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Diff for /imach/src/imach.c between versions 1.149 and 1.184

version 1.149, 2014/06/18 15:51:14	version 1.184, 2015/03/11 11:52:39
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	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
	Summary: Problem with macro SQR on Intel compiler

	Revision 1.160 2014/09/02 09:24:05 brouard
	* empty log message *

	Revision 1.159 2014/09/01 10:34:10 brouard
	Summary: WIN32
	Author: Brouard

	Revision 1.158 2014/08/27 17:11:51 brouard
	* empty log message *

	Revision 1.157 2014/08/27 16:26:55 brouard
	Summary: Preparing windows Visual studio version
	Author: Brouard

	In order to compile on Visual studio, time.h is now correct and time_t
	and tm struct should be used. difftime should be used but sometimes I
	just make the differences in raw time format (time(&now).
	Trying to suppress #ifdef LINUX
	Add xdg-open for __linux in order to open default browser.

	Revision 1.156 2014/08/25 20:10:10 brouard
	* empty log message *

	Revision 1.155 2014/08/25 18:32:34 brouard
	Summary: New compile, minor changes
	Author: Brouard

	Revision 1.154 2014/06/20 17:32:08 brouard
	Summary: Outputs now all graphs of convergence to period prevalence

	Revision 1.153 2014/06/20 16:45:46 brouard
	Summary: If 3 live state, convergence to period prevalence on same graph
	Author: Brouard

	Revision 1.152 2014/06/18 17:54:09 brouard
	Summary: open browser, use gnuplot on same dir than imach if not found in the path

	Revision 1.151 2014/06/18 16:43:30 brouard
	* empty log message *

	Revision 1.150 2014/06/18 16:42:35 brouard
	Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
	Author: brouard

Revision 1.149 2014/06/18 15:51:14 brouard	Revision 1.149 2014/06/18 15:51:14 brouard
Summary: Some fixes in parameter files errors	Summary: Some fixes in parameter files errors
Author: Nicolas Brouard	Author: Nicolas Brouard
Line 434	Line 575
end	end
*/	*/

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



#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
#include <stdlib.h>	#include <stdlib.h>
#include <string.h>	#include <string.h>

	#ifdef _WIN32
	#include <io.h>
	#include <windows.h>
	#include <tchar.h>
	#else
#include <unistd.h>	#include <unistd.h>
	#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; */

	/* #ifdef LINUX */
	/* #include <time.h> */
	/* #include "timeval.h" */
	/* #else */
	/* #include <sys/time.h> */
	/* #endif */

#ifdef LINUX
#include <time.h>	#include <time.h>
#include "timeval.h"
#else
#include <sys/time.h>
#endif

#ifdef GSL	#ifdef GSL
#include <gsl/gsl_errno.h>	#include <gsl/gsl_errno.h>
#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 485 extern int errno;	Line 649 extern int errno;
#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 AGEGOMP 10 /*< Minimal age for Gompertz adjustment /
#ifdef UNIX	#ifdef _WIN32
#define DIRSEPARATOR '/'
#define CHARSEPARATOR "/"
#define ODIRSEPARATOR '\\'
#else
#define DIRSEPARATOR '\\'	#define DIRSEPARATOR '\\'
#define CHARSEPARATOR "\\"	#define CHARSEPARATOR "\\"
#define ODIRSEPARATOR '/'	#define ODIRSEPARATOR '/'
	#else
	#define DIRSEPARATOR '/'
	#define CHARSEPARATOR "/"
	#define ODIRSEPARATOR '\\'
#endif	#endif

/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */

char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";	char version[]="Imach version 0.98q0, March 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];
Line 530 int *mw; / mw[mi][i] is number of the	Line 694 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 573 char popfile[FILENAMELENGTH];	Line 738 char popfile[FILENAMELENGTH];

char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;	char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;

struct timeval start_time, end_time, curr_time, last_time, forecast_time;	/* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
struct timezone tzp;	/* struct timezone tzp; */
extern int gettimeofday();	/* extern int gettimeofday(); */
struct tm tmg, tm, tmf, gmtime(), localtime();	struct tm tml, gmtime(), localtime();
long time_value;
extern long time();	extern time_t time();

	struct tm start_time, end_time, curr_time, last_time, forecast_time;
	time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
	struct tm tm;

char strcurr[80], strfor[80];	char strcurr[80], strfor[80];

char *endptr;	char *endptr;
Line 608 static double maxarg1,maxarg2;	Line 778 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 663 static int split( char path, char dirc	Line 838 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 char cutl(char blocc, char *alocc, cha	Line 912 char cutl(char blocc, char *alocc, cha
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 blocc	If occ is not found blocc is null and alocc is equal to in. Returns blocc
*/	*/
char s, t, *bl;	char s, t;
t=in;s=in;	t=in;s=in;
while ((in != occ) && (in != '\0')){	while ((in != occ) && (in != '\0')){
alocc++ = in++;	alocc++ = in++;
Line 817 int nbocc(char *s, char occ)	Line 996 int nbocc(char *s, char occ)
/* } */	/* } */
/* } */	/* } */

	#ifdef _WIN32
	char * strsep(char *pp, const char delim)
	{
	char p, q;

	if ((p = *pp) == NULL)
	return 0;
	if ((q = strpbrk (p, delim)) != NULL)
	{
	*pp = q + 1;
	*q = '\0';
	}
	else
	*pp = 0;
	return p;
	}
	#endif

/******************** nrerror ******************/	/******************** nrerror ******************/

void nrerror(char error_text[])	void nrerror(char error_text[])
Line 1016 char subdirf3(char fileres[], char pre	Line 1213 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 1039 double brent(double ax, double bx, doubl	Line 1249 double brent(double ax, double bx, doubl
{	{
int iter;	int iter;
double a,b,d,etemp;	double a,b,d,etemp;
double fu,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 1054 double brent(double ax, double bx, doubl	Line 1264 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 1089 double brent(double ax, double bx, doubl	Line 1299 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 1112 double brent(double ax, double bx, doubl	Line 1322 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;

Line 1120 void mnbrak(double ax, double bx, doub	Line 1334 void mnbrak(double ax, double bx, doub
fb=(func)(*bx);	fb=(func)(*bx);
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;
	}
	#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 1177 void linmin(double p[], double xi[], int	Line 1459 void linmin(double p[], double xi[], int
}	}
ax=0.0;	ax=0.0;
xx=1.0;	xx=1.0;
mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);	mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);	fret=brent(ax,xx,bx,f1dim,TOL,&xmin); / Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
#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);
Line 1191 void linmin(double p[], double xi[], int	Line 1473 void linmin(double p[], double xi[], int
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 1212 void powell(double p[], double **xi, int	Line 1490 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 1222 void powell(double p[], double **xi, int	Line 1501 void powell(double p[], double **xi, int
xits=vector(1,n);	xits=vector(1,n);
fret=(func)(p);	fret=(func)(p);
for (j=1;j<=n;j++) pt[j]=p[j];	for (j=1;j<=n;j++) pt[j]=p[j];
	rcurr_time = time(NULL);
for (iter=1;;++(iter)) {	for (iter=1;;++(iter)) {
fp=(*fret);	fp=(*fret);
ibig=0;	ibig=0;
del=0.0;	del=0.0;
last_time=curr_time;	rlast_time=rcurr_time;
(void) gettimeofday(&curr_time,&tzp);	/* (void) gettimeofday(&curr_time,&tzp); */
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);	rcurr_time = time(NULL);
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);	curr_time = *localtime(&rcurr_time);
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tv_sec-start_time.tv_sec); */	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(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]);
Line 1240 void powell(double p[], double **xi, int	Line 1522 void powell(double p[], double **xi, int
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficrespow,"\n");fflush(ficrespow);	fprintf(ficrespow,"\n");fflush(ficrespow);
if(*iter <=3){	if(*iter <=3){
tm = *localtime(&curr_time.tv_sec);	tml = *localtime(&rcurr_time);
strcpy(strcurr,asctime(&tm));	strcpy(strcurr,asctime(&tml));
/* asctime_r(&tm,strcurr); */	rforecast_time=rcurr_time;
forecast_time=curr_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,curr_time.tv_sec-last_time.tv_sec);	printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);	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){
forecast_time.tv_sec=curr_time.tv_sec+(niterf-iter)(curr_time.tv_sec-last_time.tv_sec);	rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);
tmf = *localtime(&forecast_time.tv_sec);	forecast_time = *localtime(&rforecast_time);
/* asctime_r(&tmf,strfor); */	strcpy(strfor,asctime(&forecast_time));
strcpy(strfor,asctime(&tmf));
itmp = strlen(strfor);	itmp = strlen(strfor);
if(strfor[itmp-1]=='\n')	if(strfor[itmp-1]=='\n')
strfor[itmp-1]='\0';	strfor[itmp-1]='\0';
printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);	printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);	fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
}	}
}	}
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];	for (j=1;j<=n;j++) xit[j]=xi[j][i];
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);
fprintf(ficlog,"%d",i);fflush(ficlog);	fprintf(ficlog,"%d",i);fflush(ficlog);
linmin(p,xit,n,fret,func);	linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
if (fabs(fptt-(*fret)) > del) {	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 1284 void powell(double p[], double **xi, int	Line 1569 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 i */
if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) {	if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /* Did we reach enough precision? */
#ifdef DEBUG	#ifdef DEBUG
int k[2],l;	int k[2],l;
k[0]=1;	k[0]=1;
Line 1323 void powell(double p[], double **xi, int	Line 1608 void powell(double p[], double **xi, int
return;	return;
}	}
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");	if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
ptt[j]=2.0*p[j]-pt[j];	ptt[j]=2.0*p[j]-pt[j];
xit[j]=p[j]-pt[j];	xit[j]=p[j]-pt[j];
pt[j]=p[j];	pt[j]=p[j];
}	}
fptt=(*func)(ptt);	fptt=(func)(ptt); / f_3 */
if (fptt < fp) {	if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)-delSQR(fp-fptt);	/* (x1 f1=fp), (x2 f2=fret), (x3 f3=fptt), (xm fm) /
if (t < 0.0) {	/* From x1 (P0) distance of x2 is at h and x3 is 2h */
linmin(p,xit,n,fret,func);	/* Let f"(x2) be the 2nd derivative equal everywhere. */
	/* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
	/* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h*2 /
	/* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
	/* t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)-delSQR(fp-fptt); */
	#ifdef NRCORIGINAL
	t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)- 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);
	#endif
	directest = fp-2.0(fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
	#ifdef DEBUG
	printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),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),
	(fp-(fret)-del)(fp-(fret)-del),(fp-fptt)(fp-fptt));
	fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3= %.12lf, t4= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
	(fp-(fret)-del)(fp-(fret)-del),(fp-fptt)(fp-fptt));
	printf("tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);
	fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);
	#endif
	#ifdef POWELLORIGINAL
	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
	linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n];	xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
xi[j][n]=xit[j];	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);	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);	fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 1347 void powell(double p[], double **xi, int	Line 1668 void powell(double p[], double **xi, int
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
}	} /* end of t negative */
}	} /* end if (fptt < fp) */
}	}
}	}

Line 1358 double prevalim(double prlim, int nl	Line 1679 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 */
Line 1410 double prevalim(double prlim, int nl	Line 1731 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 1436 double pmij(double ps, double *cov,	Line 1758 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 1578 double *hpxij(double *po, int nhstep	Line 1900 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 1596 double func( double *x)	Line 1937 double func( double *x)
/*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 1675 double func( double *x)	Line 2019 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 1707 double func( double *x)	Line 2070 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){
Line 1977 void likelione(FILE *ficres,double p[],	Line 2344 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 1998 void mlikeli(FILE *ficres,double p[], in	Line 2377 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 2014 void hesscov(double **matcov, double p[]	Line 2420 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 2148 double hessii(double x[], double delta,	Line 2554 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 2163 double hessii(double x[], double delta,	Line 2569 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 2278 void pstamp(FILE *fichier)	Line 2684 void pstamp(FILE *fichier)
void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, char strstart[])	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 2302 void freqsummary(char fileres[], int ia	Line 2708 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 2459 void prevalence(double ***probs, double	Line 2864 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 2553 void concatwav(int wav[], int **dh, int	Line 2958 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 2682 void tricode(int Tvar, int *nbcode, in	Line 3087 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 2793 void evsij(double ***eij, double x[], in	Line 3198 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 3112 void varevsij(char optionfilefiname[], d	Line 3517 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 3389 void varevsij(char optionfilefiname[], d	Line 3797 void varevsij(char optionfilefiname[], d
/* 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.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
Line 3415 void varprevlim(char fileres[], double *	Line 3823 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 3497 void varprevlim(char fileres[], double *	Line 3904 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 3507 void varprob(char optionfilefiname[], do	Line 3914 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 3811 To be simple, these graphs help to under	Line 4218 To be simple, these graphs help to under
} /* 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 3878 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4285 fprintf(fichtm," \n<ul><li><b>Graphs</b>
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.png\">%s%d_2.png</a><br> \
<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Period (stable) prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \	fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
<img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);	<img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);	<img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}	}
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
Line 3965 true period expectancies (those weighted	Line 4372 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 3980 void printinggnuplot(char fileres[], cha	Line 4387 void printinggnuplot(char fileres[], cha
strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
	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.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
Line 3987 void printinggnuplot(char fileres[], cha	Line 4395 void printinggnuplot(char fileres[], cha
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 png small size 320, 240\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);	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));
}	}
}	}
/2 eme/	/2 eme/
	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.png\" \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 png small size 320, 240\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 4064 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4472 plot [%.f:%.f] \"%s\" every :::%d::%d u
}	}

/* CV preval stable (period) */	/* CV preval stable (period) */
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
for (cpt=1; cpt<=nlstate ; cpt ++) {	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,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d_%d.png\" \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 png small size 320, 240\n\
unset log y\n\	unset log y\n\
plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);	plot [%.f:%.f] ", ageminpar, agemaxpar);
	for (i=1; i<= nlstate ; i ++){
for (i=1; i< nlstate ; i ++)	if(i==1)
fprintf(ficgp,"+$%d",k+i+1);	fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);	else
	fprintf(ficgp,", '' ");
l=3+(nlstate+ndeath)*cpt;	l=(nlstate+ndeath)*(i-1)+1;
fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
for (i=1; i< nlstate ; i ++) {	for (j=1; j<= (nlstate-1) ; j ++)
l=3+(nlstate+ndeath)*cpt;	fprintf(ficgp,"+$%d",k+l+j);
fprintf(ficgp,"+$%d",l+i+1);	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
}	} /* nlstate */
fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);	fprintf(ficgp,"\n");
}	} /* end cpt state*/
}	} /* end covariate */

/* proba elementaires */	/* proba elementaires */
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
Line 4149 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4558 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
} /* end k2 */	} /* end k2 */
} /* end jk */	} /* end jk */
} /* end ng */	} /* end ng */
avoid:	/* avoid: */
fflush(ficgp);	fflush(ficgp);
} /* end gnuplot */	} /* end gnuplot */

Line 4197 int movingaverage(double ***probs, doubl	Line 4606 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 4321 prevforecast(char fileres[], double anpr	Line 4729 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 4498 void prwizard(int ncovmodel, int nlstate	Line 4906 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 4720 fprintf(fichtm,"<ul><li><h4>Life table</	Line 5128 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 4745 int readdata(char datafile[], int firsto	Line 5153 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;

Line 4776 int readdata(char datafile[], int firsto	Line 5184 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 4799 int readdata(char datafile[], int firsto	Line 5205 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 4815 int readdata(char datafile[], int firsto	Line 5221 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 4830 int readdata(char datafile[], int firsto	Line 5236 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 5323 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 4930 void removespace(char *str) {	Line 5336 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:
Line 4948 int decodemodel ( char model[], int last	Line 5354 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];

Line 4960 int decodemodel ( char model[], int last	Line 5366 int decodemodel ( char model[], int last
cptcovs=j+1-j1; /*< Number of simple covariates V1+V2age+V3 +V3V4=> V1 + V3 =2 /	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*/	cptcovt= j+1; /* Number of total covariates in the model V1 + V2age+ V3 + V3V4=> 4*/
/* including age products which are counted in cptcovage.	/* including age products which are counted in cptcovage.
/* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */	* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /	cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /
cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */	cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */
strcpy(modelsav,model);	strcpy(modelsav,model);
Line 5097 int decodemodel ( char model[], int last	Line 5503 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 5113 calandcheckages(int imx, int maxwav, dou	Line 5519 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 5132 calandcheckages(int imx, int maxwav, dou	Line 5538 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 5144 calandcheckages(int imx, int maxwav, dou	Line 5550 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 5156 calandcheckages(int imx, int maxwav, dou	Line 5563 calandcheckages(int imx, int maxwav, dou
}	}
else if(agev[m][i] >*agemax){	else if(agev[m][i] >*agemax){
*agemax=agev[m][i];	*agemax=agev[m][i];
printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);	/* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], agemax);/
}	}
/agev[m][i]=anint[m][i]-annais[i];/	/agev[m][i]=anint[m][i]-annais[i];/
/* agev[m][i] = age[i]+2m;/	/* agev[m][i] = age[i]+2m;/
Line 5174 calandcheckages(int imx, int maxwav, dou	Line 5581 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 5194 calandcheckages(int imx, int maxwav, dou	Line 5601 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()
	{
	/* #include "syscompilerinfo.h"*/
	/* command line Intel compiler 64bit windows:
	/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" */
	/*
	/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" */
	#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-");
	fprintf(ficlog, "Cross-");
	}
	#endif

	#include <stdint.h>

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

	// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
	#ifdef _WIN32 // note the underscore: without it, it's not msdn official!
	// Windows (x64 and x86)
	printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
	#elif __unix__ // all unices, not all compilers
	// Unix
	printf("Unix ");fprintf(ficlog,"Unix ");
	#elif __linux__
	// linux
	printf("linux ");fprintf(ficlog,"linux ");
	#elif __APPLE__
	// Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
	printf("Mac OS ");fprintf(ficlog,"Mac OS ");
	#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"); fprintf(ficlog," 32-bit");/* 32-bit */
	#elif UINTPTR_MAX == 0xffffffffffffffff
	printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
	#else
	printf(" wtf-bit"); 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__);
	fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);

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

	// void main()
	// {
	#if defined(_MSC_VER)
	if (IsWow64()){
	printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
	fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
	}
	else{
	printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
	fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
	}
	// printf("\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,codtab[cptcod][cptcov]);
	fprintf(ficrespl,"\n#******");
	printf("\n#******");
	fprintf(ficlog,"\n#******");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
	fprintf(ficrespl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");

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

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

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

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

	double agedeb;
	double ***p3mat;

	strcpy(filerespij,"pij"); strcat(filerespij,fileres);
	if((ficrespij=fopen(filerespij,"w"))==NULL) {
	printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
	fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
	}
	printf("Computing pij: result on file '%s' \n", filerespij);
	fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);

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

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

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

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

	/* nhstepm=nhstepmYEARM; aff par mois/

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


/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
Line 5214 int main(int argc, char *argv[])	Line 5932 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 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;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;	double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

double fret;	double fret;
double **xi,tmp,delta;

double dum; /* Dummy variable */	double dum; /* 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],model[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;
int c, h , cpt,l;	int jl;
int ju,jl, mi;	int i1, j1, jk, stepsize;
int i1,j1, jk,aa,bb, stepsize, ij;	int *tab;
int jnais,jdc,jint4,jint1,jint2,jint3,*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, nhstepm;
Line 5254 int main(int argc, char *argv[])	Line 5969 int main(int argc, char *argv[])
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, agebase;
double ftolpl=FTOL;	double ftolpl=FTOL;
double **prlim;	double **prlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters */
Line 5265 int main(int argc, char *argv[])	Line 5980 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 5285 int main(int argc, char *argv[])	Line 5999 int main(int argc, char *argv[])
/* setlocale (LC_MESSAGES, ""); */	/* setlocale (LC_MESSAGES, ""); */

/* gettimeofday(&start_time, (struct timezone)0); / /* at first time */	/* gettimeofday(&start_time, (struct timezone)0); / /* at first time */
(void) gettimeofday(&start_time,&tzp);	rstart_time = time(NULL);
	/* (void) gettimeofday(&start_time,&tzp);*/
	start_time = *localtime(&rstart_time);
curr_time=start_time;	curr_time=start_time;
tm = *localtime(&start_time.tv_sec);	/tml = localtime(&start_time.tm_sec);*/
tmg = *gmtime(&start_time.tv_sec);	/* strcpy(strstart,asctime(&tml)); */
strcpy(strstart,asctime(&tm));	strcpy(strstart,asctime(&start_time));

/* printf("Localtime (at start)=%s",strstart); */	/* printf("Localtime (at start)=%s",strstart); */
/* tp.tv_sec = tp.tv_sec +86400; */	/* tp.tm_sec = tp.tm_sec +86400; */
/* tm = localtime(&start_time.tv_sec); /	/* tm = localtime(&start_time.tm_sec); /
/* tmg.tm_year=tmg.tm_year +dsigndyear; /	/* tmg.tm_year=tmg.tm_year +dsigndyear; /
/* tmg.tm_mon=tmg.tm_mon +dsigndmonth; /	/* tmg.tm_mon=tmg.tm_mon +dsigndmonth; /
/* tmg.tm_hour=tmg.tm_hour + 1; */	/* tmg.tm_hour=tmg.tm_hour + 1; */
/* tp.tv_sec = mktime(&tmg); */	/* tp.tm_sec = mktime(&tmg); */
/* strt=asctime(&tmg); */	/* strt=asctime(&tmg); */
/* printf("Time(after) =%s",strstart); */	/* printf("Time(after) =%s",strstart); */
/* (void) time (&time_value);	/* (void) time (&time_value);
Line 5309 int main(int argc, char *argv[])	Line 6025 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);	printf("\n%s\n%s",version,fullversion);
if(argc <=1){	if(argc <=1){
Line 5318 int main(int argc, char *argv[])	Line 6038 int main(int argc, char *argv[])
i=strlen(pathr);	i=strlen(pathr);
if(pathr[i-1]=='\n')	if(pathr[i-1]=='\n')
pathr[i-1]='\0';	pathr[i-1]='\0';
	i=strlen(pathr);
	if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
	pathr[i-1]='\0';
for (tok = pathr; tok != NULL; ){	for (tok = pathr; tok != NULL; ){
printf("Pathr \|%s\|\n",pathr);	printf("Pathr \|%s\|\n",pathr);
while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');	while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
Line 5342 int main(int argc, char *argv[])	Line 6065 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 5373 int main(int argc, char *argv[])	Line 6101 int main(int argc, char *argv[])
path=%s \n\	path=%s \n\
optionfile=%s\n\	optionfile=%s\n\
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();

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);
/* (void) gettimeofday(&curr_time,&tzp); */	/* (void) gettimeofday(&curr_time,&tzp); */
/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */	/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */

/* */	/* */
strcpy(fileres,"r");	strcpy(fileres,"r");
Line 5389 int main(int argc, char *argv[])	Line 6119 int main(int argc, char *argv[])
/---------arguments file --------/	/---------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));
fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));	fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
fflush(ficlog);	fflush(ficlog);
/* goto end; */	/* goto end; */
exit(70);	exit(70);
Line 5543 run imach with mle=-1 to get a correct t	Line 6273 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 5842 Title=%s <br>Datafile=%s Firstpass=%d La	Line 6572 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 5912 Interval (in months) between two waves:	Line 6647 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 5923 Interval (in months) between two waves:	Line 6658 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 6326 Interval (in months) between two waves:	Line 7061 Interval (in months) between two waves:


/--------------- 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 6334 Interval (in months) between two waves:	Line 7071 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 6485 Interval (in months) between two waves:	Line 7223 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; /* Segmentation fault */
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);	cptcod= 0; /* To be deleted */
	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
if(vpopbased==1)	if(vpopbased==1)
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
Line 6577 Interval (in months) between two waves:	Line 7316 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 6611 Interval (in months) between two waves:	Line 7350 Interval (in months) between two waves:
}	}
printf("See log file on %s\n",filelog);	printf("See log file on %s\n",filelog);
/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */	/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */
(void) gettimeofday(&end_time,&tzp);	/(void) gettimeofday(&end_time,&tzp);/
tm = *localtime(&end_time.tv_sec);	rend_time = time(NULL);
tmg = *gmtime(&end_time.tv_sec);	end_time = *localtime(&rend_time);
strcpy(strtend,asctime(&tm));	/* tml = localtime(&end_time.tm_sec); /
	strcpy(strtend,asctime(&end_time));
printf("Local time at start %s\nLocal time at end %s",strstart, strtend);	printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);	fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));	printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));

printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);	printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));	fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);	fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
/* printf("Total time was %d uSec.\n", total_usecs);*/	/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */	/* if(fileappend(fichtm,optionfilehtm)){ */
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);	fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
Line 6634 Interval (in months) between two waves:	Line 7374 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");
#ifndef UNIX	#ifdef _WIN32
sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);	sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
#endif	#endif
if(!stat(plotcmd,&info)){	if(!stat(plotcmd,&info)){
printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);	printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
if(!stat(getenv("GNUPLOTBIN"),&info)){	if(!stat(getenv("GNUPLOTBIN"),&info)){
printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);	printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
}else	}else
strcpy(pplotcmd,plotcmd);	strcpy(pplotcmd,plotcmd);
#ifdef UNIX	#ifdef __unix
strcpy(plotcmd,GNUPLOTPROGRAM);	strcpy(plotcmd,GNUPLOTPROGRAM);
if(!stat(plotcmd,&info)){	if(!stat(plotcmd,&info)){
printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);	printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
}else	}else
strcpy(pplotcmd,plotcmd);	strcpy(pplotcmd,plotcmd);
#endif	#endif
Line 6660 Interval (in months) between two waves:	Line 7406 Interval (in months) between two waves:
strcpy(pplotcmd,plotcmd);	strcpy(pplotcmd,plotcmd);

sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);	sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);	printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);

if((outcmd=system(plotcmd)) != 0){	if((outcmd=system(plotcmd)) != 0){
printf("\n Problem with gnuplot\n");	printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
	printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
	sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
	if((outcmd=system(plotcmd)) != 0)
	printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
}	}
printf(" Wait...");	printf(" Successful, please wait...");
while (z[0] != 'q') {	while (z[0] != 'q') {
/* chdir(path); */	/* chdir(path); */
printf("\nType e to edit output files, g to graph again and q for exiting: ");	printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
scanf("%s",z);	scanf("%s",z);
/* if (z[0] == 'c') system("./imach"); */	/* if (z[0] == 'c') system("./imach"); */
if (z[0] == 'e') {	if (z[0] == 'e') {
printf("Starting browser with: %s",optionfilehtm);fflush(stdout);	#ifdef __APPLE__
system(optionfilehtm);	sprintf(pplotcmd, "open %s", optionfilehtm);
	#elif __linux
	sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
	#else
	sprintf(pplotcmd, "%s", optionfilehtm);
	#endif
	printf("Starting browser with: %s",pplotcmd);fflush(stdout);
	system(pplotcmd);
}	}
else if (z[0] == 'g') system(plotcmd);	else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);	else if (z[0] == 'q') exit(0);
Line 6684 Interval (in months) between two waves:	Line 7441 Interval (in months) between two waves:
scanf("%s",z);	scanf("%s",z);
}	}
}	}

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>

Removed from v.1.149
changed lines
	Added in v.1.184