	/* command line Intel compiler 32bit windows, XP compatible:*/
	/* /GS /W3 /Gy
	/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
	"_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
	"UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
	/Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
	*/
	/* 64 bits */
	/*
	/GS /W3 /Gy
	/Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
	/D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
	/Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
	"x64\Release\" /Fp"x64\Release\IMaCh.pch" */
	/* Optimization are useless and O3 is slower than O2 */
	/*
	/GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
	/D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
	/Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
	/Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
	*/
	/* Link is / / /OUT:"visual studio
	2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
	/PDB:"visual studio
	2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
	"kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
	"comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
	"oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
	/MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
	/SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
	uiAccess='false'"
	/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
	/NOLOGO /TLBID:1
	*/
#if defined __INTEL_COMPILER	#if defined __INTEL_COMPILER
struct utsname sysInfo;	#if defined(__GNUC__)
	struct utsname sysInfo; /* For Intel on Linux and OS/X */
	#endif
#elif defined(__GNUC__)	#elif defined(__GNUC__)
	#ifndef __APPLE__
#include <gnu/libc-version.h> /* Only on gnu */	#include <gnu/libc-version.h> /* Only on gnu */
struct utsname sysInfo;
#endif	#endif
	struct utsname sysInfo;
#include <stdint.h>
int cross = CROSS;	int cross = CROSS;
if (cross){	if (cross){
printf("Cross-");	printf("Cross-");
fprintf(ficlog,"Cross-");	if(logged) fprintf(ficlog, "Cross-");
}	}
printf("Compiled with:");fprintf(ficlog,"Compiled with:");	#endif

	#include <stdint.h>

	printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
#if defined(__clang__)	#if defined(__clang__)
printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */	printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
#endif	#endif
#if defined(__ICC) \|\| defined(__INTEL_COMPILER)	#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	#endif
#if defined(__GNUC__) \|\| defined(__GNUG__)	#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	#endif
#if defined(__HP_cc) \|\| defined(__HP_aCC)	#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	#endif
#if defined(__IBMC__) \|\| defined(__IBMCPP__)	#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	#endif
#if defined(_MSC_VER)	#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	#endif
#if defined(__PGI)	#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	#endif
#if defined(__SUNPRO_C) \|\| defined(__SUNPRO_CC)	#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	#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	// 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!	#ifdef _WIN32 // note the underscore: without it, it's not msdn official!
// Windows (x64 and x86)	// 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	#elif __unix__ // all unices, not all compilers
// Unix	// Unix
printf("Unix ");fprintf(ficlog,"Unix ");	printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
#elif __linux__	#elif __linux__
// linux	// linux
printf("linux ");fprintf(ficlog,"linux ");	printf("linux ");if(logged) fprintf(ficlog,"linux ");
#elif __APPLE__	#elif __APPLE__
// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..	// 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	#endif

/* __MINGW32__ */	/* __MINGW32__ */
Line 5578 void syscompilerinfo()	Line 6013 void syscompilerinfo()
/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */	/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */

#if UINTPTR_MAX == 0xffffffff	#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	#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	#else
printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */	printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
#endif	#endif

#if defined(__GNUC__)	#if defined(__GNUC__)
Line 5595 void syscompilerinfo()	Line 6030 void syscompilerinfo()
+ __GNUC_MINOR__ * 100)	+ __GNUC_MINOR__ * 100)
# endif	# endif
printf(" using GNU C version %d.\n", __GNUC_VERSION__);	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) {	if (uname(&sysInfo) != -1) {
printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);	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	else
perror("uname() error");	perror("uname() error");
#ifndef __INTEL_COMPILER	//#ifndef __INTEL_COMPILER
	#if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
printf("GNU libc version: %s\n", gnu_get_libc_version());	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
#endif	#endif

Line 5613 void syscompilerinfo()	Line 6049 void syscompilerinfo()
// {	// {
#if defined(_MSC_VER)	#if defined(_MSC_VER)
if (IsWow64()){	if (IsWow64()){
printf("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");
fprintf(ficlog, "The 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{	else{
printf("The process 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");
frintf(ficlog,"The programm 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...");	// printf("\nPress Enter to continue...");
// getchar();	// getchar();
Line 5629 void syscompilerinfo()	Line 6065 void syscompilerinfo()

}	}

	int prevalence_limit(double p, double *prlim, double ageminpar, double agemaxpar){
	/--------------- Prevalence limit (period or stable prevalence) --------------/
	int i, j, k, i1 ;
	double ftolpl = 1.e-10;
	double age, agebase, agelim;

	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");

	/* prlim=matrix(1,nlstate,1,nlstate);/ / back in main */

	agebase=ageminpar;
	agelim=agemaxpar;

	i1=pow(2,cptcoveff);
	if (cptcovn < 1){i1=1;}

	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
	/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
	//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#******");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
	fprintf(ficrespl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");

	fprintf(ficrespl,"#Age ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
	fprintf(ficrespl,"\n");

	for (age=agebase; age<=agelim; age++){
	/* for (age=agebase; age<=agebase; age++){ */
	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
	fprintf(ficrespl,"%.0f ",age );
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	for(i=1; i<=nlstate;i++)
	fprintf(ficrespl," %.5f", prlim[i][i]);
	fprintf(ficrespl,"\n");
	} /* Age */
	/* was end of cptcod */
	} /* cptcov */
	return 0;
	}

	int hPijx(double *p, int bage, int fage){
	/------------- h Pij x at various ages ------------/

	int stepsize;
	int agelim;
	int hstepm;
	int nhstepm;
	int h, i, i1, j, k;

	double agedeb;
	double ***p3mat;

	strcpy(filerespij,"pij"); strcat(filerespij,fileres);
	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;
	}
	printf("Computing pij: result on file '%s' \n", filerespij);
	fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);

	stepsize=(int) (stepm+YEARM-1)/YEARM;
	/if (stepm<=24) stepsize=2;/

	agelim=AGESUP;
	hstepm=stepsizeYEARM; / Every year of age */
	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

	/* hstepm=1; aff par mois*/
	pstamp(ficrespij);
	fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
	i1= pow(2,cptcoveff);
	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
	/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */
	/* k=k+1; */
	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,"******\n");

	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
	nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /
	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */

	/* nhstepm=nhstepmYEARM; aff par mois/

	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	oldm=oldms;savm=savms;
	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
	fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
	for(i=1; i<=nlstate;i++)
	for(j=1; j<=nlstate+ndeath;j++)
	fprintf(ficrespij," %1d-%1d",i,j);
	fprintf(ficrespij,"\n");
	for (h=0; h<=nhstepm; h++){
	/agedebphstep = agedeb + hhstepm/YEARMstepm;/
	fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm );
	for(i=1; i<=nlstate;i++)
	for(j=1; j<=nlstate+ndeath;j++)
	fprintf(ficrespij," %.5f", p3mat[i][j][h]);
	fprintf(ficrespij,"\n");
	}
	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	fprintf(ficrespij,"\n");
	}
	/}/
	}
	return 0;
	}


/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
/***********************************************/	/***********************************************/
Line 5655 int main(int argc, char *argv[])	Line 6230 int main(int argc, char *argv[])
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
struct stat info;	struct stat info;
double agedeb;	double agedeb=0.;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;	double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

double fret;	double fret;
double dum; /* Dummy variable */	double dum=0.; /* Dummy variable */
double ***p3mat;	double ***p3mat;
double ***mobaverage;	double ***mobaverage;

Line 5669 int main(int argc, char *argv[])	Line 6244 int main(int argc, char *argv[])
char tok, val; /* pathtot */	char tok, val; /* pathtot */
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10;
int c, h , cpt;	int c, h , cpt;
int jl;	int jl=0;
int i1, j1, jk, stepsize;	int i1, j1, jk, stepsize=0;
int *tab;	int *tab;
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */	int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm, nhstepm;	int hstepm=0, nhstepm=0;
int agemortsup;	int agemortsup;
float sumlpop=0.;	float sumlpop=0.;
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;	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 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 ftolpl=FTOL;
double **prlim;	double **prlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters */
Line 5736 int main(int argc, char *argv[])	Line 6311 int main(int argc, char *argv[])

nberr=0; /* Number of errors and warnings */	nberr=0; /* Number of errors and warnings */
nbwarn=0;	nbwarn=0;
	#ifdef WIN32
	_getcwd(pathcd, size);
	#else
getcwd(pathcd, size);	getcwd(pathcd, size);
	#endif
	syscompilerinfo(0);
printf("\n%s\n%s",version,fullversion);	printf("\n%s\n%s",version,fullversion);
if(argc <=1){	if(argc <=1){
printf("\nEnter the parameter file name: ");	printf("\nEnter the parameter file name: ");
Line 5772 int main(int argc, char *argv[])	Line 6351 int main(int argc, char *argv[])
/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */	/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);	split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);	printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
	#ifdef WIN32
	_chdir(path); /* Can be a relative path */
	if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
	#else
chdir(path); /* Can be a relative path */	chdir(path); /* Can be a relative path */
if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */	if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
printf("Current directory %s!\n",pathcd);	#endif
	printf("Current directory %s!\n",pathcd);
strcpy(command,"mkdir ");	strcpy(command,"mkdir ");
strcat(command,optionfilefiname);	strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){	if((outcmd=system(command)) != 0){
Line 5789 int main(int argc, char *argv[])	Line 6373 int main(int argc, char *argv[])

/-------- arguments in the command line --------/	/-------- arguments in the command line --------/

/* Log file */	/* Main Log file */
strcat(filelog, optionfilefiname);	strcat(filelog, optionfilefiname);
strcat(filelog,".log"); /* */	strcat(filelog,".log"); /* */
if((ficlog=fopen(filelog,"w"))==NULL) {	if((ficlog=fopen(filelog,"w"))==NULL) {
Line 5805 int main(int argc, char *argv[])	Line 6389 int main(int argc, char *argv[])
optionfilext=%s\n\	optionfilext=%s\n\
optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);	optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);

syscompilerinfo();	syscompilerinfo(0);

printf("Local time (at start):%s",strstart);	printf("Local time (at start):%s",strstart);
fprintf(ficlog,"Local time (at start): %s",strstart);	fprintf(ficlog,"Local time (at start): %s",strstart);
Line 5818 int main(int argc, char *argv[])	Line 6402 int main(int argc, char *argv[])
strcat(fileres, optionfilefiname);	strcat(fileres, optionfilefiname);
strcat(fileres,".txt"); /* Other files have txt extension */	strcat(fileres,".txt"); /* Other files have txt extension */

/---------arguments file --------/	/* Main ---------arguments file --------*/

if((ficpar=fopen(optionfile,"r"))==NULL) {	if((ficpar=fopen(optionfile,"r"))==NULL) {
printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));	printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
Line 5851 int main(int argc, char *argv[])	Line 6435 int main(int argc, char *argv[])
}	}
ungetc(c,ficpar);	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);	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++;
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\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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);	if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the 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);	model[strlen(model)-1]='\0';
	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);	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+ageage+V1+V1age.' 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){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
Line 5875 int main(int argc, char *argv[])	Line 6471 int main(int argc, char *argv[])
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
*/	*/
if (strlen(model)>1)	if (strlen(model)>1)
ncovmodel=2+nbocc(model,'+')+1; /Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2v4+v5age makes 5+2=7/	ncovmodel=2+nbocc(model,'+')+1; /Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2v4+v5age makes 5+2=7,ageage makes 3*/
else	else
ncovmodel=2;	ncovmodel=2; /* Constant and age */
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
nforce= (nlstate+ndeath-1)nlstate; / Number of forces ij from state i to j */	nforce= (nlstate+ndeath-1)nlstate; / Number of forces ij from state i to j */
npar= nforcencovmodel; / Number of parameters like aij*/	npar= nforcencovmodel; / Number of parameters like aij*/
if(npar >MAXPARM \|\| nlstate >NLSTATEMAX \|\| ndeath >NDEATHMAX \|\| ncovmodel>NCOVMAX){	if(npar >MAXPARM \|\| nlstate >NLSTATEMAX \|\| ndeath >NDEATHMAX \|\| ncovmodel>NCOVMAX){
Line 5893 int main(int argc, char *argv[])	Line 6488 int main(int argc, char *argv[])
/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/	/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/
if(mle==-1){ /* Print a wizard for help writing covariance matrix */	if(mle==-1){ /* Print a wizard for help writing covariance matrix */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" 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 choose 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);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);	fclose (ficparo);
fclose (ficlog);	fclose (ficlog);
goto end;	goto end;
exit(0);	exit(0);
}	}
else if(mle==-3) {	else if(mle==-3) { /* Main Wizard */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);	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);	fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
Line 6061 run imach with mle=-1 to get a correct t	Line 6656 run imach with mle=-1 to get a correct t
fprintf(ficres,"#%s\n",version);	fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */	} /* End of mle != -3 */

	/* Main data
	*/
n= lastobs;	n= lastobs;
num=lvector(1,n);	num=lvector(1,n);
moisnais=vector(1,n);	moisnais=vector(1,n);
Line 6112 run imach with mle=-1 to get a correct t	Line 6708 run imach with mle=-1 to get a correct t
Tage[1=V3age]= 4; Tage[2=ageV4] = 3	Tage[1=V3age]= 4; Tage[2=ageV4] = 3
*/	*/

	/* Main decodemodel */


if(decodemodel(model, lastobs) == 1)	if(decodemodel(model, lastobs) == 1)
goto end;	goto end;

Line 6155 run imach with mle=-1 to get a correct t	Line 6754 run imach with mle=-1 to get a correct t
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;	ncodemax[1]=1;
Ndum =ivector(-1,NCOVMAX);	Ndum =ivector(-1,NCOVMAX);
if (ncovmodel > 2)	if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and ageage /
tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /	tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /
	/* Nbcode gives the value of the lth modality of jth covariate, in
	V2+V1age, 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) */	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]);/	/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);/
	/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
h=0;	h=0;


Line 6176 run imach with mle=-1 to get a correct t	Line 6779 run imach with mle=-1 to get a correct t
if (h>m)	if (h>m)
h=1;	h=1;
/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1	/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1
* h 1 2 3 4	* For k=4 covariates, h goes from 1 to 2**k
	* codtabm(h,k)= 1 & (h-1) >> (k-1) ;
	* h\k 1 2 3 4
*______________________________	*______________________________
* 1 i=1 1 i=1 1 i=1 1 i=1 1	* 1 i=1 1 i=1 1 i=1 1 i=1 1
* 2 2 1 1 1	* 2 2 1 1 1
Line 6196 run imach with mle=-1 to get a correct t	Line 6801 run imach with mle=-1 to get a correct t
* 16 2 2 2 1	* 16 2 2 2 1
*/	*/
codtab[h][k]=j;	codtab[h][k]=j;
	/* codtab[12][3]=1; */
/codtab[h][Tvar[k]]=j;/	/codtab[h][Tvar[k]]=j;/
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);	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]]);
}	}
Line 6216 run imach with mle=-1 to get a correct t	Line 6822 run imach with mle=-1 to get a correct t



/------------ gnuplot -------------/	/* Initialisation of ----------- gnuplot -------------*/
strcpy(optionfilegnuplot,optionfilefiname);	strcpy(optionfilegnuplot,optionfilefiname);
if(mle==-3)	if(mle==-3)
strcat(optionfilegnuplot,"-mort");	strcat(optionfilegnuplot,"-mort");
Line 6232 run imach with mle=-1 to get a correct t	Line 6838 run imach with mle=-1 to get a correct t
fprintf(ficgp,"set datafile missing 'NaNq'\n");	fprintf(ficgp,"set datafile missing 'NaNq'\n");
}	}
/* fclose(ficgp);*/	/* fclose(ficgp);*/
/--------- index.htm --------/

	/* Initialisation of --------- index.htm --------*/

strcpy(optionfilehtm,optionfilefiname); /* Main html file */	strcpy(optionfilehtm,optionfilefiname); /* Main html file */
if(mle==-3)	if(mle==-3)
Line 6274 Title=%s <br>Datafile=%s Firstpass=%d La	Line 6882 Title=%s <br>Datafile=%s Firstpass=%d La

strcpy(pathr,path);	strcpy(pathr,path);
strcat(pathr,optionfilefiname);	strcat(pathr,optionfilefiname);
	#ifdef WIN32
	_chdir(optionfilefiname); /* Move to directory named optionfile */
	#else
chdir(optionfilefiname); /* Move to directory named optionfile */	chdir(optionfilefiname); /* Move to directory named optionfile */
	#endif


/* Calculates basic frequencies. Computes observed prevalence at single age	/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */	and prints on file fileres'p'. */
Line 6297 Interval (in months) between two waves:	Line 6910 Interval (in months) between two waves:
p=param[1][1]; /* (((param +1)+1)+0) /	p=param[1][1]; /* (((param +1)+1)+0) /

globpr=0; /* To get the number ipmx of contributions and the sum of weights*/	globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
	/* For mortality only */
if (mle==-3){	if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);	ximort=matrix(1,NDIM,1,NDIM);
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */	/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);	cens=ivector(1,n);
ageexmed=vector(1,n);	ageexmed=vector(1,n);
agecens=vector(1,n);	agecens=vector(1,n);
Line 6390 Interval (in months) between two waves:	Line 7003 Interval (in months) between two waves:

/* Initialize method and iterate */	/* Initialize method and iterate */
/* p[1]=0.0268; p[NDIM]=0.083; */	/* p[1]=0.0268; p[NDIM]=0.083; */
/* gsl_vector_set(x, 0, 0.0268); */	/* gsl_vector_set(x, 0, 0.0268); */
/* gsl_vector_set(x, 1, 0.083); */	/* gsl_vector_set(x, 1, 0.083); */
gsl_vector_set(x, 0, p[1]);	gsl_vector_set(x, 0, p[1]);
gsl_vector_set(x, 1, p[2]);	gsl_vector_set(x, 1, p[2]);

Line 6508 Interval (in months) between two waves:	Line 7121 Interval (in months) between two waves:
free_ivector(dcwave,1,n);	free_ivector(dcwave,1,n);
free_matrix(ximort,1,NDIM,1,NDIM);	free_matrix(ximort,1,NDIM,1,NDIM);
#endif	#endif
} /* Endof if mle==-3 */	} /* Endof if mle==-3 mortality only */
	/* Standard maximisation */
else{ /* For mle >=1 */	else{ /* For mle >=1 */
globpr=0;/* debug */	globpr=0;/* debug */
	/* Computes likelihood for initial parameters */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);	printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
printf("\n");	printf("\n");
globpr=1; /* to print the contributions */	globpr=1; /* again, to print the contributions */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);	printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
printf("\n");	printf("\n");
if(mle>=1){ /* Could be 1 or 2 */	if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}	}

/--------- results files --------------/	/--------- 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 nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
Line 6541 Interval (in months) between two waves:	Line 7155 Interval (in months) between two waves:
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%lf ",p[jk]);	printf("%12.7f ",p[jk]);
fprintf(ficlog,"%lf ",p[jk]);	fprintf(ficlog,"%12.7f ",p[jk]);
fprintf(ficres,"%lf ",p[jk]);	fprintf(ficres,"%12.7f ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
Line 6684 Interval (in months) between two waves:	Line 7298 Interval (in months) between two waves:
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");	fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);

	/* Other stuffs, more or less useful */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
Line 6757 Interval (in months) between two waves:	Line 7372 Interval (in months) between two waves:
fclose(ficres);	fclose(ficres);


	/* Other results (useful)*/


/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
#include "prevlim.h" /* Use ficrespl, ficlog */	/#include "prevlim.h"/ /* Use ficrespl, ficlog */
	prlim=matrix(1,nlstate,1,nlstate);
	prevalence_limit(p, prlim, ageminpar, agemaxpar);
fclose(ficrespl);	fclose(ficrespl);

#ifdef FREEEXIT2	#ifdef FREEEXIT2
Line 6766 Interval (in months) between two waves:	Line 7386 Interval (in months) between two waves:
#endif	#endif

/------------- h Pij x at various ages ------------/	/------------- h Pij x at various ages ------------/
#include "hpijx.h"	/#include "hpijx.h"/
	hPijx(p, bage, fage);
fclose(ficrespij);	fclose(ficrespij);

/-------------- Variance of one-step probabilities---/	/-------------- Variance of one-step probabilities---/
Line 6793 Interval (in months) between two waves:	Line 7414 Interval (in months) between two waves:
/* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */	/* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
/* } */	/* } */
}	}

	/* ------ Other prevalence ratios------------ */

/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */	/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */

Line 7068 Interval (in months) between two waves:	Line 7690 Interval (in months) between two waves:


printf("Before Current directory %s!\n",pathcd);	printf("Before Current directory %s!\n",pathcd);
	#ifdef WIN32
	if (_chdir(pathcd) != 0)
	printf("Can't move to directory %s!\n",path);
	if(_getcwd(pathcd,MAXLINE) > 0)
	#else
if(chdir(pathcd) != 0)	if(chdir(pathcd) != 0)
printf("Can't move to directory %s!\n",path);	printf("Can't move to directory %s!\n", path);
if(getcwd(pathcd,MAXLINE) > 0)	if (getcwd(pathcd, MAXLINE) > 0)
	#endif
printf("Current directory %s!\n",pathcd);	printf("Current directory %s!\n",pathcd);
/strcat(plotcmd,CHARSEPARATOR);/	/strcat(plotcmd,CHARSEPARATOR);/
sprintf(plotcmd,"gnuplot");	sprintf(plotcmd,"gnuplot");

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Removed from v.1.177
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	Added in v.1.191