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Diff for /imach/src/imach.c between versions 1.161 and 1.200

version 1.161, 2014/09/15 20:41:41	version 1.200, 2015/09/09 16:53:55
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.200 2015/09/09 16:53:55 brouard
	Summary: Big bug thanks to Flavia

	Even model=1+age+V2. did not work anymore

	Revision 1.199 2015/09/07 14:09:23 brouard
	Summary: 0.98q6 changing default small png format for graph to vectorized svg.

	Revision 1.198 2015/09/03 07:14:39 brouard
	Summary: 0.98q5 Flavia

	Revision 1.197 2015/09/01 18:24:39 brouard
	* empty log message *

	Revision 1.196 2015/08/18 23:17:52 brouard
	Summary: 0.98q5

	Revision 1.195 2015/08/18 16:28:39 brouard
	Summary: Adding a hack for testing purpose

	After reading the title, ftol and model lines, if the comment line has
	a q, starting with #q, the answer at the end of the run is quit. It
	permits to run test files in batch with ctest. The former workaround was
	$ echo q \| imach foo.imach

	Revision 1.194 2015/08/18 13:32:00 brouard
	Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.

	Revision 1.193 2015/08/04 07:17:42 brouard
	Summary: 0.98q4

	Revision 1.192 2015/07/16 16:49:02 brouard
	Summary: Fixing some outputs

	Revision 1.191 2015/07/14 10:00:33 brouard
	Summary: Some fixes

	Revision 1.190 2015/05/05 08:51:13 brouard
	Summary: Adding digits in output parameters (7 digits instead of 6)

	Fix 1+age+.

	Revision 1.189 2015/04/30 14:45:16 brouard
	Summary: 0.98q2

	Revision 1.188 2015/04/30 08:27:53 brouard
	* empty log message *

	Revision 1.187 2015/04/29 09:11:15 brouard
	* empty log message *

	Revision 1.186 2015/04/23 12:01:52 brouard
	Summary: V1*age is working now, version 0.98q1

	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
	Summary: Still testing ilc32 on OSX

	Revision 1.176 2015/01/03 16:45:04 brouard
	* empty log message *

	Revision 1.175 2015/01/03 16:33:42 brouard
	* empty log message *

	Revision 1.174 2015/01/03 16:15:49 brouard
	Summary: Still in cross-compilation

	Revision 1.173 2015/01/03 12:06:26 brouard
	Summary: trying to detect cross-compilation

	Revision 1.172 2014/12/27 12:07:47 brouard
	Summary: Back from Visual Studio and Intel, options for compiling for Windows XP

	Revision 1.171 2014/12/23 13:26:59 brouard
	Summary: Back from Visual C

	Still problem with utsname.h on Windows

	Revision 1.170 2014/12/23 11:17:12 brouard
	Summary: Cleaning some \%% back to %%

	The escape was mandatory for a specific compiler (which one?), but too many warnings.

	Revision 1.169 2014/12/22 23:08:31 brouard
	Summary: 0.98p

	Outputs some informations on compiler used, OS etc. Testing on different platforms.

	Revision 1.168 2014/12/22 15:17:42 brouard
	Summary: update

	Revision 1.167 2014/12/22 13:50:56 brouard
	Summary: Testing uname and compiler version and if compiled 32 or 64

	Testing on Linux 64

	Revision 1.166 2014/12/22 11:40:47 brouard
	* empty log message *

	Revision 1.165 2014/12/16 11:20:36 brouard
	Summary: After compiling on Visual C

	* imach.c (Module): Merging 1.61 to 1.162

	Revision 1.164 2014/12/16 10:52:11 brouard
	Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn

	* imach.c (Module): Merging 1.61 to 1.162

	Revision 1.163 2014/12/16 10:30:11 brouard
	* imach.c (Module): Merging 1.61 to 1.162

	Revision 1.162 2014/09/25 11:43:39 brouard
	Summary: temporary backup 0.99!

	Revision 1.1 2014/09/16 11:06:58 brouard
	Summary: With some code (wrong) for nlopt

	Author:

Revision 1.161 2014/09/15 20:41:41 brouard	Revision 1.161 2014/09/15 20:41:41 brouard
Summary: Problem with macro SQR on Intel compiler	Summary: Problem with macro SQR on Intel compiler

Line 481	Line 636
end	end
*/	*/

	/* #define DEBUG */
	/* #define DEBUGBRENT */
	#define POWELL /* Instead of NLOPT */
	#define POWELLF1F3 /* Skip test */
	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /



#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
#include <stdlib.h>	#include <stdlib.h>
Line 491	Line 650

#ifdef _WIN32	#ifdef _WIN32
#include <io.h>	#include <io.h>
	#include <windows.h>
	#include <tchar.h>
#else	#else
#include <unistd.h>	#include <unistd.h>
#endif	#endif

#include <limits.h>	#include <limits.h>
#include <sys/types.h>	#include <sys/types.h>

	#if defined(__GNUC__)
	#include <sys/utsname.h> /* Doesn't work on Windows */
	#endif

#include <sys/stat.h>	#include <sys/stat.h>
#include <errno.h>	#include <errno.h>
/* extern int errno; */	/* extern int errno; */
Line 515	Line 681
#include <gsl/gsl_multimin.h>	#include <gsl/gsl_multimin.h>
#endif	#endif


	#ifdef NLOPT
	#include <nlopt.h>
	typedef struct {
	double (* function)(double [] );
	} myfunc_data ;
	#endif

/* #include <libintl.h> */	/* #include <libintl.h> */
/* #define _(String) gettext (String) */	/* #define _(String) gettext (String) */

Line 534	Line 708
#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /	#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /
#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */	#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */
#define codtabm(h,k) 1 & (h-1) >> (k-1) ;	#define codtabm(h,k) (1 & (h-1) >> (k-1))+1
#define MAXN 20000	#define MAXN 20000
#define YEARM 12. /*< Number of months per year /	#define YEARM 12. /*< Number of months per year /
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
#define AGEGOMP 10. /*< Minimal age for Gompertz adjustment /	#define AGEOVERFLOW 1.e20
	#define AGEGOMP 10 /*< Minimal age for Gompertz adjustment /
#ifdef _WIN32	#ifdef _WIN32
#define DIRSEPARATOR '\\'	#define DIRSEPARATOR '\\'
#define CHARSEPARATOR "\\"	#define CHARSEPARATOR "\\"
Line 552	Line 727

/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */
	#include "version.h"
char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";	char version[]=__IMACH_VERSION__;
	char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
char fullversion[]="$Revision$ $Date$";	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 584 int *mw; / mw[mi][i] is number of the	Line 760 int *mw; / mw[mi][i] is number of the
int *dh; / dh[mi][i] is number of steps between mi,mi+1 for this individual */	int *dh; / dh[mi][i] is number of steps between mi,mi+1 for this individual */
int *bh; / bh[mi][i] is the bias (+ or -) for this individual if the delay between	int *bh; / bh[mi][i] is the bias (+ or -) for this individual if the delay between
* wave mi and wave mi+1 is not an exact multiple of stepm. */	* wave mi and wave mi+1 is not an exact multiple of stepm. */
	int countcallfunc=0; /* Count the number of calls to func */
double jmean=1; /* Mean space between 2 waves */	double jmean=1; /* Mean space between 2 waves */
double *matprod2(); / test */	double *matprod2(); / test */
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
Line 667 static double maxarg1,maxarg2;	Line 844 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 */
	#define mytinydouble 1.0e-16
	/* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
	/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
	/* static double dsqrarg; */
	/* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrargdsqrarg) /
static double sqrarg;	static double sqrarg;
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)	#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}	#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
Line 682 int estepm;	Line 864 int estepm;

int m,nb;	int m,nb;
long *num;	long *num;
int firstpass=0, lastpass=4,cod, ncodemax, Tage,cens;	int firstpass=0, lastpass=4,cod, cens;
	int ncodemax; / ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered excluding
	undefined. Usually 2: 0 and 1. */
	int ncodemaxwundef; / ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered including
	undefined. Usually 3: -1, 0 and 1. */
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
double pmmij, *probs;	double pmmij, *probs;
double ageexmed,agecens;	double ageexmed,agecens;
Line 693 int *s; / Status */	Line 881 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 *Tage;
int Ndum; /* Freq of modality (tricode */	int Ndum; /* Freq of modality (tricode */
int codtab; /< codtab=imatrix(1,100,1,10); */	/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /
int *Tvard, Tprod, cptcovprod, *Tvaraff;	int *Tvard, Tprod, cptcovprod, *Tvaraff;
double lsurv, lpop, *tpop;	double lsurv, lpop, *tpop;

Line 711 static int split( char path, char dirc	Line 900 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 722 static int split( char path, char dirc	Line 911 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 733 static int split( char path, char dirc	Line 926 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 785 char trimbb(char out, char *in)	Line 978 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 815 char cutl(char blocc, char *alocc, cha	Line 1051 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 1093 char subdirf3(char fileres[], char pre	Line 1329 char subdirf3(char fileres[], char pre
return tmpout;	return tmpout;
}	}

	char *asc_diff_time(long time_sec, char ascdiff[])
	{
	long sec_left, days, hours, minutes;
	days = (time_sec) / (606024);
	sec_left = (time_sec) % (606024);
	hours = (sec_left) / (60*60) ;
	sec_left = (sec_left) %(60*60);
	minutes = (sec_left) /60;
	sec_left = (sec_left) % (60);
	sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
	return ascdiff;
	}

/*************** f1dim ***********************/	/*************** f1dim ***********************/
extern int ncom;	extern int ncom;
extern double pcom,xicom;	extern double pcom,xicom;
Line 1113 double f1dim(double x)	Line 1362 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;
double ftemp;	double ftemp=0.;
double p,q,r,tol1,tol2,u,v,w,x,xm;	double p,q,r,tol1,tol2,u,v,w,x,xm;
double e=0.0;	double e=0.0;

Line 1131 double brent(double ax, double bx, doubl	Line 1386 double brent(double ax, double bx, doubl
/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret)))*/	/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret)))*/
printf(".");fflush(stdout);	printf(".");fflush(stdout);
fprintf(ficlog,".");fflush(ficlog);	fprintf(ficlog,".");fflush(ficlog);
#ifdef DEBUG	#ifdef DEBUGBRENT
printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);	printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);	fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
/* if ((fabs(x-xm) <= (tol2-0.5(b-a)))\|\|(2.0fabs(fu-ftemp) <= ftol1.e-2(fabs(fu)+fabs(ftemp)))) { */	/* if ((fabs(x-xm) <= (tol2-0.5(b-a)))\|\|(2.0fabs(fu-ftemp) <= ftol1.e-2(fabs(fu)+fabs(ftemp)))) { */
Line 1166 double brent(double ax, double bx, doubl	Line 1421 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 1189 double brent(double ax, double bx, doubl	Line 1444 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) {	#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)/
(2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));	(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);	ulim=(bx)+GLIMIT(cx-bx); /* Maximum abscissa where function should be evaluated */
if ((bx-u)(u-*cx) > 0.0) {	if ((bx-u)(u-cx) > 0.0) { / if u_p is between b and c */
fu=(*func)(u);	fu=(*func)(u);
} else if ((cx-u)(u-ulim) > 0.0) {	#ifdef DEBUG
	/* f(x)=A(x-u)*2+f(u) /
	double A, fparabu;
	A= (fb - fa)/(bx-ax)/(bx+ax-2*u);
	fparabu= fa - A(ax-u)(*ax-u);
	printf("mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);
	fprintf(ficlog, "mnbrak (ax=%.12f, fa=%.12lf), (bx=%.12f, fb=%.12lf), (cx=%.12f, fc=%.12lf), (u=%.12f, fu=%.12lf, fparabu=%.12f)\n",ax,fa,bx,fb,cx,*fc,u,fu, fparabu);
	/* 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
	#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 */
	#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) {	} 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 **********************/
	/* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
	resets p to where the function func(p) takes on a minimum along the direction xi from p ,
	and replaces xi by the actual vector displacement that p was moved. Also returns as fret
	the value of func at the returned location p . This is actually all accomplished by calling the
	routines mnbrak and brent .*/
int ncom;	int ncom;
double pcom,xicom;	double pcom,xicom;
double (*nrfunc)(double []);	double (*nrfunc)(double []);
Line 1243 void linmin(double p[], double xi[], int	Line 1591 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 1252 void linmin(double p[], double xi[], int	Line 1602 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);	/* xxss=1; /\* 1 and using scale \/ /
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);	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);
}	}

char *asc_diff_time(long time_sec, char ascdiff[])
{
long sec_left, days, hours, minutes;
days = (time_sec) / (606024);
sec_left = (time_sec) % (606024);
hours = (sec_left) / (60*60) ;
sec_left = (sec_left) %(60*60);
minutes = (sec_left) /60;
sec_left = (sec_left) % (60);
sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
return ascdiff;
}

/************* powell **********************/	/************* powell **********************/
	/*
	Minimization of a function func of n variables. Input consists of an initial starting point
	p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
	rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
	such that failure to decrease by more than this amount on one iteration signals doneness. On
	output, p is set to the best point found, xi is the then-current direction set, fret is the returned
	function value at p , and iter is the number of iterations taken. The routine linmin is used.
	*/
void powell(double p[], double *xi, int n, double ftol, int iter, double *fret,	void powell(double p[], double *xi, int n, double ftol, int iter, double *fret,
double (*func)(double []))	double (*func)(double []))
{	{
Line 1289 void powell(double p[], double **xi, int	Line 1674 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 1301 void powell(double p[], double **xi, int	Line 1687 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 1311 void powell(double p[], double **xi, int	Line 1697 void powell(double p[], double **xi, int
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);	printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);	fprintf(ficlog," %d %.12lf",i, p[i]);
fprintf(ficrespow," %.12lf", p[i]);	fprintf(ficrespow," %.12lf", p[i]);
Line 1322 void powell(double p[], double **xi, int	Line 1708 void powell(double p[], double **xi, int
if(*iter <=3){	if(*iter <=3){
tml = *localtime(&rcurr_time);	tml = *localtime(&rcurr_time);
strcpy(strcurr,asctime(&tml));	strcpy(strcurr,asctime(&tml));
/* asctime_r(&tm,strcurr); */
rforecast_time=rcurr_time;	rforecast_time=rcurr_time;
itmp = strlen(strcurr);	itmp = strlen(strcurr);
if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */	if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
strcurr[itmp-1]='\0';	strcurr[itmp-1]='\0';
printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
for(niterf=10;niterf<=30;niterf+=10){	for(niterf=10;niterf<=30;niterf+=10){
rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);	rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);
forecast_time = *localtime(&rforecast_time);	forecast_time = *localtime(&rforecast_time);
/* asctime_r(&tmf,strfor); */
strcpy(strfor,asctime(&forecast_time));	strcpy(strfor,asctime(&forecast_time));
itmp = strlen(strfor);	itmp = strlen(strfor);
if(strfor[itmp-1]=='\n')	if(strfor[itmp-1]=='\n')
Line 1341 void powell(double p[], double **xi, int	Line 1725 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 \n",*fret);	printf("fret=%lf, %lf, %lf \n", fret, fret, *fret);
fprintf(ficlog,"fret=%lf \n",*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 1364 void powell(double p[], double **xi, int	Line 1753 void powell(double p[], double **xi, int
fprintf(ficlog," x(%d)=%.12e",j,xit[j]);	fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
}	}
for(j=1;j<=n;j++) {	for(j=1;j<=n;j++) {
printf(" p=%.12e",p[j]);	printf(" p(%d)=%.12e",j,p[j]);
fprintf(ficlog," p=%.12e",p[j]);	fprintf(ficlog," p(%d)=%.12e",j,p[j]);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
}	} /* 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 1401 void powell(double p[], double **xi, int	Line 1805 void powell(double p[], double **xi, int
free_vector(ptt,1,n);	free_vector(ptt,1,n);
free_vector(pt,1,n);	free_vector(pt,1,n);
return;	return;
}	} /* enough precision */
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 */
	#ifdef POWELLF1F3
	#else
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 /	#endif
	/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /
/* From x1 (P0) distance of x2 is at h and x3 is 2h */	/* From x1 (P0) distance of x2 is at h and x3 is 2h */
/* Let f"(x2) be the 2nd derivative equal everywhere. Then the parabolic through (x1,f1), (x2,f2) and (x3,f3)	/* Let f"(x2) be the 2nd derivative equal everywhere. */
will reach at f3 = fm + h^2/2 f''m ; f" = (f1 -2f2 +f3 ) / h*2 /	/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
/* f1-f3 = delta(2h) = 2 h*2 f'' = 2(f1- 2f2 +f3) /	/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h*2 /
/* Thus we compare delta(2h) with observed f1-f3 */	/* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
/* 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); */
t=2.0(fp-2.0(fret)+fptt)SQR(fp-(*fret)-del);	#ifdef NRCORIGINAL
	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 1430 void powell(double p[], double **xi, int	Line 1841 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++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */	printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
xi[j][n]=xit[j]; /* and nth direction by the extrapolated */	if(j % ncovmodel == 0)
	printf("\n");
}	}
printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	#endif
fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);	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++) {
	xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
	}
	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 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);
	fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
for(j=1;j<=n;j++){	for(j=1;j<=n;j++){
printf(" %.12e",xit[j]);	printf(" %.12e",xit[j]);
fprintf(ficlog," %.12e",xit[j]);	fprintf(ficlog," %.12e",xit[j]);
Line 1447 void powell(double p[], double **xi, int	Line 1885 void powell(double p[], double **xi, int
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
}	} /* end of t or directest negative */
}	#ifdef POWELLF1F3
}	#else
	} /* end if (fptt < fp) */
	#endif
	} /* loop iteration */
}	}

/** Prevalence limit (stable or period prevalence) **************/	/** Prevalence limit (stable or period prevalence) **************/
Line 1458 double prevalim(double prlim, int nl	Line 1899 double prevalim(double prlim, int nl
{	{
/* Computes the prevalence limit in each live state at age x by left multiplying the unit	/* Computes the prevalence limit in each live state at age x by left multiplying the unit
matrix by transitions matrix until convergence is reached */	matrix by transitions matrix until convergence is reached */

int i, ii,j,k;	int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;	double min, max, maxmin, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], pmij();	double out, cov[NCOVMAX+1], pmij();
double **newm;	double **newm;
double agefin, delaymax=50 ; /* Max number of years to converge */	double agefin, delaymax=50 ; /* Max number of years to converge */

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++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}

cov[1]=1.;	cov[1]=1.;

/* Even if hstepm = 1, at least one multiplication by the unit matrix */	/* Even if hstepm = 1, at least one multiplication by the unit matrix */
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){	for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
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]][codtabm(ij,Tvar[k])]; */
/printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);/	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
}	/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	}
/* for (k=1; k<=cptcovprod;k++) /\* Useless \/ /	/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[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<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]cov[2]; /
	for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
	for (k=1; k<=cptcovprod;k++) /* Useless */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d 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 1510 double prevalim(double prlim, int nl	Line 1956 double prevalim(double prlim, int nl
}	}
maxmin=max-min;	maxmin=max-min;
maxmax=FMAX(maxmax,maxmin);	maxmax=FMAX(maxmax,maxmin);
}	} /* j loop */
if(maxmax < ftolpl){	if(maxmax < ftolpl){
return prlim;	return prlim;
}	}
}	} /* age loop */
	return prlim; /* should not reach here */
}	}

/************* transition probabilities *************/	/************* transition probabilities *************/
Line 1536 double pmij(double ps, double *cov,	Line 1983 double pmij(double ps, double *cov,
*/	*/
double s1, lnpijopii;	double s1, lnpijopii;
/double t34;/	/double t34;/
int i,j,j1, nc, ii, jj;	int i,j, nc, ii, jj;

for(i=1; i<= nlstate; i++){	for(i=1; i<= nlstate; i++){
for(j=1; j<i;j++){	for(j=1; j<i;j++){
Line 1638 double *hpxij(double *po, int nhstep	Line 2085 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 1651 double *hpxij(double *po, int nhstep	Line 2099 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]][codtabm(ij,k)];
for (k=1; k<=cptcovage;k++)	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
	/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */	for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
Line 1678 double *hpxij(double *po, int nhstep	Line 2133 double *hpxij(double *po, int nhstep
return po;	return po;
}	}

	#ifdef NLOPT
	double myfunc(unsigned n, const double p1, double grad, void *pd){
	double fret;
	double *xt;
	int j;
	myfunc_data d2 = (myfunc_data ) pd;
	/* xt = (p1-1); */
	xt=vector(1,n);
	for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */

	fret=(d2->function)(xt); /* p xt[1]@8 is fine */
	/* fret=(func)(xt); /\ p xt[1]@8 is fine \/ /
	printf("Function = %.12lf ",fret);
	for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
	printf("\n");
	free_vector(xt,1,n);
	return fret;
	}
	#endif

/************* log-likelihood ***********/	/************* log-likelihood ***********/
double func( double *x)	double func( double *x)
Line 1690 double func( double *x)	Line 2164 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]);*/
/*for(i=1;i<imx;i++)	/*for(i=1;i<imx;i++)
printf(" %d\n",s[4][i]);	printf(" %d\n",s[4][i]);
*/	*/

	++countcallfunc;

cov[1]=1.;	cov[1]=1.;

for(k=1; k<=nlstate; k++) ll[k]=0.;	for(k=1; k<=nlstate; k++) ll[k]=0.;
Line 1708 double func( double *x)	Line 2186 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 1721 double func( double *x)	Line 2199 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 1775 double func( double *x)	Line 2256 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 1807 double func( double *x)	Line 2307 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 1820 double func( double *x)	Line 2324 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 1841 double func( double *x)	Line 2348 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 1850 double func( double *x)	Line 2357 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 1871 double func( double *x)	Line 2381 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 1880 double func( double *x)	Line 2390 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 1906 double func( double *x)	Line 2419 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 1915 double func( double *x)	Line 2428 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 1953 double funcone( double *x)	Line 2469 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 1964 double funcone( double *x)	Line 2481 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 1973 double funcone( double *x)	Line 2490 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 2077 void likelione(FILE *ficres,double p[],	Line 2598 void likelione(FILE *ficres,double p[],

void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))	void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))
{	{
int i,j, iter;	int i,j, iter=0;
double **xi;	double **xi;
double fret;	double fret;
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
/* char filerespow[FILENAMELENGTH];*/	/* char filerespow[FILENAMELENGTH];*/

	#ifdef NLOPT
	int creturn;
	nlopt_opt opt;
	/* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds \/ /
	double *lb;
	double minf; /* the minimum objective value, upon return */
	double * p1; /* Shifted parameters from 0 instead of 1 */
	myfunc_data dinst, *d = &dinst;
	#endif


xi=matrix(1,npar,1,npar);	xi=matrix(1,npar,1,npar);
for (i=1;i<=npar;i++)	for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++)	for (j=1;j<=npar;j++)
Line 2098 void mlikeli(FILE *ficres,double p[], in	Line 2631 void mlikeli(FILE *ficres,double p[], in
for(j=1;j<=nlstate+ndeath;j++)	for(j=1;j<=nlstate+ndeath;j++)
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
fprintf(ficrespow,"\n");	fprintf(ficrespow,"\n");
	#ifdef POWELL
powell(p,xi,npar,ftol,&iter,&fret,func);	powell(p,xi,npar,ftol,&iter,&fret,func);
	#endif

	#ifdef NLOPT
	#ifdef NEWUOA
	opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
	#else
	opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
	#endif
	lb=vector(0,npar-1);
	for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
	nlopt_set_lower_bounds(opt, lb);
	nlopt_set_initial_step1(opt, 0.1);

	p1= (p+1); /* p (p+1)@8 and p (p1)@8 are equal p1[0]=p[1] */
	d->function = func;
	printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
	nlopt_set_min_objective(opt, myfunc, d);
	nlopt_set_xtol_rel(opt, ftol);
	if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
	printf("nlopt failed! %d\n",creturn);
	}
	else {
	printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
	printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
	iter=1; /* not equal */
	}
	nlopt_destroy(opt);
	#endif
free_matrix(xi,1,npar,1,npar);	free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);	fclose(ficrespow);
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,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 = %d, -2 Log likelihood = %.12f \n",iter,func(p));	fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));	fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));

}	}

Line 2114 void hesscov(double **matcov, double p[]	Line 2674 void hesscov(double **matcov, double p[]
{	{
double a,y,*x,pd;	double a,y,*x,pd;
double **hess;	double **hess;
int i, j,jk;	int i, j;
int *indx;	int *indx;

double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);	double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
Line 2248 double hessii(double x[], double delta,	Line 2808 double hessii(double x[], double delta,
k=kmax;	k=kmax;
}	}
else if((k1 >khi/nkhif) \|\| (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */	else if((k1 >khi/nkhif) \|\| (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
k=kmax; l=lmax*10.;	k=kmax; l=lmax*10;
}	}
else if((k1 >khi/nkhi) \|\| (k2 >khi/nkhi)){	else if((k1 >khi/nkhi) \|\| (k2 >khi/nkhi)){
delts=delt;	delts=delt;
Line 2263 double hessii(double x[], double delta,	Line 2823 double hessii(double x[], double delta,
double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)	double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
{	{
int i;	int i;
int l=1, l1, lmax=20;	int l=1, lmax=20;
double k1,k2,k3,k4,res,fx;	double k1,k2,k3,k4,res,fx;
double p2[MAXPARM+1];	double p2[MAXPARM+1];
int k;	int k;
Line 2371 void lubksb(double *a, int n, int indx	Line 2931 void lubksb(double *a, int n, int indx

void pstamp(FILE *fichier)	void pstamp(FILE *fichier)
{	{
fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);	fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
}	}

/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, char strstart[])	void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, char strstart[])
{ /* Some frequencies */	{ /* Some frequencies */

int i, m, jk, k1,i1, j1, bool, z1,j;	int i, m, jk, j1, bool, z1,j;
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
Line 2402 void freqsummary(char fileres[], int ia	Line 2962 void freqsummary(char fileres[], int ia

first=1;	first=1;

/* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */	/* for(k1=1; k1<=j ; k1++){ / / Loop on covariates */
/* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */	/* for(i1=1; i1<=ncodemax[k1];i1++){ / / Now it is 2 */
/* j1++;	/* j1++; */
*/
for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){	for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
Line 2424 void freqsummary(char fileres[], int ia	Line 2983 void freqsummary(char fileres[], int ia
bool=1;	bool=1;
if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
/* Tests if the value of each of the covariates of i is equal to filter j1 */	/* Tests if the value of each of the covariates of i is equal to filter j1 */
bool=0;	bool=0;
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/	j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
}	}
}	}

Line 2459 void freqsummary(char fileres[], int ia	Line 3018 void freqsummary(char fileres[], int ia
pstamp(ficresp);	pstamp(ficresp);
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresp, "**********\n#");	fprintf(ficresp, "**********\n#");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "**********\n#");	fprintf(ficlog, "**********\n#");
}	}
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 2559 void prevalence(double ***probs, double	Line 3118 void prevalence(double ***probs, double
We still use firstpass and lastpass as another selection.	We still use firstpass and lastpass as another selection.
*/	*/

int i, m, jk, k1, i1, j1, bool, z1,j;	int i, m, jk, j1, bool, z1,j;
double **freq; / Frequencies */
double pp, *prop;	double **prop;
double pos,posprop;	double posprop;
double y2; /* in fractional years */	double y2; /* in fractional years */
int iagemin, iagemax;	int iagemin, iagemax;
int first; /** to stop verbosity which is redirected to log file */	int first; /** to stop verbosity which is redirected to log file */
Line 2590 void prevalence(double ***probs, double	Line 3149 void prevalence(double ***probs, double
bool=1;	bool=1;
if (cptcovn>0) {	if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
bool=0;	bool=0;
}	}
if (bool==1) {	if (bool==1) {
Line 2653 void concatwav(int wav[], int **dh, int	Line 3212 void concatwav(int wav[], int **dh, int
int j, k=0,jk, ju, jl;	int j, k=0,jk, ju, jl;
double sum=0.;	double sum=0.;
first=0;	first=0;
jmin=1e+5;	jmin=100000;
jmax=-1;	jmax=-1;
jmean=0.;	jmean=0.;
for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
Line 2782 void tricode(int Tvar, int *nbcode, in	Line 3341 void tricode(int Tvar, int *nbcode, in
{	{
/*< Uses cptcovn+2cptcovprod as the number of covariates */	/*< Uses cptcovn+2cptcovprod as the number of covariates */
/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1	/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
/* Boring subroutine which should only output nbcode[Tvar[j]][k]	* Boring subroutine which should only output nbcode[Tvar[j]][k]
* Tvar[5] in V2+V1+V3age+V2V4 is 2 (V2)	* Tvar[5] in V2+V1+V3age+V2V4 is 2 (V2)
/* nbcode[Tvar[j]][1]=	* nbcode[Tvar[j]][1]=
*/	*/

int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;	int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
Line 2795 void tricode(int Tvar, int *nbcode, in	Line 3354 void tricode(int Tvar, int *nbcode, in

cptcoveff=0;	cptcoveff=0;

for (k=-1; k < maxncov; k++) Ndum[k]=0;
for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */	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 (k=-1; k < maxncov; k++) Ndum[k]=0;
	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
modality of this covariate Vj*/	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 2822 void tricode(int Tvar, int *nbcode, in	Line 3381 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 i */
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);
	fprintf(ficlog," 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 (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1// For each value k of the modality of model-cov j */
printf("Frequencies of covariates %d 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], k, Ndum[k]);
if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */	fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */	if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
	if( k != -1){
	ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered excluding
	undefined. Usually 2: 0 and 1. */
	}
	ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
	covariate for which somebody answered including
	undefined. Usually 3: -1, 0 and 1. */
}	}
/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for	/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */	historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
} /* 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;
nbcode[Tvar[j]][3]=2;	nbcode[Tvar[j]][3]=2;
	To be continued (not working yet).
*/	*/
ij=1; /* ij is similar to i but can jumps over null modalities */	ij=0; /* ij is similar to i but can jump over null modalities */
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */	for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
/recode from 0 /	break;
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.	ij++;
k is a modality. If we have model=V1+V1*sex	nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */	cptcode = ij; /* New max modality for covar j */
ij++;	} /* end of loop on modality i=-1 to 1 or more */
}
if (ij > ncodemax[j]) break;	/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /
} /* end of loop on */	/* /\recode from 0 \/ */
} /* end of loop on modality */	/* k is a modality. If we have model=V1+V1sex /
	/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
	/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /
	/* } */
	/* /\* cptcode = ij; \/ /\ New max modality for covar j \/ /
	/* if (ij > ncodemax[j]) { */
	/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
	/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
	/* break; */
	/* } */
	/* } /\* end of loop on modality k \/ /
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/	} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/

for (k=-1; k< maxncov; k++) Ndum[k]=0;	for (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=0;
for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /	for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /
/printf("Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("Ndum[%d]=%d\n",i, Ndum[i]);/
if((Ndum[i]!=0) && (i<=ncovcol)){	if((Ndum[i]!=0) && (i<=ncovcol)){
	ij++;
/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/
Tvaraff[ij]=i; /For printing (unclear) /	Tvaraff[ij]=i; /For printing (unclear) /
ij++;	}else{
}else	/* Tvaraff[ij]=0; */
Tvaraff[ij]=0;	}
}	}
ij--;	/* ij--; */
cptcoveff=ij; /Number of total covariates/	cptcoveff=ij; /Number of total covariates/

}	}
Line 2893 void evsij(double ***eij, double x[], in	Line 3473 void evsij(double ***eij, double x[], in

{	{
/* Health expectancies, no variances */	/* Health expectancies, no variances */
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;	int i, j, nhstepm, hstepm, h, nstepm;
int nhstepma, nstepma; /* Decreasing with age */	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
double ***p3mat;	double ***p3mat;
Line 3212 void varevsij(char optionfilefiname[], d	Line 3792 void varevsij(char optionfilefiname[], d
/* Variance of health expectancies */	/* Variance of health expectancies */
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/
/* double *newm;/	/* double *newm;/
	/* int movingaverage(double *probs, double bage,double fage, double mobaverage, int mobilav)/

	int movingaverage();
double dnewm,doldm;	double dnewm,doldm;
double dnewmp,doldmp;	double dnewmp,doldmp;
int i, j, nhstepm, hstepm, h, nstepm ;	int i, j, nhstepm, hstepm, h, nstepm ;
int k, cptcode;	int k;
double *xp;	double *xp;
double gp, gm; /* for var eij */	double gp, gm; /* for var eij */
double *gradg, trgradg; /for var eij */	double *gradg, trgradg; /for var eij */
Line 3270 void varevsij(char optionfilefiname[], d	Line 3853 void varevsij(char optionfilefiname[], d
}	}
fprintf(ficresprobmorprev,"\n");	fprintf(ficresprobmorprev,"\n");
fprintf(ficgp,"\n# Routine varevsij");	fprintf(ficgp,"\n# Routine varevsij");
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/	fprintf(ficgp,"\nunset title \n");
	/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */	/* } */
Line 3482 void varevsij(char optionfilefiname[], d	Line 4066 void varevsij(char optionfilefiname[], d
free_vector(gmp,nlstate+1,nlstate+ndeath);	free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);	free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/	free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");	/* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
	fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */	/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");	fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
	fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /	/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));	fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));	fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);	fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);	/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
*/	*/
/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */	/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);	fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,nlstate);	free_matrix(doldm,1,nlstate,1,nlstate);
Line 3515 void varprevlim(char fileres[], double *	Line 4101 void varprevlim(char fileres[], double *
{	{
/* Variance of prevalence limit */	/* Variance of prevalence limit */
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/
double **newm;
double dnewm,doldm;	double dnewm,doldm;
int i, j, nhstepm, hstepm;	int i, j, nhstepm, hstepm;
int k, cptcode;
double *xp;	double *xp;
double gp, gm;	double gp, gm;
double gradg, trgradg;	double gradg, trgradg;
Line 3597 void varprevlim(char fileres[], double *	Line 4182 void varprevlim(char fileres[], double *
/********** Variance of one-step probabilities ****************/	/********** Variance of one-step probabilities ****************/
void varprob(char optionfilefiname[], double *matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int Tvar, int *nbcode, int ncodemax, char strstart[])	void varprob(char optionfilefiname[], double *matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int Tvar, int *nbcode, int ncodemax, char strstart[])
{	{
int i, j=0, i1, k1, l1, t, tj;	int i, j=0, k1, l1, tj;
int k2, l2, j1, z1;	int k2, l2, j1, z1;
int k=0,l, cptcode;	int k=0, l;
int first=1, first1, first2;	int first=1, first1, first2;
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;	double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
double dnewm,doldm;	double dnewm,doldm;
Line 3607 void varprob(char optionfilefiname[], do	Line 4192 void varprob(char optionfilefiname[], do
double gp, gm;	double gp, gm;
double gradg, trgradg;	double gradg, trgradg;
double **mu;	double **mu;
double age,agelim, cov[NCOVMAX+1];	double age, cov[NCOVMAX+1];
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */	double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
int theta;	int theta;
char fileresprob[FILENAMELENGTH];	char fileresprob[FILENAMELENGTH];
Line 3670 void varprob(char optionfilefiname[], do	Line 4255 void varprob(char optionfilefiname[], do
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");	fprintf(fichtm,"\n");

fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);	fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\	fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
file %s<br>\n",optionfilehtmcov);	fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
and drawn. It helps understanding how is the covariance between two incidences.\	and drawn. It helps understanding how is the covariance between two incidences.\
They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");	They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \	fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
Line 3694 To be simple, these graphs help to under	Line 4278 To be simple, these graphs help to under
/j1++;/	/j1++;/
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");	fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprob, "**********\n#\n");	fprintf(ficresprob, "**********\n#\n");
fprintf(ficresprobcov, "\n#********** Variable ");	fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcov, "**********\n#\n");	fprintf(ficresprobcov, "**********\n#\n");

fprintf(ficgp, "\n#********** Variable ");	fprintf(ficgp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficgp, "**********\n#\n");	fprintf(ficgp, "**********\n#\n");


fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");	fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");

fprintf(ficresprobcor, "\n#********** Variable ");	fprintf(ficresprobcor, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcor, "**********\n#");	fprintf(ficresprobcor, "**********\n#");
}	}

Line 3720 To be simple, these graphs help to under	Line 4304 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]][codtabm(j1,k)];
	/cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(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]]][codtabm(ij,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]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];


for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
Line 3878 To be simple, these graphs help to under	Line 4466 To be simple, these graphs help to under
/* mu2+ v21lc1cost + v22lc2sin(t) */	/* mu2+ v21lc1cost + v22lc2sin(t) */
if(first==1){	if(first==1){
first=0;	first=0;
	fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small size 320, 240");	fprintf(ficgp,"\nset ter svg size 640, 480");
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\	fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s%d%1d%1d-%1d%1d.png\">\	:<a href=\"%s%d%1d%1d-%1d%1d.svg\">\
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\	%s%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\	subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);	fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
Line 3905 To be simple, these graphs help to under	Line 4494 To be simple, these graphs help to under
}/* if first */	}/* if first */
} /* age mod 5 */	} /* age mod 5 */
} /* end loop age */	} /* end loop age */
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);	fprintf(ficgp,"\nset out;\nset out \"%s%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
first=1;	first=1;
} /l12 /	} /l12 /
} /* k12 */	} /* k12 */
} /l1 /	} /l1 /
}/* k1 */	}/* k1 */
/* } /* loop covariates */	/* } / / loop covariates */
}	}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);	free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);	free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
Line 3962 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4551 fprintf(fichtm," \n<ul><li><b>Graphs</b>

jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)	for (cpt=1; cpt<=cptcoveff;cpt++){
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
	printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
	}
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.svg\">%s%d_1.svg</a><br> \
<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_1.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \	before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.svg\">%s%d_2.svg</a><br> \
<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_2.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Period (stable) prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \	fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
<img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);	<img src=\"%s%d_%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);	<img src=\"%s%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}	}
} /* end i1 */	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");


fprintf(fichtm,"\	fprintf(fichtm,"\
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\	\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
	- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
	But because parameters are usually highly correlated (a higher incidence of disability \
	and a higher incidence of recovery can give very close observed transition) it might \
	be very useful to look not only at linear confidence intervals estimated from the \
	variances but at the covariance matrix. And instead of looking at the estimated coefficients \
	(parameters) of the logistic regression, it might be more meaningful to visualize the \
	covariance matrix of the one-step probabilities. \
	See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);

fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));	subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 4036 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4634 fprintf(fichtm," \n<ul><li><b>Graphs</b>

jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)	for (cpt=1; cpt<=cptcoveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\	prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
<img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);	<img src=\"%s%d_%d.svg\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\	true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\	drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: %s%d.png<br>\	observed and cahotic prevalences: %s%d.svg<br>\
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);	<img src=\"%s%d.svg\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");
fflush(fichtm);	fflush(fichtm);
Line 4065 true period expectancies (those weighted	Line 4663 true period expectancies (those weighted
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){	void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
int ng=0;	int ng=0;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
Line 4083 void printinggnuplot(char fileres[], cha	Line 4681 void printinggnuplot(char fileres[], cha
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);	fprintf(ficgp,"\n#set out \"v%s%d_%d.svg\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\	fprintf(ficgp,"set xlabel \"Age\" \n\
set ylabel \"Probability\" \n\	set ylabel \"Probability\" \n\
set ter png small size 320, 240\n\	set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
}	}
Line 4110 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4708 plot [%.f:%.f] \"%s\" every :::%d::%d u
/2 eme/	/2 eme/
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);	fprintf(ficgp,"\nset out \"%s%d.svg\" \n",subdirf2(optionfilefiname,"e"),k1);
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);

for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 0,");	fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
else fprintf(ficgp,"\" t\"\" w l lt 0,");	else fprintf(ficgp,"\" t\"\" w l lt 0,");
Line 4144 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4742 plot [%.f:%.f] \"%s\" every :::%d::%d u
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.svg\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small size 320, 240\n\	fprintf(ficgp,"set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
Line 4169 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4767 plot [%.f:%.f] \"%s\" every :::%d::%d u
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
k=3;	k=3;
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter png small size 320, 240\n\	set ter svg size 640, 480\n\
unset log y\n\	unset log y\n\
plot [%.f:%.f] ", ageminpar, agemaxpar);	plot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
Line 4190 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4788 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 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,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);	fprintf(ficgp,"# jk=%d\n",jk);
	fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \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");
else	else
fprintf(ficgp,"\nset title \"Probability\"\n");	fprintf(ficgp,"\nunset title \n");
fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);	fprintf(ficgp,"\nset ter svg size 640, 480\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;	i=1;
for(k2=1; k2<=nlstate; k2++) {	for(k2=1; k2<=nlstate; k2++) {
k3=i;	k3=i;
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 \/ /	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
/* /\fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\/ */	if(ij <=cptcovage) { /* Bug valgrind */
/* ij++; */	if((j-2)==Tage[ij]) { /* Bug valgrind */
/* } */	fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
/* else */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	ij++;
	}
	}
	else
	fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(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(ij <=cptcovage) { /* Bug valgrind */
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); /	if((j-2)==Tage[ij]) { /* Bug valgrind */
/* ij++; */	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
/* } */	/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /
/* else */	ij++;
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	}
	}
	else
	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 4251 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 4888 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* end k2 */	} /* end k2 */
} /* end jk */	} /* end jk */
} /* end ng */	} /* end ng */
avoid:	/* avoid: */
fflush(ficgp);	fflush(ficgp);
} /* end gnuplot */	} /* end gnuplot */

Line 4299 int movingaverage(double ***probs, doubl	Line 4936 int movingaverage(double ***probs, doubl


/************ Forecasting ****************/	/************ Forecasting ****************/
prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){	void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
/* proj1, year, month, day of starting projection	/* proj1, year, month, day of starting projection
agemin, agemax range of age	agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed	dateprev1 dateprev2 range of dates during which prevalence is computed
anproj2 year of en of projection (same day and month as proj1).	anproj2 year of en of projection (same day and month as proj1).
*/	*/
int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;	int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
int *popage;
double agec; /* generic age */	double agec; /* generic age */
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double popeffectif,popcount;	double popeffectif,popcount;
Line 4367 prevforecast(char fileres[], double anpr	Line 5003 prevforecast(char fileres[], double anpr
k=k+1;	k=k+1;
fprintf(ficresf,"\n#******");	fprintf(ficresf,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficresf,"******\n");	fprintf(ficresf,"******\n");
fprintf(ficresf,"# Covariate valuofcovar yearproj age");	fprintf(ficresf,"# Covariate valuofcovar yearproj age");
Line 4391 prevforecast(char fileres[], double anpr	Line 5027 prevforecast(char fileres[], double anpr
if (hhstepm/YEARMstepm ==yearp) {	if (hhstepm/YEARMstepm ==yearp) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
Line 4423 prevforecast(char fileres[], double anpr	Line 5059 prevforecast(char fileres[], double anpr
}	}

/************ Forecasting *not tested NB***********/	/************ Forecasting *not tested NB***********/
populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){	void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){

int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;	int *popage;
Line 4489 populforecast(char fileres[], double anp	Line 5125 populforecast(char fileres[], double anp
k=k+1;	k=k+1;
fprintf(ficrespop,"\n#******");	fprintf(ficrespop,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficrespop,"******\n");	fprintf(ficrespop,"******\n");
fprintf(ficrespop,"# Age");	fprintf(ficrespop,"# Age");
Line 4600 void prwizard(int ncovmodel, int nlstate	Line 5236 void prwizard(int ncovmodel, int nlstate

/* Wizard to print covariance matrix template */	/* Wizard to print covariance matrix template */

char ca[32], cb[32], cc[32];	char ca[32], cb[32];
int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;	int i,j, k, li, lj, lk, ll, jj, npar, itimes;
int numlinepar;	int numlinepar;

printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
Line 4804 void printinghtmlmort(char fileres[], ch	Line 5440 void printinghtmlmort(char fileres[], ch
fprintf(fichtm," mu(age) =%lfexp(%lf(age-%d)) per year<br><br>",p[1],p[2],agegomp);	fprintf(fichtm," mu(age) =%lfexp(%lf(age-%d)) per year<br><br>",p[1],p[2],agegomp);
for (i=1;i<=2;i++)	for (i=1;i<=2;i++)
fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");	fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");

fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");	fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
Line 4822 fprintf(fichtm,"<ul><li><h4>Life table</	Line 5458 fprintf(fichtm,"<ul><li><h4>Life table</
void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){	void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
int ng;	int ng;


Line 4833 void printinggnuplotmort(char fileres[],	Line 5469 void printinggnuplotmort(char fileres[],

strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
fprintf(ficgp,"set out \"graphmort.png\"\n ");	fprintf(ficgp,"set out \"graphmort.svg\"\n ");
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");	fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");	fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
/* fprintf(ficgp, "set size 0.65,0.65\n"); */	/* fprintf(ficgp, "set size 0.65,0.65\n"); */
fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);	fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);

Line 4847 int readdata(char datafile[], int firsto	Line 5483 int readdata(char datafile[], int firsto
/-------- data file ----------/	/-------- data file ----------/
FILE *fic;	FILE *fic;
char dummy[]=" ";	char dummy[]=" ";
int i, j, n;	int i=0, j=0, n=0;
int linei, month, year,iout;	int linei, month, year,iout;
char line[MAXLINE], linetmp[MAXLINE];	char line[MAXLINE], linetmp[MAXLINE];
char stra[80], strb[80];	char stra[MAXLINE], strb[MAXLINE];
char *stratrunc;	char *stratrunc;
int lstra;	int lstra;


if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem while opening datafile: %s\n", datafile);return 1;	printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;	fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
}	}

i=1;	i=1;
Line 4878 int readdata(char datafile[], int firsto	Line 5514 int readdata(char datafile[], int firsto
continue;	continue;
}	}
trimbb(linetmp,line); /* Trims multiple blanks in line */	trimbb(linetmp,line); /* Trims multiple blanks in line */
for (j=0; line[j]!='\0';j++){	strcpy(line, linetmp);
line[j]=linetmp[j];
}


for (j=maxwav;j>=1;j--){	for (j=maxwav;j>=1;j--){
Line 4901 int readdata(char datafile[], int firsto	Line 5535 int readdata(char datafile[], int firsto

strcpy(line,stra);	strcpy(line,stra);
cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){	if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}	}
else if(iout=sscanf(strb,"%s.",dummy) != 0){	else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
Line 4917 int readdata(char datafile[], int firsto	Line 5551 int readdata(char datafile[], int firsto
} /* ENd Waves */	} /* ENd Waves */

cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){	if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}	}
else if(iout=sscanf(strb,"%s.",dummy) != 0){	else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
Line 4932 int readdata(char datafile[], int firsto	Line 5566 int readdata(char datafile[], int firsto
strcpy(line,stra);	strcpy(line,stra);

cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){	if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
}	}
else if(iout=sscanf(strb,"%s.", dummy) != 0){	else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
Line 5019 int readdata(char datafile[], int firsto	Line 5653 int readdata(char datafile[], int firsto
fclose(fic);	fclose(fic);

return (0);	return (0);
endread:	/* endread: */
printf("Exiting readdata: ");	printf("Exiting readdata: ");
fclose(fic);	fclose(fic);
return (1);	return (1);
Line 5032 void removespace(char *str) {	Line 5666 void removespace(char *str) {
do	do
while (*p2 == ' ')	while (*p2 == ' ')
p2++;	p2++;
while (p1++ = p2++);	while (p1++ == p2++);
}	}

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 5050 int decodemodel ( char model[], int last	Line 5685 int decodemodel ( char model[], int last
*/	*/
{	{
int i, j, k, ks;	int i, j, k, ks;
int i1, 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 5076 int decodemodel ( char model[], int last	Line 5703 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]][codtabm(ij,Tvar[k])]; */
	/* } */
	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]cov[2]; /
	/*
	* Treating invertedly V2+V1+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 5199 int decodemodel ( char model[], int last	Line 5862 int decodemodel ( char model[], int last


return (0); /* with covar[new additional covariate if product] and Tage if age */	return (0); /* with covar[new additional covariate if product] and Tage if age */
endread:	/endread:/
printf("Exiting decodemodel: ");	printf("Exiting decodemodel: ");
return (1);	return (1);
}	}

calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )	int calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )
{	{
int i, m;	int i, m;

Line 5215 calandcheckages(int imx, int maxwav, dou	Line 5878 calandcheckages(int imx, int maxwav, dou
s[m][i]=-1;	s[m][i]=-1;
}	}
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){	if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
*nberr++;	nberr = nberr + 1;
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);	printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
s[m][i]=-1;	s[m][i]=-1;
}	}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){	if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
*nberr++;	(*nberr)++;
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);	printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);	fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */	s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
Line 5234 calandcheckages(int imx, int maxwav, dou	Line 5897 calandcheckages(int imx, int maxwav, dou
for(m=firstpass; (m<= lastpass); m++){	for(m=firstpass; (m<= lastpass); m++){
if(s[m][i] >0 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5){	if(s[m][i] >0 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5){
if (s[m][i] >= nlstate+1) {	if (s[m][i] >= nlstate+1) {
if(agedc[i]>0)	if(agedc[i]>0){
if((int)moisdc[i]!=99 && (int)andc[i]!=9999)	if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
agev[m][i]=agedc[i];	agev[m][i]=agedc[i];
/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/	/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/
else {	}else {
if ((int)andc[i]!=9999){	if ((int)andc[i]!=9999){
nbwarn++;	nbwarn++;
printf("Warning negative age at death: %ld line:%d\n",num[i],i);	printf("Warning negative age at death: %ld line:%d\n",num[i],i);
Line 5246 calandcheckages(int imx, int maxwav, dou	Line 5909 calandcheckages(int imx, int maxwav, dou
agev[m][i]=-1;	agev[m][i]=-1;
}	}
}	}
	} /* agedc > 0 */
}	}
else if(s[m][i] !=9){ /* Standard case, age in fractional	else if(s[m][i] !=9){ /* Standard case, age in fractional
years but with the precision of a month */	years but with the precision of a month */
Line 5276 calandcheckages(int imx, int maxwav, dou	Line 5940 calandcheckages(int imx, int maxwav, dou
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=firstpass; (m<=lastpass); m++){	for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
*nberr++;	(*nberr)++;
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
return 1;	return 1;
Line 5296 calandcheckages(int imx, int maxwav, dou	Line 5960 calandcheckages(int imx, int maxwav, dou
fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);	fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);

return (0);	return (0);
endread:	/* endread:*/
printf("Exiting calandcheckages: ");	printf("Exiting calandcheckages: ");
return (1);	return (1);
}	}

	#if defined(_MSC_VER)
	/printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);/
	/fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);/
	//#include "stdafx.h"
	//#include <stdio.h>
	//#include <tchar.h>
	//#include <windows.h>
	//#include <iostream>
	typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);

	LPFN_ISWOW64PROCESS fnIsWow64Process;

	BOOL IsWow64()
	{
	BOOL bIsWow64 = FALSE;

	//typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
	// (HANDLE, PBOOL);

	//LPFN_ISWOW64PROCESS fnIsWow64Process;

	HMODULE module = GetModuleHandle(_T("kernel32"));
	const char funcName[] = "IsWow64Process";
	fnIsWow64Process = (LPFN_ISWOW64PROCESS)
	GetProcAddress(module, funcName);

	if (NULL != fnIsWow64Process)
	{
	if (!fnIsWow64Process(GetCurrentProcess(),
	&bIsWow64))
	//throw std::exception("Unknown error");
	printf("Unknown error\n");
	}
	return bIsWow64 != FALSE;
	}
	#endif

	void syscompilerinfo(int logged)
	{
	/* #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(__GNUC__)
	struct utsname sysInfo; /* For Intel on Linux and OS/X */
	#endif
	#elif defined(__GNUC__)
	#ifndef __APPLE__
	#include <gnu/libc-version.h> /* Only on gnu */
	#endif
	struct utsname sysInfo;
	int cross = CROSS;
	if (cross){
	printf("Cross-");
	if(logged) fprintf(ficlog, "Cross-");
	}
	#endif

	#include <stdint.h>

	printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
	#if defined(__clang__)
	printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
	#endif
	#if defined(__ICC) \|\| defined(__INTEL_COMPILER)
	printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
	#endif
	#if defined(__GNUC__) \|\| defined(__GNUG__)
	printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
	#endif
	#if defined(__HP_cc) \|\| defined(__HP_aCC)
	printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
	#endif
	#if defined(__IBMC__) \|\| defined(__IBMCPP__)
	printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
	#endif
	#if defined(_MSC_VER)
	printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
	#endif
	#if defined(__PGI)
	printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
	#endif
	#if defined(__SUNPRO_C) \|\| defined(__SUNPRO_CC)
	printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
	#endif
	printf(" for "); if (logged) fprintf(ficlog, " for ");

	// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
	#ifdef _WIN32 // note the underscore: without it, it's not msdn official!
	// Windows (x64 and x86)
	printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
	#elif __unix__ // all unices, not all compilers
	// Unix
	printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
	#elif __linux__
	// linux
	printf("linux ");if(logged) fprintf(ficlog,"linux ");
	#elif __APPLE__
	// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
	printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
	#endif

	/* __MINGW32__ */
	/* __CYGWIN__ */
	/* __MINGW64__ */
	// http://msdn.microsoft.com/en-us/library/b0084kay.aspx
	/* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
	/* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
	/* _WIN64 // Defined for applications for Win64. */
	/* _M_X64 // Defined for compilations that target x64 processors. */
	/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */

	#if UINTPTR_MAX == 0xffffffff
	printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
	#elif UINTPTR_MAX == 0xffffffffffffffff
	printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
	#else
	printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
	#endif

	#if defined(__GNUC__)
	# if defined(__GNUC_PATCHLEVEL__)
	# define __GNUC_VERSION__ (__GNUC__ * 10000 \
	+ __GNUC_MINOR__ * 100 \
	+ __GNUC_PATCHLEVEL__)
	# else
	# define __GNUC_VERSION__ (__GNUC__ * 10000 \
	+ __GNUC_MINOR__ * 100)
	# endif
	printf(" using GNU C version %d.\n", __GNUC_VERSION__);
	if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);

	if (uname(&sysInfo) != -1) {
	printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
	if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
	}
	else
	perror("uname() error");
	//#ifndef __INTEL_COMPILER
	#if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
	printf("GNU libc version: %s\n", gnu_get_libc_version());
	if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
	#endif
	#endif

	// void main()
	// {
	#if defined(_MSC_VER)
	if (IsWow64()){
	printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
	if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
	}
	else{
	printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
	if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
	}
	// printf("\nPress Enter to continue...");
	// getchar();
	// }

	#endif


	}

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

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

	for (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]][codtabm(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]][codtabm(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 5316 int main(int argc, char *argv[])	Line 6315 int main(int argc, char *argv[])
double ssval;	double ssval;
#endif	#endif
int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);	int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);
int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;	int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
int linei, month, year,iout;
int jj, ll, li, lj, lk, imk;	int jj, ll, li, lj, lk;
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
	int num_filled;
int itimes;	int itimes;
int NDIM=2;	int NDIM=2;
int vpopbased=0;	int vpopbased=0;

char ca[32], cb[32], cc[32];	char ca[32], cb[32];
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
struct stat info;	struct stat info;
double agedeb, agefin,hf;	double agedeb=0.;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

double fret;	double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
double **xi,tmp,delta;

double dum; /* Dummy variable */	double fret;
	double dum=0.; /* Dummy variable */
double ***p3mat;	double ***p3mat;
double ***mobaverage;	double ***mobaverage;
int *indx;
char line[MAXLINE], linepar[MAXLINE];	char line[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];

	char model[MAXLINE], modeltemp[MAXLINE];
char pathr[MAXLINE], pathimach[MAXLINE];	char pathr[MAXLINE], pathimach[MAXLINE];
char *bp, tok, val; / pathtot */	char tok, val; /* pathtot */
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */	int c, h , cpt, c2;
int c, h , cpt,l;	int jl=0;
int ju,jl, mi;	int i1, j1, jk, stepsize=0;
int i1,j1, jk,aa,bb, stepsize, ij;	int count=0;
int jnais,jdc,jint4,jint1,jint2,jint3,*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, fage, 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 5367 int main(int argc, char *argv[])	Line 6369 int main(int argc, char *argv[])
double *eij, *vareij;	double *eij, *vareij;
double *varpl; / Variances of prevalence limits by age */	double *varpl; / Variances of prevalence limits by age */
double *epj, vepp;	double *epj, vepp;
double kk1, kk2;
double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;	double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
double **ximort;	double **ximort;
char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";	char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
int *dcwave;	int *dcwave;

char z[1]="c", occ;	char z[1]="c";

/char strt;*/	/char strt;*/
char strtend[80];	char strtend[80];

long total_usecs;

/* setlocale (LC_ALL, ""); */	/* setlocale (LC_ALL, ""); */
/* bindtextdomain (PACKAGE, LOCALEDIR); */	/* bindtextdomain (PACKAGE, LOCALEDIR); */
/* textdomain (PACKAGE); */	/* textdomain (PACKAGE); */
Line 5413 int main(int argc, char *argv[])	Line 6414 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
printf("\n%s\n%s",version,fullversion);	syscompilerinfo(0);
	printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
if(argc <=1){	if(argc <=1){
printf("\nEnter the parameter file name: ");	printf("\nEnter the parameter file name: ");
fgets(pathr,FILENAMELENGTH,stdin);	fgets(pathr,FILENAMELENGTH,stdin);
Line 5449 int main(int argc, char *argv[])	Line 6454 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){
printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);	printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
/* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */	/* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
/* fclose(ficlog); */	/* fclose(ficlog); */
/* exit(1); */	/* exit(1); */
Line 5466 int main(int argc, char *argv[])	Line 6476 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 5474 int main(int argc, char *argv[])	Line 6484 int main(int argc, char *argv[])
goto end;	goto end;
}	}
fprintf(ficlog,"Log filename:%s\n",filelog);	fprintf(ficlog,"Log filename:%s\n",filelog);
fprintf(ficlog,"\n%s\n%s",version,fullversion);	fprintf(ficlog,"Version %s %s",version,fullversion);
fprintf(ficlog,"\nEnter the parameter file name: \n");	fprintf(ficlog,"\nEnter the parameter file name: \n");
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\	fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
path=%s \n\	path=%s \n\
Line 5482 int main(int argc, char *argv[])	Line 6492 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(1);

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);
fflush(ficlog);	fflush(ficlog);
Line 5493 int main(int argc, char *argv[])	Line 6505 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 5516 int main(int argc, char *argv[])	Line 6528 int main(int argc, char *argv[])

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
numlinepar=0;	numlinepar=0;
while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	/* First parameter line */
fgets(line, MAXLINE, ficpar);	while(fgets(line, MAXLINE, ficpar)) {
	/* If line starts with a # it is a comment */
	if (line[0] == '#') {
	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	continue;
	}else
	break;
	}
	if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
	title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
	if (num_filled != 5) {
	printf("Should be 5 parameters\n");
	}
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
fputs(line,ficparo);	}
fputs(line,ficlog);	/* Second parameter line */
	while(fgets(line, MAXLINE, ficpar)) {
	/* If line starts with a # it is a comment */
	if (line[0] == '#') {
	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	continue;
	}else
	break;
	}
	if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
	&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
	if (num_filled != 8) {
	printf("Not 8\n");
	}
	printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
}	}
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);	/* Third parameter line */
numlinepar++;	while(fgets(line, MAXLINE, ficpar)) {
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);	/* If line starts with a # it is a comment */
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 (line[0] == '#') {
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);	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	continue;
	}else
	break;
	}
	if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
	if (num_filled != 1) {
	printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
	model[0]='\0';
	goto end;
	}
	else{
	if (model[0]=='+'){
	for(i=1; i<=strlen(model);i++)
	modeltemp[i-1]=model[i];
	}
	strcpy(model,modeltemp);
	}
	/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
	}
	/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
	/* numlinepar=numlinepar+3; /\* In general \/ /
	/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
	if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the 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);
numlinepar++;	numlinepar++;
	if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
	z[0]=line[1];
	}
	/* printf("***line [1] = %c \n",line[1]); /
fputs(line, stdout);	fputs(line, stdout);
//puts(line);	//puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
Line 5550 int main(int argc, char *argv[])	Line 6637 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 5568 int main(int argc, char *argv[])	Line 6654 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 chose 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 chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
}	}
Line 5603 int main(int argc, char *argv[])	Line 6689 int main(int argc, char *argv[])
if(jj==i) continue;	if(jj==i) continue;
j++;	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) && (j1 != j)){	if ((i1 != i) \|\| (j1 != jj)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
It might be a problem of design; if ncovcol and the model are correct\n \	It might be a problem of design; if ncovcol and the model are correct\n \
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);	run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
Line 5611 run imach with mle=-1 to get a correct t	Line 6697 run imach with mle=-1 to get a correct t
}	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
if(mle==1)	if(mle==1)
printf("%1d%1d",i,j);	printf("%1d%1d",i,jj);
fprintf(ficlog,"%1d%1d",i,j);	fprintf(ficlog,"%1d%1d",i,jj);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar," %lf",&param[i][j][k]);	fscanf(ficpar," %lf",&param[i][j][k]);
if(mle==1){	if(mle==1){
Line 5650 run imach with mle=-1 to get a correct t	Line 6736 run imach with mle=-1 to get a correct t
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){	for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1-i)*(j1-j)!=0){	if ( (i1-i) * (j1-j) != 0){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
exit(1);	exit(1);
}	}
Line 5693 run imach with mle=-1 to get a correct t	Line 6779 run imach with mle=-1 to get a correct t
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=1; j <=npar; j++) matcov[i][j]=0.;	for(j=1; j <=npar; j++) matcov[i][j]=0.;

	/* Scans npar lines */
for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",str);	count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
	if(count != 3){
	printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
	This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
	fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
	This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
	exit(1);
	}else
if(mle==1)	if(mle==1)
printf("%s",str);	printf("%1d%1d%1d",i1,j1,jk);
fprintf(ficlog,"%s",str);	fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
fprintf(ficparo,"%s",str);	fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
for(j=1; j <=i; j++){	for(j=1; j <=i; j++){
fscanf(ficpar," %le",&matcov[i][j]);	fscanf(ficpar," %le",&matcov[i][j]);
if(mle==1){	if(mle==1){
Line 5714 run imach with mle=-1 to get a correct t	Line 6810 run imach with mle=-1 to get a correct t
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
	/* End of read covariance matrix npar lines */
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=i+1;j<=npar;j++)	for(j=i+1;j<=npar;j++)
matcov[i][j]=matcov[j][i];	matcov[i][j]=matcov[j][i];
Line 5736 run imach with mle=-1 to get a correct t	Line 6833 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 5752 run imach with mle=-1 to get a correct t	Line 6850 run imach with mle=-1 to get a correct t
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
	ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /

/* Reads data from file datafile */	/* Reads data from file datafile */
if (readdata(datafile, firstobs, lastobs, &imx)==1)	if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 5787 run imach with mle=-1 to get a correct t	Line 6886 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 5830 run imach with mle=-1 to get a correct t	Line 6932 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
codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2(k-1) */	V2+V1age, there are 3 covariates Tvar[2]=1 (V1)./
/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);/	/* 1 to ncodemax[j] is the maximum value of this jth covariate */

	/* codtab=imatrix(1,100,1,10);/ / codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2(k-1) */
	/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));/
	/* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
h=0;	h=0;


Line 5843 run imach with mle=-1 to get a correct t	Line 6949 run imach with mle=-1 to get a correct t

m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 /
h++;
if (h>m)
h=1;
/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1	/< 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 5861 run imach with mle=-1 to get a correct t	Line 6962 run imach with mle=-1 to get a correct t
* 6 2 1 2 1	* 6 2 1 2 1
* 7 i=4 1 2 2 1	* 7 i=4 1 2 2 1
* 8 2 2 2 1	* 8 2 2 2 1
* 9 i=5 1 i=3 1 i=2 1 1	* 9 i=5 1 i=3 1 i=2 1 2
* 10 2 1 1 1	* 10 2 1 1 2
* 11 i=6 1 2 1 1	* 11 i=6 1 2 1 2
* 12 2 2 1 1	* 12 2 2 1 2
* 13 i=7 1 i=4 1 2 1	* 13 i=7 1 i=4 1 2 2
* 14 2 1 2 1	* 14 2 1 2 2
* 15 i=8 1 2 2 1	* 15 i=8 1 2 2 2
* 16 2 2 2 1	* 16 2 2 2 2
*/	*/
codtab[h][k]=j;	for(h=1; h <=100 ;h++){
/codtab[h][Tvar[k]]=j;/	/* printf("h=%2d ", h); */
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);	/* for(k=1; k <=10; k++){ */
}	/* printf("k=%d %d ",k,codtabm(h,k)); */
}	/* codtab[h][k]=codtabm(h,k); */
}	/* } */
}	/* printf("\n"); */
	}
	/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate \/ /
	/* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 \/ /
	/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2\/ /
	/* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 \/ */
	/* h++; */
	/* if (h>m) */
	/* h=1; */
	/* codtab[h][k]=j; */
	/* /\* codtab[12][3]=1; \/ /
	/* /\codtab[h][Tvar[k]]=j;\/ */
	/* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); \/ /
	/* } */
	/* } */
	/* } */
	/* } */
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);	/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
codtab[1][2]=1;codtab[2][2]=2; */	codtab[1][2]=1;codtab[2][2]=2; */
/* for(i=1; i <=m ;i++){	/* for(i=1; i <=m ;i++){ */
for(k=1; k <=cptcovn; k++){	/* for(k=1; k <=cptcovn; k++){ */
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);	/* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
}	/* } */
printf("\n");	/* printf("\n"); */
}	/* } */
scanf("%d",i);*/	/* scanf("%d",i);*/

free_ivector(Ndum,-1,NCOVMAX);	free_ivector(Ndum,-1,NCOVMAX);



/------------ gnuplot -------------/	/* Initialisation of ----------- gnuplot -------------*/
strcpy(optionfilegnuplot,optionfilefiname);	strcpy(optionfilegnuplot,optionfilefiname);
if(mle==-3)	if(mle==-3)
strcat(optionfilegnuplot,"-mort");	strcat(optionfilegnuplot,"-mort");
Line 5907 run imach with mle=-1 to get a correct t	Line 7024 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 5949 Title=%s <br>Datafile=%s Firstpass=%d La	Line 7068 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 5972 Interval (in months) between two waves:	Line 7096 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 6019 Interval (in months) between two waves:	Line 7143 Interval (in months) between two waves:

#ifdef GSL	#ifdef GSL
printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");	printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
#elsedef	#else
printf("Powell\n"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
#endif	#endif
strcpy(filerespow,"pow-mort");	strcpy(filerespow,"pow-mort");
Line 6030 Interval (in months) between two waves:	Line 7154 Interval (in months) between two waves:
}	}
#ifdef GSL	#ifdef GSL
fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");	fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
#elsedef	#else
fprintf(ficrespow,"# Powell\n# iter -2*LL");	fprintf(ficrespow,"# Powell\n# iter -2*LL");
#endif	#endif
/* for (i=1;i<=nlstate;i++)	/* for (i=1;i<=nlstate;i++)
Line 6065 Interval (in months) between two waves:	Line 7189 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 6134 Interval (in months) between two waves:	Line 7258 Interval (in months) between two waves:
}	}

printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);	printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
for (i=1;i<=NDIM;i++)	for (i=1;i<=NDIM;i++) {
printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
	fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
	}
lsurv=vector(1,AGESUP);	lsurv=vector(1,AGESUP);
lpop=vector(1,AGESUP);	lpop=vector(1,AGESUP);
tpop=vector(1,AGESUP);	tpop=vector(1,AGESUP);
Line 6168 Interval (in months) between two waves:	Line 7293 Interval (in months) between two waves:


replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	if(ageminpar == AGEOVERFLOW \|\|agemaxpar == AGEOVERFLOW){
	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	}else
	printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \	printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov,agemortsup);	model,imx,p,matcov,agemortsup);
Line 6183 Interval (in months) between two waves:	Line 7315 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 6216 Interval (in months) between two waves:	Line 7349 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 6232 Interval (in months) between two waves:	Line 7365 Interval (in months) between two waves:
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, p, npar, delti, ftolhess, func);
}	}
	printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
	fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
	for(i=1,jk=1; i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d ",i,k);
	fprintf(ficlog,"%d%d ",i,k);
	for(j=1; j <=ncovmodel; j++){
	printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	jk++;
	}
	printf("\n");
	fprintf(ficlog,"\n");
	}
	}
	}

fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");	printf("# Scales (for hessian or gradient estimation)\n");
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
Line 6359 Interval (in months) between two waves:	Line 7510 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 6387 Interval (in months) between two waves:	Line 7539 Interval (in months) between two waves:
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;	dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;

fscanf(ficpar,"pop_based=%d\n",&popbased);	fscanf(ficpar,"pop_based=%d\n",&popbased);
	fprintf(ficlog,"pop_based=%d\n",popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);	fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficres,"pop_based=%d\n",popbased);	fprintf(ficres,"pop_based=%d\n",popbased);

Line 6411 Interval (in months) between two waves:	Line 7564 Interval (in months) between two waves:
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */	/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */

replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	if(ageminpar == AGEOVERFLOW \|\|agemaxpar == -AGEOVERFLOW){
	printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
	}else
	printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\	model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
Line 6432 Interval (in months) between two waves:	Line 7593 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 6441 Interval (in months) between two waves:	Line 7607 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 6468 Interval (in months) between two waves:	Line 7635 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 6502 Interval (in months) between two waves:	Line 7670 Interval (in months) between two waves:
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficreseij,"******\n");	fprintf(ficreseij,"******\n");

Line 6562 Interval (in months) between two waves:	Line 7730 Interval (in months) between two waves:
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficrest,"\n#****** ");	fprintf(ficrest,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");

fprintf(ficresstdeij,"\n#****** ");	fprintf(ficresstdeij,"\n#****** ");
fprintf(ficrescveij,"\n#****** ");	fprintf(ficrescveij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
fprintf(ficresstdeij,"******\n");	fprintf(ficresstdeij,"******\n");
fprintf(ficrescveij,"******\n");	fprintf(ficrescveij,"******\n");

fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresvij,"******\n");	fprintf(ficresvij,"******\n");

eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
Line 6591 Interval (in months) between two waves:	Line 7759 Interval (in months) between two waves:


for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
oldm=oldms;savm=savms; /* Segmentation fault */	oldm=oldms;savm=savms; /* ZZ Segmentation fault */
cptcod= 0; /* To be deleted */	cptcod= 0; /* To be deleted */
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
Line 6602 Interval (in months) between two waves:	Line 7770 Interval (in months) between two waves:
fprintf(ficrest,"# Age e.. (std) ");	fprintf(ficrest,"# Age e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
	/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
epj=vector(1,nlstate+1);	epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /ZZ Is it the correct prevalim /
if (vpopbased==1) {	if (vpopbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 6617 Interval (in months) between two waves:	Line 7785 Interval (in months) between two waves:
}	}

fprintf(ficrest," %4.0f",age);	fprintf(ficrest," %4.0f",age);
	/* printf(" age %4.0f ",age); */
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
for(i=1, epj[j]=0.;i <=nlstate;i++) {	for(i=1, epj[j]=0.;i <=nlstate;i++) {
epj[j] += prlim[i][i]*eij[i][j][(int)age];	epj[j] += prlim[i][i]*eij[i][j][(int)age];
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/	/ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);/
	/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
}	}
epj[nlstate+1] +=epj[j];	epj[nlstate+1] +=epj[j];
}	}
	/* printf(" age %4.0f \n",age); */

for(i=1, vepp=0.;i <=nlstate;i++)	for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)	for(j=1;j <=nlstate;j++)
Line 6669 Interval (in months) between two waves:	Line 7840 Interval (in months) between two waves:
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficresvpl,"\n#****** ");	fprintf(ficresvpl,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");

varpl=matrix(1,nlstate,(int) bage, (int) fage);	varpl=matrix(1,nlstate,(int) bage, (int) fage);
Line 6685 Interval (in months) between two waves:	Line 7856 Interval (in months) between two waves:
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
} /* mle==-3 arrives here for freeing */	} /* mle==-3 arrives here for freeing */
endfree:	/* endfree:*/
free_matrix(prlim,1,nlstate,1,nlstate); /here or after loop ? /	free_matrix(prlim,1,nlstate,1,nlstate); /here or after loop ? /
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
Line 6699 Interval (in months) between two waves:	Line 7870 Interval (in months) between two waves:
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);

free_ivector(ncodemax,1,NCOVMAX);	free_ivector(ncodemax,1,NCOVMAX);
	free_ivector(ncodemaxwundef,1,NCOVMAX);
free_ivector(Tvar,1,NCOVMAX);	free_ivector(Tvar,1,NCOVMAX);
free_ivector(Tprod,1,NCOVMAX);	free_ivector(Tprod,1,NCOVMAX);
free_ivector(Tvaraff,1,NCOVMAX);	free_ivector(Tvaraff,1,NCOVMAX);
free_ivector(Tage,1,NCOVMAX);	free_ivector(Tage,1,NCOVMAX);

free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);	free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
free_imatrix(codtab,1,100,1,10);	/* free_imatrix(codtab,1,100,1,10); */
fflush(fichtm);	fflush(fichtm);
fflush(ficgp);	fflush(ficgp);

Line 6743 Interval (in months) between two waves:	Line 7915 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");
Line 6800 Interval (in months) between two waves:	Line 7978 Interval (in months) between two waves:
}	}
end:	end:
while (z[0] != 'q') {	while (z[0] != 'q') {
printf("\nType q for exiting: ");	printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);	scanf("%s",z);
}	}
}	}

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Removed from v.1.161
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	Added in v.1.200