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Diff for /imach/src/imach.c between versions 1.140 and 1.166

version 1.140, 2011/09/02 10:37:54	version 1.166, 2014/12/22 11:40:47
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.166 2014/12/22 11:40:47 brouard
	* empty log message *

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

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

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

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

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

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

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

	Author:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

	Revision 1.148 2014/06/17 17:38:48 brouard
	Summary: Nothing new
	Author: Brouard

	Just a new packaging for OS/X version 0.98nS

	Revision 1.147 2014/06/16 10:33:11 brouard
	* empty log message *

	Revision 1.146 2014/06/16 10:20:28 brouard
	Summary: Merge
	Author: Brouard

	Merge, before building revised version.

	Revision 1.145 2014/06/10 21:23:15 brouard
	Summary: Debugging with valgrind
	Author: Nicolas Brouard

	Lot of changes in order to output the results with some covariates
	After the Edimburgh REVES conference 2014, it seems mandatory to
	improve the code.
	No more memory valgrind error but a lot has to be done in order to
	continue the work of splitting the code into subroutines.
	Also, decodemodel has been improved. Tricode is still not
	optimal. nbcode should be improved. Documentation has been added in
	the source code.

	Revision 1.143 2014/01/26 09:45:38 brouard
	Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising

	* imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
	(Module): Version 0.98nR Running ok, but output format still only works for three covariates.

	Revision 1.142 2014/01/26 03:57:36 brouard
	Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2

	* imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...

	Revision 1.141 2014/01/26 02:42:01 brouard
	* imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...

Revision 1.140 2011/09/02 10:37:54 brouard	Revision 1.140 2011/09/02 10:37:54 brouard
Summary: times.h is ok with mingw32 now.	Summary: times.h is ok with mingw32 now.

Line 360	Line 477
begin-prev-date,...	begin-prev-date,...
open gnuplot file	open gnuplot file
open html file	open html file
period (stable) prevalence	period (stable) prevalence \| pl_nom 1-1 2-2 etc by covariate
for age prevalim()	for age prevalim() \| #**** V1=0 V2=1 V3=1 V4=0 ****
h Pij x	\| 65 1 0 2 1 3 1 4 0 0.96326 0.03674
variance of p varprob	freexexit2 possible for memory heap.

	h Pij x \| pij_nom ficrestpij
	# Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
	1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
	1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907

	1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
	1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
	variance of p one-step probabilities varprob \| prob_nom ficresprob #One-step probabilities and stand. devi in ()
	Standard deviation of one-step probabilities \| probcor_nom ficresprobcor #One-step probabilities and correlation matrix
	Matrix of variance covariance of one-step probabilities \| probcov_nom ficresprobcov #One-step probabilities and covariance matrix

forecasting if prevfcast==1 prevforecast call prevalence()	forecasting if prevfcast==1 prevforecast call prevalence()
health expectancies	health expectancies
Variance-covariance of DFLE	Variance-covariance of DFLE
Line 376	Line 505
end	end
*/	*/

	#define POWELL /* Instead of NLOPT */



#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>
	#else
#include <unistd.h>	#include <unistd.h>
	#endif

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

#include <sys/time.h>
/*
#include <time.h>	#include <time.h>
#include "timeval.h"

#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) */

#define MAXLINE 256	#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */

#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
Line 413 extern int errno;	Line 557 extern int errno;
#define GLOCK_ERROR_NOPATH -1 /* empty path */	#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */	#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */

#define MAXPARM 128 /* Maximum number of parameters for the optimization */	#define MAXPARM 128 /*< Maximum number of parameters for the optimization /
#define NPARMAX 64 /* (nlstate+ndeath-1)nlstatencovmodel */	#define NPARMAX 64 /*< (nlstate+ndeath-1)nlstatencovmodel /

#define NINTERVMAX 8	#define NINTERVMAX 8
#define NLSTATEMAX 8 /* Maximum number of live states (for func) */	#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /
#define NDEATHMAX 8 /* Maximum number of dead states (for func) */	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 20 /* Maximum number of covariates */	#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */
	#define codtabm(h,k) 1 & (h-1) >> (k-1) ;
#define MAXN 20000	#define MAXN 20000
#define YEARM 12. /* Number of months per year */	#define YEARM 12. /*< Number of months per year /
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */	#define 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 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";	char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nvar=0, nforce=0; /* Number of variables, number of forces */	int nvar=0, nforce=0; /* Number of variables, number of forces */
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with 'age' /	/* Number of covariates model=V2+V1+ V3age+V2V4 */
	int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */
	int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /
	int cptcovs=0; /*< cptcovs number of simple covariates V2+V1 =2 /
	int cptcovage=0; /*< Number of covariates with age: V3age only =1 */
	int cptcovprodnoage=0; /*< Number of covariate products without age /
	int cptcoveff=0; /* Total number of covariates to vary for printing results */
	int cptcov=0; /* Working variable */
int npar=NPARMAX;	int npar=NPARMAX;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
Line 462 int *mw; / mw[mi][i] is number of the	Line 614 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 oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
/FILE fic ; / / Used in readdata only */	/FILE fic ; / / Used in readdata only */
Line 504 char popfile[FILENAMELENGTH];	Line 658 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 539 static double maxarg1,maxarg2;	Line 698 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 562 double dateintmean=0;	Line 726 double dateintmean=0;

double *weight;	double *weight;
int *s; / Status */	int *s; / Status */
double agedc, *covar, idx;	double *agedc;
int *nbcode, Tvar, codtab, Tvard, Tprod, cptcovprod, Tvaraff;	double covar; /< covar[j,i], value of jth covariate for individual i,
	* covar=matrix(0,NCOVMAX,1,n);
	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]cov[2]; /
	double idx;
	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
	int Ndum; /* Freq of modality (tricode */
	int codtab; /< codtab=imatrix(1,100,1,10); */
	int *Tvard, Tprod, cptcovprod, *Tvaraff;
double lsurv, lpop, *tpop;	double lsurv, lpop, *tpop;

double ftol=FTOL; /* Tolerance for computing Max Likelihood */	double ftol=FTOL; /*< Tolerance for computing Max Likelihood /
double ftolhess; /* Tolerance for computing hessian */	double ftolhess; /*< Tolerance for computing hessian /

/************** split ***********************/	/************** split ***********************/
static int split( char path, char dirc, char name, char ext, char *finame )	static int split( char path, char dirc, char name, char ext, char *finame )
Line 650 char trimbb(char out, char *in)	Line 821 char trimbb(char out, char *in)
return s;	return s;
}	}

	char cutl(char blocc, char alocc, char in, char occ)
	{
	/* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
	and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
	gives blocc="abcdef2ghi" and alocc="j".
	If occ is not found blocc is null and alocc is equal to in. Returns blocc
	*/
	char s, t;
	t=in;s=in;
	while ((in != occ) && (in != '\0')){
	alocc++ = in++;
	}
	if( *in == occ){
	*(alocc)='\0';
	s=++in;
	}

	if (s == t) {/* occ not found */
	*(alocc-(in-s))='\0';
	in=s;
	}
	while ( *in != '\0'){
	blocc++ = in++;
	}

	*blocc='\0';
	return t;
	}
char cutv(char blocc, char alocc, char in, char occ)	char cutv(char blocc, char alocc, char in, char occ)
{	{
/* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'	/* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
Line 713 int nbocc(char *s, char occ)	Line 912 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 820 double **matrix(long nrl, long nrh, long	Line 1037 double **matrix(long nrl, long nrh, long

for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;	for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;	return m;
/* print ((m+1)+70) or print m[1][70]; print m+1 or print &(m[1])	/* print ((m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
	m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
	that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
*/	*/
}	}

Line 910 char subdirf3(char fileres[], char pre	Line 1129 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 933 double brent(double ax, double bx, doubl	Line 1165 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 948 double brent(double ax, double bx, doubl	Line 1180 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 1018 void mnbrak(double ax, double bx, doub	Line 1250 void mnbrak(double ax, double bx, doub
}	}
cx=(bx)+GOLD(bx-*ax);	cx=(bx)+GOLD(bx-*ax);
fc=(func)(*cx);	fc=(func)(*cx);
while (fb > fc) {	while (fb > fc) { /* Declining 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 abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
ulim=(bx)+GLIMIT(cx-bx);	ulim=(bx)+GLIMIT(cx-bx); /* Maximum abscisse where function can be evaluated */
if ((bx-u)(u-*cx) > 0.0) {	if ((bx-u)(u-cx) > 0.0) { / if u 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);
	#endif
	} else if ((cx-u)(u-ulim) > 0.0) { /* u is after c but before ulim */
fu=(*func)(u);	fu=(*func)(u);
if (fu < *fc) {	if (fu < *fc) {
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) */
u=ulim;	u=ulim;
fu=(*func)(u);	fu=(*func)(u);
} else {	} else {
Line 1045 void mnbrak(double ax, double bx, doub	Line 1285 void mnbrak(double ax, double bx, doub
}	}

/************* 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 1071 void linmin(double p[], double xi[], int	Line 1315 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 1085 void linmin(double p[], double xi[], int	Line 1329 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,"%d day(s) %d hour(s) %d minute(s) %d 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 1116 void powell(double p[], double **xi, int	Line 1356 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 1134 void powell(double p[], double **xi, int	Line 1377 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);
Line 1178 void powell(double p[], double **xi, int	Line 1419 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))) {
#ifdef DEBUG	#ifdef DEBUG
int k[2],l;	int k[2],l;
Line 1217 void powell(double p[], double **xi, int	Line 1458 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 an extrapolated point */
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);
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 /
	/* f1-f3 = delta(2h) = 2 h*2 f'' = 2(f1- 2f2 +f3) /
	/* Thus we compare delta(2h) with observed f1-f3 */
	/* or best gain on one ancient line 'del' with total */
	/* gain f1-f2 = f1 - f2 - 'del' with del */
	/* t=2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del)-delSQR(fp-fptt); */

	t=2.0(fp-2.0(fret)+fptt)SQR(fp-(*fret)-del);
	t= t- del*SQR(fp-fptt);
	printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t);
	fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0(fp-2.0(fret)+fptt)SQR(fp-(fret)-del),delSQR(fp-fptt),t);
	#ifdef DEBUG
	printf("t3= %.12lf, t4= %.12lf, t3= %.12lf, t4= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
	(fp-(fret)-del)(fp-(fret)-del),(fp-fptt)(fp-fptt));
	fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3= %.12lf, t4= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
	(fp-(fret)-del)(fp-(fret)-del),(fp-fptt)(fp-fptt));
	printf("tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);
	fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0(fp-2.0(fret)+fptt)(fp-(fret)-del)(fp-(fret)-del)-del(fp-fptt)*(fp-fptt),t);
	#endif
	if (t < 0.0) { /* Then we use it for last direction */
	linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n];	xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
xi[j][n]=xit[j];	xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
}	}
	printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
	fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);

#ifdef DEBUG	#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 1241 void powell(double p[], double **xi, int	Line 1507 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 1255 double prevalim(double prlim, int nl	Line 1521 double prevalim(double prlim, int nl

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();	/* 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 */
Line 1275 double prevalim(double prlim, int nl	Line 1541 double prevalim(double prlim, int nl

for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
/* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/	/printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);/
}	}
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
for (k=1; k<=cptcovprod;k++)	/* for (k=1; k<=cptcovprod;k++) /\* Useless \/ /
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	/* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
	/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /
	out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */

savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
Line 1296 double prevalim(double prlim, int nl	Line 1564 double prevalim(double prlim, int nl
sumnew=0;	sumnew=0;
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
prlim[i][j]= newm[i][j]/(1-sumnew);	prlim[i][j]= newm[i][j]/(1-sumnew);
	/printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);/
max=FMAX(max,prlim[i][j]);	max=FMAX(max,prlim[i][j]);
min=FMIN(min,prlim[i][j]);	min=FMIN(min,prlim[i][j]);
}	}
Line 1327 double pmij(double ps, double *cov,	Line 1596 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 1376 double pmij(double ps, double *cov,	Line 1645 double pmij(double ps, double *cov,
}	}
}	}


/* for(ii=1; ii<= nlstate+ndeath; ii++){ */	/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */	/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
/* printf("ddd %lf ",ps[ii][jj]); */	/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
/* } */	/* } */
/* printf("\n "); */	/* printf("\n "); */
/* } */	/* } */
/* printf("\n ");printf("%lf ",cov[2]); */	/* printf("\n ");printf("%lf ",cov[2]);*/
/*	/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);	for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/	goto end;*/
return ps;	return ps;
Line 1392 double pmij(double ps, double *cov,	Line 1661 double pmij(double ps, double *cov,

/************** Product of 2 matrices ****************/	/************** Product of 2 matrices ****************/

double matprod2(double out, double in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double b)	double matprod2(double out, double in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double b)
{	{
/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times	/* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */	b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
/* in, b, out are matrice of pointers which should have been initialized	/* in, b, out are matrice of pointers which should have been initialized
before: only the contents of out is modified. The function returns	before: only the contents of out is modified. The function returns
a pointer to pointers identical to out */	a pointer to pointers identical to out */
long i, j, k;	int i, j, k;
for(i=nrl; i<= nrh; i++)	for(i=nrl; i<= nrh; i++)
for(k=ncolol; k<=ncoloh; k++)	for(k=ncolol; k<=ncoloh; k++){
for(j=ncl,out[i][k]=0.; j<=nch; j++)	out[i][k]=0.;
out[i][k] +=in[i][j]*b[j][k];	for(j=ncl; j<=nch; j++)
	out[i][k] +=in[i][j]*b[j][k];
	}
return out;	return out;
}	}

Line 1446 double *hpxij(double *po, int nhstep	Line 1716 double *hpxij(double *po, int nhstep
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
for (k=1; k<=cptcovage;k++)	for (k=1; k<=cptcovage;k++)
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)	for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];


Line 1468 double *hpxij(double *po, int nhstep	Line 1738 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 1486 double func( double *x)	Line 1775 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 1497 double func( double *x)	Line 1789 double func( double *x)
Then computes with function pmij which return a matrix p[i][j] giving the elementary probability	Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
to be observed in j being in i according to the model.	to be observed in j being in i according to the model.
*/	*/
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
	cov[2+k]=covar[Tvar[k]][i];
	}
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]
has been calculated etc */	has been calculated etc */
Line 1765 double funcone( double *x)	Line 2059 double funcone( double *x)
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
}	}
	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
	/* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */
Line 1800 double funcone( double *x)	Line 2097 double funcone( double *x)
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /	/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /
if(globpr){	if(globpr){
fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\	fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],	num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2weight[i]lli,out[s1][s2],savm[s1][s2]);	2weight[i]lli,out[s1][s2],savm[s1][s2]);
Line 1862 void likelione(FILE *ficres,double p[],	Line 2159 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 1883 void mlikeli(FILE *ficres,double p[], in	Line 2192 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("\n#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,"\n#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,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));

}	}

Line 1899 void hesscov(double **matcov, double p[]	Line 2235 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 2012 double hessii(double x[], double delta,	Line 2348 double hessii(double x[], double delta,

fx=func(x);	fx=func(x);
for (i=1;i<=npar;i++) p2[i]=x[i];	for (i=1;i<=npar;i++) p2[i]=x[i];
for(l=0 ; l <=lmax; l++){	for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
l1=pow(10,l);	l1=pow(10,l);
delts=delt;	delts=delt;
for(k=1 ; k <kmax; k=k+1){	for(k=1 ; k <kmax; k=k+1){
delt = delta(l1k);	delt = delta(l1k);
p2[theta]=x[theta] +delt;	p2[theta]=x[theta] +delt;
k1=func(p2)-fx;	k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
p2[theta]=x[theta]-delt;	p2[theta]=x[theta]-delt;
k2=func(p2)-fx;	k2=func(p2)-fx;
/res= (k1-2.0fx+k2)/delt/delt; */	/res= (k1-2.0fx+k2)/delt/delt; */
Line 2033 double hessii(double x[], double delta,	Line 2369 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 2048 double hessii(double x[], double delta,	Line 2384 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 2163 void pstamp(FILE *fichier)	Line 2499 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 2187 void freqsummary(char fileres[], int ia	Line 2523 void freqsummary(char fileres[], int ia

first=1;	first=1;

for(k1=1; k1<=j;k1++){	/* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
for(i1=1; i1<=ncodemax[k1];i1++){	/* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
j1++;	/* 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);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
for (jk=-5; jk<=nlstate+ndeath; jk++)	for (jk=-5; jk<=nlstate+ndeath; jk++)
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;	freq[i][jk][m]=0;

for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
prop[i][m]=0;	prop[i][m]=0;

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
bool=1;	bool=1;
if (cptcovn>0) {	if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
bool=0;	/* Tests if the value of each of the covariates of i is equal to filter j1 */
	bool=0;
	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
	j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
	}
}	}

if (bool==1){	if (bool==1){
for(m=firstpass; m<=lastpass; m++){	for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);	k2=anint[m][i]+(mint[m][i]/12.);
Line 2229 void freqsummary(char fileres[], int ia	Line 2574 void freqsummary(char fileres[], int ia
/}/	/}/
}	}
}	}
}	} /* end i */

/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
pstamp(ficresp);	pstamp(ficresp);
Line 2237 void freqsummary(char fileres[], int ia	Line 2582 void freqsummary(char fileres[], int ia
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresp, "**********\n#");	fprintf(ficresp, "**********\n#");
	fprintf(ficlog, "\n#********** Variable ");
	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
	fprintf(ficlog, "**********\n#");
}	}
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
Line 2313 void freqsummary(char fileres[], int ia	Line 2661 void freqsummary(char fileres[], int ia
printf("Others in log...\n");	printf("Others in log...\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	/}/
}	}
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

Line 2332 void prevalence(double ***probs, double	Line 2680 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 */

iagemin= (int) agemin;	iagemin= (int) agemin;
iagemax= (int) agemax;	iagemax= (int) agemax;
Line 2346 void prevalence(double ***probs, double	Line 2695 void prevalence(double ***probs, double
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/	/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
j1=0;	j1=0;

j=cptcoveff;	/j=cptcoveff;/
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

for(k1=1; k1<=j;k1++){	first=1;
for(i1=1; i1<=ncodemax[k1];i1++){	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
j1++;	/*for(i1=1; i1<=ncodemax[k1];i1++){
	j1++;*/

for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
Line 2381 void prevalence(double ***probs, double	Line 2731 void prevalence(double ***probs, double
}	}
}	}
for(i=iagemin; i <= iagemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){

for(jk=1,posprop=0; jk <=nlstate ; jk++) {	for(jk=1,posprop=0; jk <=nlstate ; jk++) {
posprop += prop[jk][i];	posprop += prop[jk][i];
}	}

for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if( i <= iagemax){	if( i <= iagemax){
if(posprop>=1.e-5){	if(posprop>=1.e-5){
probs[i][jk][j1]= prop[jk][i]/posprop;	probs[i][jk][j1]= prop[jk][i]/posprop;
} else	} else{
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);	if(first==1){
	first=0;
	printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
	}
	}
}	}
}/* end jk */	}/* end jk */
}/* end i */	}/* end i */
} /* end i1 */	/} //* end i1 */
} /* end k1 */	} /* end j1 */

/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/	/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
/free_vector(pp,1,nlstate);/	/free_vector(pp,1,nlstate);/
Line 2421 void concatwav(int wav[], int **dh, int	Line 2774 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 2542 void concatwav(int wav[], int **dh, int	Line 2895 void concatwav(int wav[], int **dh, int
}	}
jmean=sum/k;	jmean=sum/k;
printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);	printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);	fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
}	}

/********* Tricode **************************/	/********* Tricode **************************/
void tricode(int Tvar, int *nbcode, int imx)	void tricode(int Tvar, int nbcode, int imx, int Ndum)
{	{
/* 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]
	* Tvar[5] in V2+V1+V3age+V2V4 is 2 (V2)
	/* nbcode[Tvar[j]][1]=
	*/

int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;	int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
int modmaxcovj=0; /* Modality max of covariates j */	int modmaxcovj=0; /* Modality max of covariates j */
	int cptcode=0; /* Modality max of covariates j */
	int modmincovj=0; /* Modality min of covariates j */


cptcoveff=0;	cptcoveff=0;

for (k=0; k<maxncov; k++) Ndum[k]=0;	for (k=-1; k < maxncov; k++) Ndum[k]=0;
for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */	for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */

for (j=1; j<=(cptcovn+2cptcovprod); j++) { / For each covariate j */	/* Loop on covariates without age and products */
for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the	for (j=1; j<=(cptcovs); j++) { /* model V1 + V2age+ V3 + V3V4 : V1 + V3 = 2 only */
	for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
modality of this covariate Vj*/	modality of this covariate Vj*/
ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the	ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
	* If product of VnVm, still boolean :
	* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
	* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
	/* Finds for covariate j, n=Tvar[j] of Vn . ij is the
modality of the nth covariate of individual i. */	modality of the nth covariate of individual i. */
	if (ij > modmaxcovj)
	modmaxcovj=ij;
	else if (ij < modmincovj)
	modmincovj=ij;
	if ((ij < -1) && (ij > NCOVMAX)){
	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
	exit(1);
	}else
Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/	Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/
	/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/	/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/
if (ij > modmaxcovj) modmaxcovj=ij;
/* getting the maximum value of the modality of the covariate	/* getting the maximum value of the modality of the covariate
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and	(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
female is 1, then modmaxcovj=1.*/	female is 1, then modmaxcovj=1.*/
}	}
	printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
	cptcode=modmaxcovj;
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */	/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1// For each modality of model-cov j */	/for (i=0; i<=cptcode; i++) {/
if( Ndum[i] != 0 )	for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1// For each value of the modality of model-cov j */
ncodemax[j]++;	printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
/* Number of modalities of the j th covariate. In fact	if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
ncodemax[j]=2 (dichotom. variables only) but it could be more for	ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
historical reasons */	}
	/* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
	historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
} /* Ndum[-1] number of undefined modalities */	} /* Ndum[-1] number of undefined modalities */

/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */	/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
ij=1;	/* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */	/* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX// maxncov or modmaxcovj */	modmincovj=3; modmaxcovj = 7;
	There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
	which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
	variables V1_1 and V1_2.
	nbcode[Tvar[j]][ij]=k;
	nbcode[Tvar[j]][1]=0;
	nbcode[Tvar[j]][2]=1;
	nbcode[Tvar[j]][3]=2;
	*/
	ij=1; /* ij is similar to i but can jumps over null modalities */
	for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
	for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 // Could be 1 to 4 */
	/recode from 0 /
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */	if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.	nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
k is a modality. If we have model=V1+V1*sex	k is a modality. If we have model=V1+V1*sex
Line 2594 void tricode(int Tvar, int *nbcode, in	Line 2984 void tricode(int Tvar, int *nbcode, in
} /* end of loop on modality */	} /* end of loop on modality */
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/	} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/

for (k=0; k< maxncov; k++) Ndum[k]=0;	for (k=-1; k< maxncov; k++) Ndum[k]=0;

for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */	for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./	/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./
ij=Tvar[i]; /* Tvar might be -1 if status was unknown */	ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
Ndum[ij]++;	Ndum[ij]++;
}	}

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

}	}


/********* Health Expectancies **************/	/********* Health Expectancies **************/

void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )	void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )

{	{
/* Health expectancies, no variances */	/* 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 2941 void varevsij(char optionfilefiname[], d	Line 3336 void varevsij(char optionfilefiname[], d
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 3208 void varevsij(char optionfilefiname[], d	Line 3603 void varevsij(char optionfilefiname[], d
free_vector(gmp,nlstate+1,nlstate+ndeath);	free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);	free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/	free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");	fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */	/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */
fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");	fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /	/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 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 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 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);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);	/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
Line 3241 void varprevlim(char fileres[], double *	Line 3636 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 3323 void varprevlim(char fileres[], double *	Line 3717 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;	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;
double *xp;	double *xp;
double gp, gm;	double gp, gm;
double gradg, trgradg;	double gradg, trgradg;
double **mu;	double **mu;
double age,agelim, cov[NCOVMAX];	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];
char fileresprobcov[FILENAMELENGTH];	char fileresprobcov[FILENAMELENGTH];
char fileresprobcor[FILENAMELENGTH];	char fileresprobcor[FILENAMELENGTH];

double ***varpij;	double ***varpij;

strcpy(fileresprob,"prob");	strcpy(fileresprob,"prob");
Line 3412 standard deviations wide on each axis. <	Line 3805 standard deviations wide on each axis. <
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");	To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");

cov[1]=1;	cov[1]=1;
tj=cptcoveff;	/* tj=cptcoveff; */
	tj = (int) pow(2,cptcoveff);
if (cptcovn<1) {tj=1;ncodemax[1]=1;}	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;	j1=0;
for(t=1; t<=tj;t++){	for(j1=1; j1<=tj;j1++){
for(i1=1; i1<=ncodemax[t];i1++){	/for(i1=1; i1<=ncodemax[t];i1++){ /
j1++;	/j1++;/
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");	fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 3440 To be simple, these graphs help to under	Line 3834 To be simple, these graphs help to under
fprintf(ficresprobcor, "**********\n#");	fprintf(ficresprobcor, "**********\n#");
}	}

	gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
	gp=vector(1,(nlstate)*(nlstate+ndeath));
	gm=vector(1,(nlstate)*(nlstate+ndeath));
for (age=bage; age<=fage; age ++){	for (age=bage; age<=fage; age ++){
cov[2]=age;	cov[2]=age;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];	cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
	* 1 1 1 1 1
	* 2 2 1 1 1
	* 3 1 2 1 1
	*/
	/* nbcode[1][1]=0 nbcode[1][2]=1;*/
}	}
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)	for (k=1; k<=cptcovprod;k++)
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];

gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
gp=vector(1,(nlstate)*(nlstate+ndeath));
gm=vector(1,(nlstate)*(nlstate+ndeath));

for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)	for(i=1; i<=npar; i++)
Line 3490 To be simple, these graphs help to under	Line 3889 To be simple, these graphs help to under

matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);	matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);

pmij(pmmij,cov,ncovmodel,x,nlstate);	pmij(pmmij,cov,ncovmodel,x,nlstate);

Line 3527 To be simple, these graphs help to under	Line 3922 To be simple, these graphs help to under
i=0;	i=0;
for (k=1; k<=(nlstate);k++){	for (k=1; k<=(nlstate);k++){
for (l=1; l<=(nlstate+ndeath);l++){	for (l=1; l<=(nlstate+ndeath);l++){
i=i++;	i++;
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);	fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);	fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
for (j=1; j<=i;j++){	for (j=1; j<=i;j++){
	/* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);	fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));	fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
}	}
}	}
}/* end of loop for state */	}/* end of loop for state */
} /* end of loop for age */	} /* end of loop for age */
	free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
	free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
	free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
	free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);

/* Confidence intervalle of pij */	/* Confidence intervalle of pij */
/*	/*
fprintf(ficgp,"\nunset parametric;unset label");	fprintf(ficgp,"\nunset parametric;unset label");
Line 3550 To be simple, these graphs help to under	Line 3950 To be simple, these graphs help to under
*/	*/

/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
first1=1;	first1=1;first2=2;
for (k2=1; k2<=(nlstate);k2++){	for (k2=1; k2<=(nlstate);k2++){
for (l2=1; l2<=(nlstate+ndeath);l2++){	for (l2=1; l2<=(nlstate+ndeath);l2++){
if(l2==k2) continue;	if(l2==k2) continue;
Line 3572 To be simple, these graphs help to under	Line 3972 To be simple, these graphs help to under
lc1=((v1+v2)+sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;	lc1=((v1+v2)+sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;
lc2=((v1+v2)-sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;	lc2=((v1+v2)-sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12)))/2.;
if ((lc2 <0) \|\| (lc1 <0) ){	if ((lc2 <0) \|\| (lc1 <0) ){
printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);	if(first2==1){
fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);	first1=0;
lc1=fabs(lc1);	printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
lc2=fabs(lc2);	}
	fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
	/* lc1=fabs(lc1); / / If we want to have them positive */
	/* lc2=fabs(lc2); */
}	}

/* Eigen vectors */	/* Eigen vectors */
Line 3597 To be simple, these graphs help to under	Line 4000 To be simple, these graphs help to under
first=0;	first=0;
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");	fprintf(ficgp,"\nset ter png small size 320, 240");
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\	fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s%d%1d%1d-%1d%1d.png\">\	:<a href=\"%s%d%1d%1d-%1d%1d.png\">\
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\	%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
Line 3628 To be simple, these graphs help to under	Line 4031 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 3674 void printinghtml(char fileres[], char t	Line 4077 void printinghtml(char fileres[], char t

fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");	fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");

m=cptcoveff;	m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;
Line 3688 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4091 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.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%d2.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 3748 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4151 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fflush(fichtm);	fflush(fichtm);
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");	fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

m=cptcoveff;	m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;
Line 3763 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 4166 fprintf(fichtm," \n<ul><li><b>Graphs</b>
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\	prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);	<img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
Line 3782 true period expectancies (those weighted	Line 4185 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 3797 void printinggnuplot(char fileres[], cha	Line 4200 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 ++) {	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);
fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);	fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\	fprintf(ficgp,"set xlabel \"Age\" \n\
set ylabel \"Probability\" \n\	set ylabel \"Probability\" \n\
set ter png small\n\	set ter png small size 320, 240\n\
set size 0.65,0.65\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 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 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*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
}	}
}	}
/2 eme/	/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\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);

for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
Line 3844 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4247 plot [%.f:%.f] \"%s\" every :::%d::%d u
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 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 0");	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
else fprintf(ficgp,"\" t\"\" w l 0,");	else fprintf(ficgp,"\" t\"\" w l lt 0,");
}	}
}	}

Line 3862 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4265 plot [%.f:%.f] \"%s\" every :::%d::%d u
/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small\n\	fprintf(ficgp,"set ter png small size 320, 240\n\
set size 0.65,0.65\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
Line 3883 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 4285 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,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
	fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter png small\nset size 0.65,0.65\n\	set ter png small size 320, 240\n\
unset log y\n\	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 3918 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4321 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
}	}
}	}
}	}
	/goto avoid;/
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/	for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
for(jk=1; jk <=m; jk++) {	for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);	fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
if (ng==2)	if (ng==2)
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
else	else
fprintf(ficgp,"\nset title \"Probability\"\n");	fprintf(ficgp,"\nset title \"Probability\"\n");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);	fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;	i=1;
for(k2=1; k2<=nlstate; k2++) {	for(k2=1; k2<=nlstate; k2++) {
k3=i;	k3=i;
Line 3936 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4339 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);	fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);
else	else
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
ij=1;	ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel; j++) {	for(j=3; j <=ncovmodel; j++) {
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {	/* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind \/ /
fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);	/* /\fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\/ */
ij++;	/* ij++; */
}	/* } */
else	/* else */
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");
Line 3951 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4354 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);	fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
ij=1;	ij=1;
for(j=3; j <=ncovmodel; j++){	for(j=3; j <=ncovmodel; j++){
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {	/* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);	/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); /
ij++;	/* ij++; */
}	/* } */
else	/* else */
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
Line 3968 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1	Line 4371 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
} /* end k2 */	} /* end k2 */
} /* end jk */	} /* end jk */
} /* end ng */	} /* end ng */
	/* avoid: */
fflush(ficgp);	fflush(ficgp);
} /* end gnuplot */	} /* end gnuplot */

Line 4021 prevforecast(char fileres[], double anpr	Line 4425 prevforecast(char fileres[], double anpr
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 4316 void prwizard(int ncovmodel, int nlstate	Line 4719 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 4538 fprintf(fichtm,"<ul><li><h4>Life table</	Line 4941 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 4551 void printinggnuplotmort(char fileres[],	Line 4954 void printinggnuplotmort(char fileres[],
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
fprintf(ficgp,"set out \"graphmort.png\"\n ");	fprintf(ficgp,"set out \"graphmort.png\"\n ");
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");	fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
fprintf(ficgp, "set ter png small\n set log y\n");	fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
fprintf(ficgp, "set size 0.65,0.65\n");	/* fprintf(ficgp, "set size 0.65,0.65\n"); */
fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);	fprintf(ficgp,"plot [%d:100] %lfexp(%lf(x-%d))",agegomp,p[1],p[2],agegomp);

}	}
Line 4563 int readdata(char datafile[], int firsto	Line 4966 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 4594 int readdata(char datafile[], int firsto	Line 4997 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 4608 int readdata(char datafile[], int firsto	Line 5009 int readdata(char datafile[], int firsto
lval=strtol(strb,&endptr,10);	lval=strtol(strb,&endptr,10);
/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0')){
printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
return 1;	return 1;
}	}
}	}
Line 4619 int readdata(char datafile[], int firsto	Line 5020 int readdata(char datafile[], int firsto
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.") != 0){	else if(iout=sscanf(strb,"%s.",dummy) != 0){
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
return 1;	return 1;
}	}
anint[j][i]= (double) year;	anint[j][i]= (double) year;
Line 4639 int readdata(char datafile[], int firsto	Line 5040 int readdata(char datafile[], int firsto
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;	return 1;
}	}
andc[i]=(double) year;	andc[i]=(double) year;
Line 4650 int readdata(char datafile[], int firsto	Line 5051 int readdata(char datafile[], int firsto
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.") != 0){	else if(iout=sscanf(strb,"%s.", dummy) != 0){
month=99;	month=99;
year=9999;	year=9999;
}else{	}else{
printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;	return 1;
}	}
if (year==9999) {	if (year==9999) {
printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
return 1;	return 1;

}	}
Line 4672 int readdata(char datafile[], int firsto	Line 5073 int readdata(char datafile[], int firsto
errno=0;	errno=0;
dval=strtod(strb,&endptr);	dval=strtod(strb,&endptr);
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0')){
printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);	printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);	fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
fflush(ficlog);	fflush(ficlog);
return 1;	return 1;
}	}
Line 4688 int readdata(char datafile[], int firsto	Line 5089 int readdata(char datafile[], int firsto
errno=0;	errno=0;
lval=strtol(strb,&endptr,10);	lval=strtol(strb,&endptr,10);
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0')){
printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
return 1;	return 1;
}	}
}	}
if(lval <-1 \|\| lval >1){	if(lval <-1 \|\| lval >1){
printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
Line 4703 int readdata(char datafile[], int firsto	Line 5104 int readdata(char datafile[], int firsto
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);	Exiting.\n",lval,linei, i,line,j);
fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
Line 4735 int readdata(char datafile[], int firsto	Line 5136 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 4743 int readdata(char datafile[], int firsto	Line 5144 int readdata(char datafile[], int firsto


}	}
	void removespace(char *str) {
int decodemodel ( char model[], int lastobs)	char p1 = str, p2 = str;
	do
	while (*p2 == ' ')
	p2++;
	while (p1++ = p2++);
	}

	int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
	* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age
	* - cptcovt total number of covariates of the model nbocc(+)+1 = 8
	* - cptcovn or number of covariates k of the models excluding age*products =6
	* - cptcovage number of covariates with age*products =2
	* - cptcovs number of simple covariates
	* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
	* which is a new column after the 9 (ncovcol) variables.
	* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
	* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
	* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.
	* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .
	*/
{	{
int i, j, k;	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];

	/removespace(model);/
if (strlen(model) >1){ /* If there is at least 1 covariate */	if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=1, k2=1;	j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
j=nbocc(model,'+'); /* j=Number of '+' */	j=nbocc(model,'+'); /*< j=Number of '+' /
j1=nbocc(model,''); / j1=Number of '' /	j1=nbocc(model,''); /< j1=Number of '' */
cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3	cptcovs=j+1-j1; /*< Number of simple covariates V1+V2age+V3 +V3V4=> V1 + V3 =2 /
but the covariates which are product must be computed and stored. */	cptcovt= j+1; /* Number of total covariates in the model V1 + V2age+ V3 + V3V4=> 4*/
cptcovprod=j1; /Number of products V1V2 +v3age = 2 /	/* including age products which are counted in cptcovage.
	/* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
	cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /
	cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */
strcpy(modelsav,model);	strcpy(modelsav,model);
if (strstr(model,"AGE") !=0){	if (strstr(model,"AGE") !=0){
printf("Error. AGE must be in lower case 'age' model=%s ",model);	printf("Error. AGE must be in lower case 'age' model=%s ",model);
fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);	fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
return 1;	return 1;
}	}
	if (strstr(model,"v") !=0){
	printf("Error. 'v' must be in upper case 'V' model=%s ",model);
	fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
	return 1;
	}

	/* Design
	* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
	* < ncovcol=8 >
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8
	* k= 1 2 3 4 5 6 7 8
	* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
	* covar[k,i], value of kth covariate if not including age for individual i:
	* covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
	* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
	* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and
	* Tage[++cptcovage]=k
	* if products, new covar are created after ncovcol with k1
	* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
	* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
	* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
	* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
	* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
	* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
	* < ncovcol=8 >
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2
	* k= 1 2 3 4 5 6 7 8 9 10 11 12
	* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
	* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
	* p Tprod[1]@2={ 6, 5}
	*p Tvard[1][1]@4= {7, 8, 5, 6}
	* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8
	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	*How to reorganize?
	* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
	* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
	* {2, 1, 4, 8, 5, 6, 3, 7}
	* Struct []
	*/

/* This loop fills the array Tvar from the string 'model'.*/	/* This loop fills the array Tvar from the string 'model'.*/
/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */	/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */	/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4 */
Line 4778 int decodemodel ( char model[], int last	Line 5240 int decodemodel ( char model[], int last
/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */	/* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
/* } */	/* } */
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
for(k=cptcovn; k>=1;k--){	/*
cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	* Treating invertedly V2+V1+V3age+V2V4 is as if written V2V4 +V3age + V1 + V2 */
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4	for(k=cptcovt; k>=1;k--) /*< Number of covariates /
*/	Tvar[k]=0;
	cptcovage=0;
	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
	modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { / Model includes a product V2+V1+V4+V3age strb=V3age */	if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /
cutv(strd,strc,strb,''); / strdstrc VmVn: strb=V3age strc=age strd=V3 ; V3V2 strc=V2, strd=V3 */	cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /
if (strcmp(strc,"age")==0) { /* Vnage /	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strd,'V'); /* stre="V3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=2 ; V1+V2age Tvar[2]=2 */	Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2 */
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Sums the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tage[1] = 4 */	Tage[cptcovage]=k; /* Tage[1] = 4 */
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
} else if (strcmp(strd,"age")==0) { /* or ageVn /	} else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strc,'V');	cutl(stre,strb,strc,'V');
Tvar[k]=atoi(stre);	Tvar[k]=atoi(stre);
cptcovage++;	cptcovage++;
Tage[cptcovage]=k;	Tage[cptcovage]=k;
} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/	} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/
/* loops on k1=1 (V3V2) and k1=2 V4V3 */	/* loops on k1=1 (V3V2) and k1=2 V4V3 */
cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/	cptcovn++;
Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but	cptcovprodnoage++;k1++;
	cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
	Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
because this model-covariate is a construction we invent a new column	because this model-covariate is a construction we invent a new column
ncovcol + k1	ncovcol + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */
cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tvard[k1][1]=atoi(strc); /* m 1 for V1*/	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2]=atoi(stre); /* n 4 for V4*/	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */	k2=k2+2;
Tvar[cptcovn+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */	Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
	Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
for (i=1; i<=lastobs;i++){	for (i=1; i<=lastobs;i++){
/* Computes the new covariate which is a product of	/* Computes the new covariate which is a product of
covar[n][i]* covar[m][i] and stores it at ncovol+k1 */	covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];	covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
}	}
k1++;
k2=k2+2;
} /* End age is not in the model */	} /* End age is not in the model */
} /* End if model includes a product */	} /* End if model includes a product */
else { /* no more sum */	else { /* no more sum */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutv(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
Tvar[k]=atoi(strc);	ks++; /*< Number of simple covariates /
	cptcovn++;
	Tvar[k]=atoi(strd);
}	}
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */	strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
Line 4846 int decodemodel ( char model[], int last	Line 5316 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);
}	}
Line 4905 calandcheckages(int imx, int maxwav, dou	Line 5375 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 4943 calandcheckages(int imx, int maxwav, dou	Line 5413 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);
}	}
Line 4963 int main(int argc, char *argv[])	Line 5433 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 5003 int main(int argc, char *argv[])	Line 5470 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 5014 int main(int argc, char *argv[])	Line 5481 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];	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 5034 int main(int argc, char *argv[])	Line 5500 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 5067 int main(int argc, char *argv[])	Line 5535 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 5122 int main(int argc, char *argv[])	Line 5593 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);

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 5138 int main(int argc, char *argv[])	Line 5609 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\n",optionfile);	printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
fprintf(ficlog,"Problem with optionfile %s\n",optionfile);	fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
fflush(ficlog);	fflush(ficlog);
goto end;	/* goto end; */
	exit(70);
}	}


Line 5161 int main(int argc, char *argv[])	Line 5633 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
numlinepar++;	numlinepar++;
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
}	}
Line 5177 int main(int argc, char *argv[])	Line 5649 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
numlinepar++;	numlinepar++;
puts(line);	fputs(line, stdout);
	//puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);


covar=matrix(0,NCOVMAX,1,n);	covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/
/* v1+v2+v3+v2v4+v5age makes cptcovn = 5	/* v1+v2+v3+v2v4+v5age makes cptcovn = 5
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
*/	*/
if (strlen(model)>1)	if (strlen(model)>1)
cptcovn=nbocc(model,'+')+1;	ncovmodel=2+nbocc(model,'+')+1; /Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2v4+v5age makes 5+2=7/
/* ncovprod */	else
ncovmodel=2+cptcovn; /Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2v4+v5age makes 5+2=7/	ncovmodel=2;
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */	nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
nforce= (nlstate+ndeath-1)nlstate; / Number of forces ij from state i to j */	nforce= (nlstate+ndeath-1)nlstate; / Number of forces ij from state i to j */
npar= nforcencovmodel; / Number of parameters like aij*/	npar= nforcencovmodel; / Number of parameters like aij*/
Line 5224 int main(int argc, char *argv[])	Line 5697 int main(int argc, char *argv[])
matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
}	}
else{	else{
/* Read guess parameters */	/* Read guessed parameters */
/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
numlinepar++;	numlinepar++;
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
}	}
Line 5273 run imach with mle=-1 to get a correct t	Line 5746 run imach with mle=-1 to get a correct t
}	}
fflush(ficlog);	fflush(ficlog);

	/* Reads scales values */
p=param[1][1];	p=param[1][1];

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
Line 5280 run imach with mle=-1 to get a correct t	Line 5754 run imach with mle=-1 to get a correct t
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
numlinepar++;	numlinepar++;
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
}	}
Line 5289 run imach with mle=-1 to get a correct t	Line 5763 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 5311 run imach with mle=-1 to get a correct t	Line 5785 run imach with mle=-1 to get a correct t
}	}
fflush(ficlog);	fflush(ficlog);

	/* Reads covariance matrix */
delti=delti3[1][1];	delti=delti3[1][1];


Line 5321 run imach with mle=-1 to get a correct t	Line 5796 run imach with mle=-1 to get a correct t
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
numlinepar++;	numlinepar++;
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
}	}
Line 5332 run imach with mle=-1 to get a correct t	Line 5807 run imach with mle=-1 to get a correct t
for(j=1; j <=npar; j++) matcov[i][j]=0.;	for(j=1; j <=npar; j++) matcov[i][j]=0.;

for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",&str);	fscanf(ficpar,"%s",str);
if(mle==1)	if(mle==1)
printf("%s",str);	printf("%s",str);
fprintf(ficlog,"%s",str);	fprintf(ficlog,"%s",str);
Line 5389 run imach with mle=-1 to get a correct t	Line 5864 run imach with mle=-1 to get a correct t
anint=matrix(1,maxwav,1,n);	anint=matrix(1,maxwav,1,n);
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,8); /* hard coded ? */	ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /

/* Reads data from file datafile */	/* Reads data from file datafile */
if (readdata(datafile, firstobs, lastobs, &imx)==1)	if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 5412 run imach with mle=-1 to get a correct t	Line 5887 run imach with mle=-1 to get a correct t
ncovcol + k1	ncovcol + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3	If already ncovcol=4 and model=V2+V1+V1V4+ageV3
Tvar[3=V1V4]=4+1 etc /	Tvar[3=V1V4]=4+1 etc /
Tprod=ivector(1,15);	Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+age*V3	/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+age*V3
if V2+V1+V1V4+ageV3+V3V2 TProd[k1=2]=5 (V3V2)	if V2+V1+V1V4+ageV3+V3V2 TProd[k1=2]=5 (V3V2)
*/	*/
Tvaraff=ivector(1,15);	Tvaraff=ivector(1,NCOVMAX); /* Unclear */
Tvard=imatrix(1,15,1,2); /* For V3V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) /	Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age	* For V3V2 (in V2+V1+V1V4+ageV3+V3V2), V3*V2 position is 2nd.
	* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
	Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age
4 covariates (3 plus signs)	4 covariates (3 plus signs)
Tage[1=V3age]= 4; Tage[2=ageV4] = 3	Tage[1=V3age]= 4; Tage[2=ageV4] = 3
*/	*/
Line 5450 run imach with mle=-1 to get a correct t	Line 5927 run imach with mle=-1 to get a correct t
free_matrix(anint,1,maxwav,1,n);*/	free_matrix(anint,1,maxwav,1,n);*/
free_vector(moisdc,1,n);	free_vector(moisdc,1,n);
free_vector(andc,1,n);	free_vector(andc,1,n);
	/* */

wav=ivector(1,imx);	wav=ivector(1,imx);
dh=imatrix(1,lastpass-firstpass+1,1,imx);	dh=imatrix(1,lastpass-firstpass+1,1,imx);
bh=imatrix(1,lastpass-firstpass+1,1,imx);	bh=imatrix(1,lastpass-firstpass+1,1,imx);
Line 5459 run imach with mle=-1 to get a correct t	Line 5936 run imach with mle=-1 to get a correct t

/* Concatenates waves */	/* Concatenates waves */
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);	concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
	/* */

/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */	/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */

nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;	ncodemax[1]=1;
if (cptcovn > 0) tricode(Tvar,nbcode,imx);	Ndum =ivector(-1,NCOVMAX);
	if (ncovmodel > 2)
codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of	tricode(Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /
the estimations*/
	codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2(k-1) */
	/printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);/
h=0;	h=0;


	/if (cptcovn > 0) /


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

for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */	for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */	for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */	for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 /	for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 /
h++;	h++;
if (h>m) {	if (h>m)
h=1;	h=1;
codtab[h][k]=j;	/< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2(k-1) )/2**(k-1) + 1
codtab[h][Tvar[k]]=j;	* h 1 2 3 4
}	*______________________________
	* 1 i=1 1 i=1 1 i=1 1 i=1 1
	* 2 2 1 1 1
	* 3 i=2 1 2 1 1
	* 4 2 2 1 1
	* 5 i=3 1 i=2 1 2 1
	* 6 2 1 2 1
	* 7 i=4 1 2 2 1
	* 8 2 2 2 1
	* 9 i=5 1 i=3 1 i=2 1 1
	* 10 2 1 1 1
	* 11 i=6 1 2 1 1
	* 12 2 2 1 1
	* 13 i=7 1 i=4 1 2 1
	* 14 2 1 2 1
	* 15 i=8 1 2 2 1
	* 16 2 2 2 1
	*/
	codtab[h][k]=j;
	/codtab[h][Tvar[k]]=j;/
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);	printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
}	}
}	}
Line 5495 run imach with mle=-1 to get a correct t	Line 5999 run imach with mle=-1 to get a correct t
printf("\n");	printf("\n");
}	}
scanf("%d",i);*/	scanf("%d",i);*/

	free_ivector(Ndum,-1,NCOVMAX);



/------------ gnuplot -------------/	/------------ gnuplot -------------/
strcpy(optionfilegnuplot,optionfilefiname);	strcpy(optionfilegnuplot,optionfilefiname);
Line 5508 run imach with mle=-1 to get a correct t	Line 6016 run imach with mle=-1 to get a correct t
else{	else{
fprintf(ficgp,"\n# %s\n", version);	fprintf(ficgp,"\n# %s\n", version);
fprintf(ficgp,"# %s\n", optionfilegnuplot);	fprintf(ficgp,"# %s\n", optionfilegnuplot);
fprintf(ficgp,"set missing 'NaNq'\n");	//fprintf(ficgp,"set missing 'NaNq'\n");
	fprintf(ficgp,"set datafile missing 'NaNq'\n");
}	}
/* fclose(ficgp);*/	/* fclose(ficgp);*/
/--------- index.htm --------/	/--------- index.htm --------/
Line 5617 Interval (in months) between two waves:	Line 6126 Interval (in months) between two waves:
ximort[i][j]=(i == j ? 1.0 : 0.0);	ximort[i][j]=(i == j ? 1.0 : 0.0);
}	}

p[1]=0.0268; p[NDIM]=0.083;	/p[1]=0.0268; p[NDIM]=0.083;/
/printf("%lf %lf", p[1], p[2]);/	/printf("%lf %lf", p[1], p[2]);/


#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 5634 Interval (in months) between two waves:	Line 6143 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 5947 Interval (in months) between two waves:	Line 6456 Interval (in months) between two waves:
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 5967 Interval (in months) between two waves:	Line 6476 Interval (in months) between two waves:
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 5981 Interval (in months) between two waves:	Line 6490 Interval (in months) between two waves:
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 5997 Interval (in months) between two waves:	Line 6506 Interval (in months) between two waves:
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
puts(line);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 6011 Interval (in months) between two waves:	Line 6520 Interval (in months) between two waves:



/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
/,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);/	/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */

replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
Line 6037 Interval (in months) between two waves:	Line 6546 Interval (in months) between two waves:


/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
	#include "prevlim.h" /* Use ficrespl, ficlog */
strcpy(filerespl,"pl");
strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
}
printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
pstamp(ficrespl);
fprintf(ficrespl,"# Period (stable) prevalence \n");
fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");

prlim=matrix(1,nlstate,1,nlstate);

agebase=ageminpar;
agelim=agemaxpar;
ftolpl=1.e-10;
i1=cptcoveff;
if (cptcovn < 1){i1=1;}

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

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

/------------- h Pij x at various ages ------------/	#ifdef FREEEXIT2
	#include "freeexit2.h"
strcpy(filerespij,"pij"); strcat(filerespij,fileres);	#endif
if((ficrespij=fopen(filerespij,"w"))==NULL) {
printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
}
printf("Computing pij: result on file '%s' \n", filerespij);
fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);

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

agelim=AGESUP;
hstepm=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 ");
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;
fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrespij,"******\n");

for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 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);	/------------- h Pij x at various ages ------------/
oldm=oldms;savm=savms;	#include "hpijx.h"
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	fclose(ficrespij);
fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %1d-%1d",i,j);
fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ 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");
}
}
}

	/-------------- Variance of one-step probabilities---/
	k=1;
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);	varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);

fclose(ficrespij);

probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
for(i=1;i<=AGESUP;i++)	for(i=1;i<=AGESUP;i++)
Line 6196 Interval (in months) between two waves:	Line 6609 Interval (in months) between two waves:
}	}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
k=k+1;
	for (k=1; k <= (int) pow(2,cptcoveff); k++){
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
Line 6210 Interval (in months) between two waves:	Line 6624 Interval (in months) between two waves:
evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);

free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
}	/}/
}	}
fclose(ficreseij);	fclose(ficreseij);

Line 6255 Interval (in months) between two waves:	Line 6669 Interval (in months) between two waves:
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
k=k+1;
fprintf(ficrest,"\n#****** ");	for (k=1; k <= (int) pow(2,cptcoveff); k++){
	fprintf(ficrest,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");
Line 6280 Interval (in months) between two waves:	Line 6695 Interval (in months) between two waves:
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
	/*
	*/
	/* goto endfree; */

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
pstamp(ficrest);	pstamp(ficrest);


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;	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); 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 ");	cptcod= 0; /* To be deleted */
	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
if(vpopbased==1)	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);
else	else
Line 6329 Interval (in months) between two waves:	Line 6751 Interval (in months) between two waves:
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_vector(epj,1,nlstate+1);	free_vector(epj,1,nlstate+1);
}	/}/
}	}
free_vector(weight,1,n);	free_vector(weight,1,n);
free_imatrix(Tvard,1,15,1,2);	free_imatrix(Tvard,1,NCOVMAX,1,2);
free_imatrix(s,1,maxwav+1,1,n);	free_imatrix(s,1,maxwav+1,1,n);
free_matrix(anint,1,maxwav,1,n);	free_matrix(anint,1,maxwav,1,n);
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,1,n);
Line 6354 Interval (in months) between two waves:	Line 6776 Interval (in months) between two waves:
}	}
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);	printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
k=k+1;
fprintf(ficresvpl,"\n#****** ");	for (k=1; k <= (int) pow(2,cptcoveff); k++){
	fprintf(ficresvpl,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");
Line 6366 Interval (in months) between two waves:	Line 6789 Interval (in months) between two waves:
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
}	/}/
}	}

fclose(ficresvpl);	fclose(ficresvpl);
Line 6374 Interval (in months) between two waves:	Line 6797 Interval (in months) between two waves:
/---------- End : free ----------------/	/---------- End : free ----------------/
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);	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);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
Line 6389 Interval (in months) between two waves:	Line 6811 Interval (in months) between two waves:
free_matrix(agev,1,maxwav,1,imx);	free_matrix(agev,1,maxwav,1,imx);
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);

free_ivector(ncodemax,1,8);	free_ivector(ncodemax,1,NCOVMAX);
free_ivector(Tvar,1,15);	free_ivector(Tvar,1,NCOVMAX);
free_ivector(Tprod,1,15);	free_ivector(Tprod,1,NCOVMAX);
free_ivector(Tvaraff,1,15);	free_ivector(Tvaraff,1,NCOVMAX);
free_ivector(Tage,1,15);	free_ivector(Tage,1,NCOVMAX);

free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);	free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
free_imatrix(codtab,1,100,1,10);	free_imatrix(codtab,1,100,1,10);
Line 6410 Interval (in months) between two waves:	Line 6832 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 %d Sec.\n", end_time.tv_sec -start_time.tv_sec);	printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
fprintf(ficlog,"Total time used %s\n", asc_diff_time(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 %d 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 6439 Interval (in months) between two waves:	Line 6862 Interval (in months) between two waves:
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 6459 Interval (in months) between two waves:	Line 6882 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 6483 Interval (in months) between two waves:	Line 6917 Interval (in months) between two waves:
scanf("%s",z);	scanf("%s",z);
}	}
}	}

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

Removed from v.1.140
changed lines
	Added in v.1.166