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Diff for /imach/src/imach.c between versions 1.99 and 1.120

version 1.99, 2004/06/05 08:57:40	version 1.120, 2006/03/16 15:10:38
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.120 2006/03/16 15:10:38 lievre
	(Module): refinements in the computation of lli if
	status=-2 in order to have more reliable computation if stepm is
	not 1 month. Version 0.98f

	Revision 1.119 2006/03/15 17:42:26 brouard
	(Module): Bug if status = -2, the loglikelihood was
	computed as likelihood omitting the logarithm. Version O.98e

	Revision 1.118 2006/03/14 18:20:07 brouard
	(Module): varevsij Comments added explaining the second
	table of variances if popbased=1 .
	(Module): Covariances of eij, ekl added, graphs fixed, new html link.
	(Module): Function pstamp added
	(Module): Version 0.98d

	Revision 1.117 2006/03/14 17:16:22 brouard
	(Module): varevsij Comments added explaining the second
	table of variances if popbased=1 .
	(Module): Covariances of eij, ekl added, graphs fixed, new html link.
	(Module): Function pstamp added
	(Module): Version 0.98d

	Revision 1.116 2006/03/06 10:29:27 brouard
	(Module): Variance-covariance wrong links and
	varian-covariance of ej. is needed (Saito).

	Revision 1.115 2006/02/27 12:17:45 brouard
	(Module): One freematrix added in mlikeli! 0.98c

	Revision 1.114 2006/02/26 12:57:58 brouard
	(Module): Some improvements in processing parameter
	filename with strsep.

	Revision 1.113 2006/02/24 14:20:24 brouard
	(Module): Memory leaks checks with valgrind and:
	datafile was not closed, some imatrix were not freed and on matrix
	allocation too.

	Revision 1.112 2006/01/30 09:55:26 brouard
	(Module): Back to gnuplot.exe instead of wgnuplot.exe

	Revision 1.111 2006/01/25 20:38:18 brouard
	(Module): Lots of cleaning and bugs added (Gompertz)
	(Module): Comments can be added in data file. Missing date values
	can be a simple dot '.'.

	Revision 1.110 2006/01/25 00:51:50 brouard
	(Module): Lots of cleaning and bugs added (Gompertz)

	Revision 1.109 2006/01/24 19:37:15 brouard
	(Module): Comments (lines starting with a #) are allowed in data.

	Revision 1.108 2006/01/19 18:05:42 lievre
	Gnuplot problem appeared...
	To be fixed

	Revision 1.107 2006/01/19 16:20:37 brouard
	Test existence of gnuplot in imach path

	Revision 1.106 2006/01/19 13:24:36 brouard
	Some cleaning and links added in html output

	Revision 1.105 2006/01/05 20:23:19 lievre
	* empty log message *

	Revision 1.104 2005/09/30 16:11:43 lievre
	(Module): sump fixed, loop imx fixed, and simplifications.
	(Module): If the status is missing at the last wave but we know
	that the person is alive, then we can code his/her status as -2
	(instead of missing=-1 in earlier versions) and his/her
	contributions to the likelihood is 1 - Prob of dying from last
	health status (= 1-p13= p11+p12 in the easiest case of somebody in
	the healthy state at last known wave). Version is 0.98

	Revision 1.103 2005/09/30 15:54:49 lievre
	(Module): sump fixed, loop imx fixed, and simplifications.

	Revision 1.102 2004/09/15 17:31:30 brouard
	Add the possibility to read data file including tab characters.

	Revision 1.101 2004/09/15 10:38:38 brouard
	Fix on curr_time

	Revision 1.100 2004/07/12 18:29:06 brouard
	Add version for Mac OS X. Just define UNIX in Makefile

Revision 1.99 2004/06/05 08:57:40 brouard	Revision 1.99 2004/06/05 08:57:40 brouard
* empty log message *	* empty log message *

Line 146	Line 233
hPijx.	hPijx.

Also this programme outputs the covariance matrix of the parameters but also	Also this programme outputs the covariance matrix of the parameters but also
of the life expectancies. It also computes the stable prevalence.	of the life expectancies. It also computes the period (stable) prevalence.

Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).	Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
Institut national d'études démographiques, Paris.	Institut national d'études démographiques, Paris.
Line 175	Line 262
begin-prev-date,...	begin-prev-date,...
open gnuplot file	open gnuplot file
open html file	open html file
stable prevalence	period (stable) prevalence
for age prevalim()	for age prevalim()
h Pij x	h Pij x
variance of p varprob	variance of p varprob
Line 187	Line 274
varevsij()	varevsij()
if popbased==1 varevsij(,popbased)	if popbased==1 varevsij(,popbased)
total life expectancies	total life expectancies
Variance of stable prevalence	Variance of period (stable) prevalence
end	end
*/	*/

Line 197	Line 284
#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
#include <stdlib.h>	#include <stdlib.h>
	#include <string.h>
#include <unistd.h>	#include <unistd.h>

	#include <limits.h>
	#include <sys/types.h>
	#include <sys/stat.h>
	#include <errno.h>
	extern int errno;

/* #include <sys/time.h> */	/* #include <sys/time.h> */
#include <time.h>	#include <time.h>
#include "timeval.h"	#include "timeval.h"
Line 207	Line 301
/* #define _(String) gettext (String) */	/* #define _(String) gettext (String) */

#define MAXLINE 256	#define MAXLINE 256

#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 132	#define FILENAMELENGTH 132
/#define DEBUG/
/#define windows/
#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 */

Line 227	Line 321
#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 UNIX
#define DIRSEPARATOR '/'	#define DIRSEPARATOR '/'
	#define CHARSEPARATOR "/"
#define ODIRSEPARATOR '\\'	#define ODIRSEPARATOR '\\'
#else	#else
#define DIRSEPARATOR '\\'	#define DIRSEPARATOR '\\'
	#define CHARSEPARATOR "\\"
#define ODIRSEPARATOR '/'	#define ODIRSEPARATOR '/'
#endif	#endif

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

char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";	char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
	char strstart[80];
	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nvar;	int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
Line 252 int popbased=0;	Line 350 int popbased=0;
int wav; / Number of waves for this individuual 0 is possible */	int wav; / Number of waves for this individuual 0 is possible */
int maxwav; /* Maxim number of waves */	int maxwav; /* Maxim number of waves */
int jmin, jmax; /* min, max spacing between 2 waves */	int jmin, jmax; /* min, max spacing between 2 waves */
	int ijmin, ijmax; /* Individuals having jmin and jmax */
int gipmx, gsw; /* Global variables on the number of contributions	int gipmx, gsw; /* Global variables on the number of contributions
to the likelihood and the sum of weights (done by funcone)*/	to the likelihood and the sum of weights (done by funcone)*/
int mle, weightopt;	int mle, weightopt;
Line 262 int *bh; / bh[mi][i] is the bias (+ or	Line 361 int *bh; / bh[mi][i] is the bias (+ or
double jmean; /* Mean space between 2 waves */	double jmean; /* Mean space between 2 waves */
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,ficpar, ficparo,ficres, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;	FILE fic,ficpar, ficparo,ficres, ficresp, ficrespl, ficrespij, ficrest,ficresf,ficrespop;
FILE ficlog, ficrespow;	FILE ficlog, ficrespow;
int globpr; /* Global variable for printing or not */	int globpr; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
Line 276 FILE *ficresprobmorprev;	Line 375 FILE *ficresprobmorprev;
FILE fichtm, fichtmcov; /* Html File */	FILE fichtm, fichtmcov; /* Html File */
FILE *ficreseij;	FILE *ficreseij;
char filerese[FILENAMELENGTH];	char filerese[FILENAMELENGTH];
	FILE *ficresstdeij;
	char fileresstde[FILENAMELENGTH];
	FILE *ficrescveij;
	char filerescve[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
char fileresv[FILENAMELENGTH];	char fileresv[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];	char title[MAXLINE];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];	char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];	char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
char command[FILENAMELENGTH];	char command[FILENAMELENGTH];
int outcmd=0;	int outcmd=0;
Line 304 long time_value;	Line 407 long time_value;
extern long time();	extern long time();
char strcurr[80], strfor[80];	char strcurr[80], strfor[80];

	char *endptr;
	long lval;

#define NR_END 1	#define NR_END 1
#define FREE_ARG char*	#define FREE_ARG char*
#define FTOL 1.0e-10	#define FTOL 1.0e-10
Line 352 double *weight;	Line 458 double *weight;
int *s; / Status */	int *s; / Status */
double agedc, *covar, idx;	double agedc, *covar, idx;
int *nbcode, Tcode, Tvar, codtab, Tvard, Tprod, cptcovprod, *Tvaraff;	int *nbcode, Tcode, Tvar, codtab, Tvard, Tprod, cptcovprod, *Tvaraff;
	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 */
Line 359 double ftolhess; /* Tolerance for comput	Line 466 double ftolhess; /* Tolerance for comput
/************** 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 )
{	{
/* From a file name with full path (either Unix or Windows) we extract the directory (dirc)	/* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
the name of the file (name), its extension only (ext) and its first part of the name (finame)	the name of the file (name), its extension only (ext) and its first part of the name (finame)
*/	*/
char ss; / pointer */	char ss; / pointer */
Line 368 static int split( char path, char dirc	Line 475 static int split( char path, char dirc
l1 = strlen(path ); /* length of path */	l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
ss= strrchr( path, DIRSEPARATOR ); /* find last / */	ss= strrchr( path, DIRSEPARATOR ); /* find last / */
if ( ss == NULL ) { /* no directory, so use current */	if ( ss == NULL ) { /* no directory, so determine current directory */
	strcpy( name, path ); /* we got the fullname name because no directory */
/*if(strrchr(path, ODIRSEPARATOR )==NULL)	/*if(strrchr(path, ODIRSEPARATOR )==NULL)
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/	printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
/* get current working directory */	/* get current working directory */
Line 376 static int split( char path, char dirc	Line 484 static int split( char path, char dirc
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {	if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
return( GLOCK_ERROR_GETCWD );	return( GLOCK_ERROR_GETCWD );
}	}
strcpy( name, path ); /* we've got it */	/* got dirc from getcwd*/
	printf(" DIRC = %s \n",dirc);
} else { /* strip direcotry from path */	} else { /* strip direcotry from path */
ss++; /* after this, the filename */	ss++; /* after this, the filename */
l2 = strlen( ss ); /* length of filename */	l2 = strlen( ss ); /* length of filename */
Line 384 static int split( char path, char dirc	Line 493 static int split( char path, char dirc
strcpy( name, ss ); /* save file name */	strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */	strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */	dirc[l1-l2] = 0; /* add zero */
	printf(" DIRC2 = %s \n",dirc);
}	}
	/* We add a separator at the end of dirc if not exists */
l1 = strlen( dirc ); /* length of directory */	l1 = strlen( dirc ); /* length of directory */
/*#ifdef windows	if( dirc[l1-1] != DIRSEPARATOR ){
if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }	dirc[l1] = DIRSEPARATOR;
#else	dirc[l1+1] = 0;
if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }	printf(" DIRC3 = %s \n",dirc);
#endif	}
*/
ss = strrchr( name, '.' ); /* find last / */	ss = strrchr( name, '.' ); /* find last / */
if (ss >0){	if (ss >0){
ss++;	ss++;
Line 401 static int split( char path, char dirc	Line 511 static int split( char path, char dirc
strncpy( finame, name, l1-l2);	strncpy( finame, name, l1-l2);
finame[l1-l2]= 0;	finame[l1-l2]= 0;
}	}

return( 0 ); /* we're done */	return( 0 ); /* we're done */
}	}

Line 433 int nbocc(char *s, char occ)	Line 544 int nbocc(char *s, char occ)

void cutv(char u,char v, char*t, char occ)	void cutv(char u,char v, char*t, char occ)
{	{
/* cuts string t into u and v where u is ended by char occ excluding it	/* cuts string t into u and v where u ends before first occurence of char 'occ'
and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)	and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
gives u="abcedf" and v="ghi2j" */	gives u="abcedf" and v="ghi2j" */
int i,lg,j,p=0;	int i,lg,j,p=0;
i=0;	i=0;
Line 876 void powell(double p[], double **xi, int	Line 987 void powell(double p[], double **xi, int
fprintf(ficrespow,"\n");fflush(ficrespow);	fprintf(ficrespow,"\n");fflush(ficrespow);
if(*iter <=3){	if(*iter <=3){
tm = *localtime(&curr_time.tv_sec);	tm = *localtime(&curr_time.tv_sec);
strcpy(strcurr,asctime(&tmf));	strcpy(strcurr,asctime(&tm));
/* asctime_r(&tm,strcurr); */	/* asctime_r(&tm,strcurr); */
forecast_time=curr_time;	forecast_time=curr_time;
itmp = strlen(strcurr);	itmp = strlen(strcurr);
if(strcurr[itmp-1]=='\n')	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 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,curr_time.tv_sec-last_time.tv_sec);	fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
Line 892 void powell(double p[], double **xi, int	Line 1003 void powell(double p[], double **xi, int
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 or\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(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 or\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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
}	}
}	}
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
Line 987 void powell(double p[], double **xi, int	Line 1098 void powell(double p[], double **xi, int
}	}
}	}

/** Prevalence limit (stable prevalence) **************/	/** Prevalence limit (stable or period prevalence) **************/

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int ij)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int ij)
{	{
Line 1232 double func( double *x)	Line 1343 double func( double *x)
} /* end mult */	} /* end mult */

/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
/* But now since version 0.9 we anticipate for bias and large stepm.	/* But now since version 0.9 we anticipate for bias at large stepm.
* If stepm is larger than one month (smallest stepm) and if the exact delay	* If stepm is larger than one month (smallest stepm) and if the exact delay
* (in months) between two waves is not a multiple of stepm, we rounded to	* (in months) between two waves is not a multiple of stepm, we rounded to
* the nearest (and in case of equal distance, to the lowest) interval but now	* the nearest (and in case of equal distance, to the lowest) interval but now
* we keep into memory the bias bh[mi][i] and also the previous matrix product	* we keep into memory the bias bh[mi][i] and also the previous matrix product
* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the	* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
* probability in order to take into account the bias as a fraction of the way	* probability in order to take into account the bias as a fraction of the way
* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies	* from savm to out if bh is negative or even beyond if bh is positive. bh varies
* -stepm/2 to stepm/2 .	* -stepm/2 to stepm/2 .
* For stepm=1 the results are the same as for previous versions of Imach.	* For stepm=1 the results are the same as for previous versions of Imach.
* For stepm > 1 the results are less biased than in previous versions.	* For stepm > 1 the results are less biased than in previous versions.
Line 1247 double func( double *x)	Line 1358 double func( double *x)
s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;	bbh=(double)bh[mi][i]/(double)stepm;
/* bias is positive if real duration	/* bias bh is positive if real duration
* is higher than the multiple of stepm and negative otherwise.	* is higher than the multiple of stepm and negative otherwise.
*/	*/
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
if( s2 > nlstate){	if( s2 > nlstate){
/* i.e. if s2 is a death state and if the date of death is known then the contribution	/* i.e. if s2 is a death state and if the date of death is known
to the likelihood is the probability to die between last step unit time and current	then the contribution to the likelihood is the probability to
step unit time, which is also the differences between probability to die before dh	die between last step unit time and current step unit time,
and probability to die before dh-stepm .	which is also equal to probability to die before dh
	minus probability to die before dh-stepm .
In version up to 0.92 likelihood was computed	In version up to 0.92 likelihood was computed
as if date of death was unknown. Death was treated as any other	as if date of death was unknown. Death was treated as any other
health state: the date of the interview describes the actual state	health state: the date of the interview describes the actual state
Line 1275 double func( double *x)	Line 1387 double func( double *x)
lower mortality.	lower mortality.
*/	*/
lli=log(out[s1][s2] - savm[s1][s2]);	lli=log(out[s1][s2] - savm[s1][s2]);
}else{

	} else if (s2==-2) {
	for (j=1,survp=0. ; j<=nlstate; j++)
	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
	/survp += out[s1][j]; /
	lli= log(survp);
	}

	else if (s2==-4) {
	for (j=3,survp=0. ; j<=nlstate; j++)
	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
	lli= log(survp);
	}

	else if (s2==-5) {
	for (j=1,survp=0. ; j<=2; j++)
	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
	lli= log(survp);
	}

	else{
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2]));/ /* linear interpolation */	/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2]));/ /* linear interpolation */
}	}
Line 1469 double funcone( double *x)	Line 1602 double funcone( double *x)
*/	*/
if( s2 > nlstate && (mle <5) ){ /* Jackson */	if( s2 > nlstate && (mle <5) ){ /* Jackson */
lli=log(out[s1][s2] - savm[s1][s2]);	lli=log(out[s1][s2] - savm[s1][s2]);
} else if (mle==1){	} else if (s2==-2) {
	for (j=1,survp=0. ; j<=nlstate; j++)
	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
	lli= log(survp);
	}else if (mle==1){
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
} else if(mle==2){	} else if(mle==2){
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */	lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */
Line 1485 double funcone( double *x)	Line 1622 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 %1d %1d %1d %1d %3d %10.6f %6.4f\	fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
%10.6f %10.6f %10.6f ", \	%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]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
Line 1571 void mlikeli(FILE *ficres,double p[], in	Line 1708 void mlikeli(FILE *ficres,double p[], in

powell(p,xi,npar,ftol,&iter,&fret,func);	powell(p,xi,npar,ftol,&iter,&fret,func);

	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 = %d, -2 Log likelihood = %.12f\n",iter,func(p));
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));	fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
Line 1838 void lubksb(double *a, int n, int indx	Line 1976 void lubksb(double *a, int n, int indx
}	}
}	}

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

/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint)	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,z2,j;	int i, m, jk, k1,i1, j1, bool, z1,z2,j;
Line 1847 void freqsummary(char fileres[], int ia	Line 1990 void freqsummary(char fileres[], int ia
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
double pos,posprop, k2, dateintsum=0,k2cpt=0;	double pos,posprop, k2, dateintsum=0,k2cpt=0;
FILE *ficresp;
char fileresp[FILENAMELENGTH];	char fileresp[FILENAMELENGTH];

pp=vector(1,nlstate);	pp=vector(1,nlstate);
Line 1859 void freqsummary(char fileres[], int ia	Line 2001 void freqsummary(char fileres[], int ia
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);	freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
j1=0;	j1=0;

j=cptcoveff;	j=cptcoveff;
Line 1872 void freqsummary(char fileres[], int ia	Line 2014 void freqsummary(char fileres[], int ia
j1++;	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=-1; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
for (jk=-1; 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;

Line 1912 void freqsummary(char fileres[], int ia	Line 2054 void freqsummary(char fileres[], int ia
}	}

/* 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);
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 1998 void freqsummary(char fileres[], int ia	Line 2140 void freqsummary(char fileres[], int ia
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

fclose(ficresp);	fclose(ficresp);
free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);	free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
free_matrix(prop,1,nlstate,iagemin, iagemax+3);	free_matrix(prop,1,nlstate,iagemin, iagemax+3);
/* End of Freq */	/* End of Freq */
Line 2107 void concatwav(int wav[], int **dh, int	Line 2249 void concatwav(int wav[], int **dh, int
mi=0;	mi=0;
m=firstpass;	m=firstpass;
while(s[m][i] <= nlstate){	while(s[m][i] <= nlstate){
if(s[m][i]>=1)	if(s[m][i]>=1 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5)
mw[++mi][i]=m;	mw[++mi][i]=m;
if(m >=lastpass)	if(m >=lastpass)
break;	break;
Line 2125 void concatwav(int wav[], int **dh, int	Line 2267 void concatwav(int wav[], int **dh, int
if(mi==0){	if(mi==0){
nbwarn++;	nbwarn++;
if(first==0){	if(first==0){
printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);	printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
first=1;	first=1;
}	}
if(first==1){	if(first==1){
fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);	fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
}	}
} /* end mi==0 */	} /* end mi==0 */
} /* End individuals */	} /* End individuals */
Line 2147 void concatwav(int wav[], int **dh, int	Line 2289 void concatwav(int wav[], int **dh, int
nberr++;	nberr++;
printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);	printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
j=1; /* Temporary Dangerous patch */	j=1; /* Temporary Dangerous patch */
printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);	printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);	fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);	fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
}	}
k=k+1;	k=k+1;
if (j >= jmax) jmax=j;	if (j >= jmax){
if (j <= jmin) jmin=j;	jmax=j;
	ijmax=i;
	}
	if (j <= jmin){
	jmin=j;
	ijmin=i;
	}
sum=sum+j;	sum=sum+j;
/if (j<0) printf("j=%d num=%d \n",j,i);/	/if (j<0) printf("j=%d num=%d \n",j,i);/
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/	/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
Line 2161 void concatwav(int wav[], int **dh, int	Line 2309 void concatwav(int wav[], int **dh, int
}	}
else{	else{
j= rint( (agev[mw[mi+1][i]][i]12 - agev[mw[mi][i]][i]12));	j= rint( (agev[mw[mi+1][i]][i]12 - agev[mw[mi][i]][i]12));
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/	/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */

k=k+1;	k=k+1;
if (j >= jmax) jmax=j;	if (j >= jmax) {
else if (j <= jmin)jmin=j;	jmax=j;
	ijmax=i;
	}
	else if (j <= jmin){
	jmin=j;
	ijmin=i;
	}
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */	/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
/printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);/	/printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);/
if(j<0){	if(j<0){
Line 2207 void concatwav(int wav[], int **dh, int	Line 2362 void concatwav(int wav[], int **dh, int
} /* end wave */	} /* end wave */
}	}
jmean=sum/k;	jmean=sum/k;
printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,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 Max=%d Mean=%f\n\n ",jmin, jmax,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);
}	}

/********* Tricode **************************/	/********* Tricode **************************/
Line 2254 void tricode(int Tvar, int *nbcode, in	Line 2409 void tricode(int Tvar, int *nbcode, in
for (k=0; k< maxncov; k++) Ndum[k]=0;	for (k=0; k< maxncov; k++) Ndum[k]=0;

for (i=1; i<=ncovmodel-2; i++) {	for (i=1; i<=ncovmodel-2; i++) {
/* Listing of all covariables in staement 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];	ij=Tvar[i];
Ndum[ij]++;	Ndum[ij]++;
}	}
Line 2272 void tricode(int Tvar, int *nbcode, in	Line 2427 void tricode(int Tvar, int *nbcode, in

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

void evsij(char fileres[], double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double savm, int ij, int estepm,double delti[],double matcov )	void evsij(char fileres[], 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 */
	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
	double age, agelim, hf;
	double ***p3mat;
	double eip;

	pstamp(ficreseij);
	fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
	fprintf(ficreseij,"# Age");
	for(i=1; i<=nlstate;i++){
	for(j=1; j<=nlstate;j++){
	fprintf(ficreseij," e%1d%1d ",i,j);
	}
	fprintf(ficreseij," e%1d. ",i);
	}
	fprintf(ficreseij,"\n");


	if(estepm < stepm){
	printf ("Problem %d lower than %d\n",estepm, stepm);
	}
	else hstepm=estepm;
	/* We compute the life expectancy from trapezoids spaced every estepm months
	* This is mainly to measure the difference between two models: for example
	* if stepm=24 months pijx are given only every 2 years and by summing them
	* we are calculating an estimate of the Life Expectancy assuming a linear
	* progression in between and thus overestimating or underestimating according
	* to the curvature of the survival function. If, for the same date, we
	* estimate the model with stepm=1 month, we can keep estepm to 24 months
	* to compare the new estimate of Life expectancy with the same linear
	* hypothesis. A more precise result, taking into account a more precise
	* curvature will be obtained if estepm is as small as stepm. */

	/* For example we decided to compute the life expectancy with the smallest unit */
	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
	nhstepm is the number of hstepm from age to agelim
	nstepm is the number of stepm from age to agelin.
	Look at hpijx to understand the reason of that which relies in memory size
	and note for a fixed period like estepm months */
	/* We decided (b) to get a life expectancy respecting the most precise curvature of the
	survival function given by stepm (the optimization length). Unfortunately it
	means that if the survival funtion is printed only each two years of age and if
	you sum them up and add 1 year (area under the trapezoids) you won't get the same
	results. So we changed our mind and took the option of the best precision.
	*/
	hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */

	agelim=AGESUP;
	/* nhstepm age range expressed in number of stepm */
	nstepm=(int) rint((agelim-age)*YEARM/stepm);
	/* Typically if 20 years nstepm = 2012/6=40 stepm /
	/* if (stepm >= YEARM) hstepm=1;*/
	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);

	for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepm matrices, stored
	in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */

	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);

	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */

	printf("%d\|",(int)age);fflush(stdout);
	fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);

	/* Computing expectancies */
	for(i=1; i<=nlstate;i++)
	for(j=1; j<=nlstate;j++)
	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
	eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;

	/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/

	}

	fprintf(ficreseij,"%3.0f",age );
	for(i=1; i<=nlstate;i++){
	eip=0;
	for(j=1; j<=nlstate;j++){
	eip +=eij[i][j][(int)age];
	fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
	}
	fprintf(ficreseij,"%9.4f", eip );
	}
	fprintf(ficreseij,"\n");

	}
	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	printf("\n");
	fprintf(ficlog,"\n");

	}

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

{	{
/* Health expectancies */	/* Covariances of health expectancies eij and of total life expectancies according
int i, j, nhstepm, hstepm, h, nstepm, k, cptj;	to initial status i, ei. .
	*/
	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
double age, agelim, hf;	double age, agelim, hf;
double *p3mat,*varhe;	double *p3matp, p3matm, **varhe;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double xp, xm;
double gp, gm;	double gp, gm;
double *gradg, *trgradg;	double *gradg, *trgradg;
int theta;	int theta;

	double eip, vip;

varhe=ma3x(1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int) fage);	varhe=ma3x(1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int) fage);
xp=vector(1,npar);	xp=vector(1,npar);
	xm=vector(1,npar);
dnewm=matrix(1,nlstate*nlstate,1,npar);	dnewm=matrix(1,nlstate*nlstate,1,npar);
doldm=matrix(1,nlstatenlstate,1,nlstatenlstate);	doldm=matrix(1,nlstatenlstate,1,nlstatenlstate);

fprintf(ficreseij,"# Health expectancies\n");	pstamp(ficresstdeij);
fprintf(ficreseij,"# Age");	fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
for(i=1; i<=nlstate;i++)	fprintf(ficresstdeij,"# Age");
	for(i=1; i<=nlstate;i++){
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
fprintf(ficreseij," %1d-%1d (SE)",i,j);	fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
fprintf(ficreseij,"\n");	fprintf(ficresstdeij," e%1d. ",i);
	}
	fprintf(ficresstdeij,"\n");

	pstamp(ficrescveij);
	fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
	fprintf(ficrescveij,"# Age");
	for(i=1; i<=nlstate;i++)
	for(j=1; j<=nlstate;j++){
	cptj= (j-1)*nlstate+i;
	for(i2=1; i2<=nlstate;i2++)
	for(j2=1; j2<=nlstate;j2++){
	cptj2= (j2-1)*nlstate+i2;
	if(cptj2 <= cptj)
	fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
	}
	}
	fprintf(ficrescveij,"\n");

if(estepm < stepm){	if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);	printf ("Problem %d lower than %d\n",estepm, stepm);
}	}
Line 2326 void evsij(char fileres[], double ***eij	Line 2601 void evsij(char fileres[], double ***eij
*/	*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */	hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */

	/* If stepm=6 months */
	/* nhstepm age range expressed in number of stepm */
agelim=AGESUP;	agelim=AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */	nstepm=(int) rint((agelim-age)*YEARM/stepm);
/* nhstepm age range expressed in number of stepm */	/* Typically if 20 years nstepm = 2012/6=40 stepm /
nstepm=(int) rint((agelim-age)*YEARM/stepm);	/* if (stepm >= YEARM) hstepm=1;*/
/* Typically if 20 years nstepm = 2012/6=40 stepm /	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);	gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
gp=matrix(0,nhstepm,1,nlstate*nlstate);	trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
gm=matrix(0,nhstepm,1,nlstate*nlstate);	gp=matrix(0,nhstepm,1,nlstate*nlstate);
	gm=matrix(0,nhstepm,1,nlstate*nlstate);

	for (age=bage; age<=fage; age ++){

/* Computed by stepm unit matrices, product of hstepm matrices, stored	/* Computed by stepm unit matrices, product of hstepm matrices, stored
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */	in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);


hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */

/* Computing Variances of health expectancies */	/* Computing Variances of health expectancies */
	/* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
for(theta=1; theta <=npar; theta++){	decrease memory allocation */
	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){	for(i=1; i<=npar; i++){
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
	xm[i] = x[i] - (i==theta ?delti[theta]:0);
}	}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);	hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
	hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);

cptj=0;
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(i=1; i<=nlstate; i++){	for(i=1; i<=nlstate; i++){
cptj=cptj+1;	for(h=0; h<=nhstepm-1; h++){
for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){	gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;	gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
}	}
}	}
}	}

	for(ij=1; ij<= nlstate*nlstate; ij++)
for(i=1; i<=npar; i++)
xp[i] = x[i] - (i==theta ?delti[theta]:0);
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);

cptj=0;
for(j=1; j<= nlstate; j++){
for(i=1;i<=nlstate;i++){
cptj=cptj+1;
for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){

gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
}
}
}
for(j=1; j<= nlstate*nlstate; j++)
for(h=0; h<=nhstepm-1; h++){	for(h=0; h<=nhstepm-1; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];	gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
}	}
}	}/* End theta */

/* End theta */
	for(h=0; h<=nhstepm-1; h++)
trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);

for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*nlstate;j++)	for(j=1; j<=nlstate*nlstate;j++)
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];	trgradg[h][j][theta]=gradg[h][theta][j];


for(i=1;i<=nlstate*nlstate;i++)	for(ij=1;ij<=nlstate*nlstate;ij++)
for(j=1;j<=nlstate*nlstate;j++)	for(ji=1;ji<=nlstate*nlstate;ji++)
varhe[i][j][(int)age] =0.;	varhe[ij][ji][(int)age] =0.;

printf("%d\|",(int)age);fflush(stdout);	printf("%d\|",(int)age);fflush(stdout);
fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);	fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);
Line 2404 void evsij(char fileres[], double ***eij	Line 2666 void evsij(char fileres[], double ***eij
for(k=0;k<=nhstepm-1;k++){	for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);	matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);
for(i=1;i<=nlstate*nlstate;i++)	for(ij=1;ij<=nlstate*nlstate;ij++)
for(j=1;j<=nlstate*nlstate;j++)	for(ji=1;ji<=nlstate*nlstate;ji++)
varhe[i][j][(int)age] += doldm[i][j]hfhf;	varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;
}	}
}	}
/* Computing expectancies */	/* Computing expectancies */
	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;	eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;

/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/	/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/

}	}

fprintf(ficreseij,"%3.0f",age );	fprintf(ficresstdeij,"%3.0f",age );
cptj=0;	for(i=1; i<=nlstate;i++){
	eip=0.;
	vip=0.;
	for(j=1; j<=nlstate;j++){
	eip += eij[i][j][(int)age];
	for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
	vip += varhe[(j-1)nlstate+i][(k-1)nlstate+i][(int)age];
	fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)nlstate+i][(j-1)nlstate+i][(int)age]) );
	}
	fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
	}
	fprintf(ficresstdeij,"\n");

	fprintf(ficrescveij,"%3.0f",age );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
cptj++;	cptj= (j-1)*nlstate+i;
fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );	for(i2=1; i2<=nlstate;i2++)
	for(j2=1; j2<=nlstate;j2++){
	cptj2= (j2-1)*nlstate+i2;
	if(cptj2 <= cptj)
	fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
	}
}	}
fprintf(ficreseij,"\n");	fprintf(ficrescveij,"\n");

free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	}
	free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
	free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
	free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
	free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
	free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");

	free_vector(xm,1,npar);
free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*nlstate,1,npar);	free_matrix(dnewm,1,nlstate*nlstate,1,npar);
free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);	free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);
Line 2444 void evsij(char fileres[], double ***eij	Line 2727 void evsij(char fileres[], double ***eij
}	}

/********** Variance ****************/	/********** Variance ****************/
void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)	void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
{	{
/* Variance of health expectancies */	/* Variance of health expectancies */
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/
Line 2495 void varevsij(char optionfilefiname[], d	Line 2778 void varevsij(char optionfilefiname[], d
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
}	}
printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);

fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);
	pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);	fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);
fprintf(ficresprobmorprev,"# Age cov=%-d",ij);	fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2505 void varevsij(char optionfilefiname[], d	Line 2790 void varevsij(char optionfilefiname[], d
}	}
fprintf(ficresprobmorprev,"\n");	fprintf(ficresprobmorprev,"\n");
fprintf(ficgp,"\n# Routine varevsij");	fprintf(ficgp,"\n# Routine varevsij");
	/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */	/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
	pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");	fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
	if(popbased==1)
	fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
	else
	fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");	fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);	fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
fprintf(ficresvij,"\n");	fprintf(ficresvij,"\n");

xp=vector(1,npar);	xp=vector(1,npar);
Line 2742 void varevsij(char optionfilefiname[], d	Line 3032 void varevsij(char optionfilefiname[], d
} /* end varevsij */	} /* end varevsij */

/********** Variance of prevlim ****************/	/********** Variance of prevlim ****************/
void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij)	void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, char strstart[])
{	{
/* 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);/
Line 2755 void varprevlim(char fileres[], double *	Line 3045 void varprevlim(char fileres[], double *
double gradg, trgradg;	double gradg, trgradg;
double age,agelim;	double age,agelim;
int theta;	int theta;

fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");	pstamp(ficresvpl);
	fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
fprintf(ficresvpl,"# Age");	fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);	fprintf(ficresvpl," %1d-%1d",i,i);
Line 2825 void varprevlim(char fileres[], double *	Line 3116 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)	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, i1, k1, l1, t, tj;
int k2, l2, j1, z1;	int k2, l2, j1, z1;
Line 2870 void varprob(char optionfilefiname[], do	Line 3161 void varprob(char optionfilefiname[], do
fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);	fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);	printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);	fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
	pstamp(ficresprob);
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");	fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");	fprintf(ficresprob,"# Age");
	pstamp(ficresprobcov);
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");	fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcov,"# Age");
	pstamp(ficresprobcor);
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");	fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcor,"# Age");


for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 3127 To be simple, these graphs help to under	Line 3420 To be simple, these graphs help to under
}	}
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);
	free_matrix(doldm,1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));
	free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
free_vector(xp,1,npar);	free_vector(xp,1,npar);
fclose(ficresprob);	fclose(ficresprob);
fclose(ficresprobcov);	fclose(ficresprobcov);
Line 3145 void printinghtml(char fileres[], char t	Line 3440 void printinghtml(char fileres[], char t
double jprev2, double mprev2,double anprev2){	double jprev2, double mprev2,double anprev2){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt;

fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
	</ul>");
	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",	- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",	- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));	stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));	subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Life expectancies by age and initial health status (estepm=%2d months): \	- (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij (estepm=%2d months): \
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n</li>",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));	estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));


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

m=cptcoveff;	m=cptcoveff;
Line 3175 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3474 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: %s%d1.png<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%d1.png\">%s%d1.png</a><br> \
<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d1.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: %s%d2.png<br> \	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> \
<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);	<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* 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>- Stable prevalence in each health state : p%s%d%d.png<br> \	fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <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);	<img src=\"%s%d%d.png\">",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>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \	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> \
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);	<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}	}
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
Line 3196 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3495 fprintf(fichtm," \n<ul><li><b>Graphs</b>


fprintf(fichtm,"\	fprintf(fichtm,"\
\n<br><li><h4> Result files (second order: variances)</h4>\n\	\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);

fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 3209 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3508 fprintf(fichtm," \n<ul><li><b>Graphs</b>
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));	subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",	- Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
	<a href=\"%s\">%s</a> <br>\n</li>",
	estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
	fprintf(fichtm,"\
	- (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
	<a href=\"%s\">%s</a> <br>\n</li>",
	estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
	fprintf(fichtm,"\
	- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));	estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",	- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"t"),subdirf2(fileres,"t"));	subdirf2(fileres,"t"),subdirf2(fileres,"t"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\	- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));	subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));

/* if(popforecast==1) fprintf(fichtm,"\n */	/* if(popforecast==1) fprintf(fichtm,"\n */
Line 3287 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3594 plot [%.f:%.f] \"%s\" every :::%d::%d u
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\"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 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)");
Line 3335 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3642 plot [%.f:%.f] \"%s\" every :::%d::%d u

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
k=2+nlstate(2cpt-2);	/* k=2+nlstate(2cpt-2); */
	k=2+(nlstate+1)*(cpt-1);
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\n\
set size 0.65,0.65\n\	set size 0.65,0.65\n\
Line 3349 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3657 plot [%.f:%.f] \"%s\" every :::%d::%d u

*/	*/
for (i=1; i< nlstate ; i ++) {	for (i=1; i< nlstate ; i ++) {
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
	/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2i,cpt,i+1);/

}	}
	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
}	}
}	}

Line 3910 double gompertz(double x[])	Line 4220 double gompertz(double x[])
{	{
double A,B,L=0.0,sump=0.,num=0.;	double A,B,L=0.0,sump=0.,num=0.;
int i,n=0; /* n is the size of the sample */	int i,n=0; /* n is the size of the sample */

for (i=0;i<=imx-1 ; i++) {	for (i=0;i<=imx-1 ; i++) {
sump=sump+weight[i];	sump=sump+weight[i];
sump=sump+1;	/* sump=sump+1;*/
num=num+1;	num=num+1;
}	}


/* for (i=1; i<=imx; i++)	/* for (i=0; i<=imx; i++)
if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/	if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/

for (i=0;i<=imx-1 ; i++)	for (i=1;i<=imx ; i++)
{	{
if (cens[i]==1 & wav[i]>1)	if (cens[i] == 1 && wav[i]>1)
A=-x[1]/(x[2])*	A=-x[1]/(x[2])(exp(x[2](agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
(exp(x[2]/YEARM(agecens[i]12-agegomp12))-exp(x[2]/YEARM(ageexmed[i]12-agegomp12)));

if (cens[i]==0 & wav[i]>1)	if (cens[i] == 0 && wav[i]>1)
A=-x[1]/(x[2])*	A=-x[1]/(x[2])(exp(x[2](agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
(exp(x[2]/YEARM(agedc[i]12-agegomp12))-exp(x[2]/YEARM(ageexmed[i]12-agegomp12)))	+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+log(x[1]/YEARM)+x[2]/YEARM(agedc[i]12-agegomp*12)+log(YEARM);

if (wav[i]>1 & agecens[i]>15) {	/if (wav[i] > 1 && agecens[i] > 15) {/ /* ??? */
	if (wav[i] > 1 ) { /* ??? */
L=L+A*weight[i];	L=L+A*weight[i];
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]12,agecens[i]12,cens[i],agedc[i]12,weight[i]);/	/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]12,agecens[i]12,cens[i],agedc[i]12,weight[i]);/
}	}
Line 3945 double gompertz(double x[])	Line 4255 double gompertz(double x[])
/***************** Printing html file *********/	/***************** Printing html file *********/
void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \	void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\	int lastpass, int stepm, int weightopt, char model[],\
int imx, double p[],double **matcov){	int imx, double p[],double **matcov,double agemortsup){
int i;	int i,k;

fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");	fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
fprintf(fichtm," mu(age) =%lfexp(%lf(age-%d)) per year<br><br>",p[1],p[2],agegomp);	fprintf(fichtm," mu(age) =%lfexp(%lf(age-%d)) per year<br><br>",p[1],p[2],agegomp);
Line 3954 void printinghtmlmort(char fileres[], ch	Line 4264 void printinghtmlmort(char fileres[], ch
fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");	fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");

	fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");

	fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");

	for (k=agegomp;k<(agemortsup-2);k++)
	fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]exp(p[2](k-agegomp)),(p[1]exp(p[2](k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);


fflush(fichtm);	fflush(fichtm);
}	}

Line 3983 void printinggnuplotmort(char fileres[],	Line 4302 void printinggnuplotmort(char fileres[],




/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
/***********************************************/	/***********************************************/
Line 3991 int main(int argc, char *argv[])	Line 4311 int main(int argc, char *argv[])
{	{
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,m,size=100,cptcode, cptcod;
	int linei, month, year,iout;
int jj, ll, li, lj, lk, imk;	int jj, ll, li, lj, lk, imk;
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;

char ca[32], cb[32], cc[32];	char ca[32], cb[32], cc[32];
	char dummy[]=" ";
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
	struct stat info;
double agedeb, agefin,hf;	double agedeb, agefin,hf;
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;

Line 4012 int main(int argc, char *argv[])	Line 4335 int main(int argc, char *argv[])
char line[MAXLINE], linepar[MAXLINE];	char line[MAXLINE], linepar[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 */
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */	int sdeb, sfin; /* Status at beginning and end */
int c, h , cpt,l;	int c, h , cpt,l;
Line 4021 int main(int argc, char *argv[])	Line 4345 int main(int argc, char *argv[])
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;
	int agemortsup;
	float sumlpop=0.;
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;	double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;	double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;

Line 4045 int main(int argc, char *argv[])	Line 4371 int main(int argc, char *argv[])
char z[1]="c", occ;	char z[1]="c", occ;

char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];	char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
char strstart[80], *strt, strtend[80];	char *strt, strtend[80];
char *stratrunc;	char *stratrunc;
int lstra;	int lstra;

Line 4087 int main(int argc, char *argv[])	Line 4413 int main(int argc, char *argv[])
printf("\n%s\n%s",version,fullversion);	printf("\n%s\n%s",version,fullversion);
if(argc <=1){	if(argc <=1){
printf("\nEnter the parameter file name: ");	printf("\nEnter the parameter file name: ");
scanf("%s",pathtot);	fgets(pathr,FILENAMELENGTH,stdin);
	i=strlen(pathr);
	if(pathr[i-1]=='\n')
	pathr[i-1]='\0';
	for (tok = pathr; tok != NULL; ){
	printf("Pathr \|%s\|\n",pathr);
	while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
	printf("val= \|%s\| pathr=%s\n",val,pathr);
	strcpy (pathtot, val);
	if(pathr[0] == '\0') break; /* Dirty */
	}
}	}
else{	else{
strcpy(pathtot,argv[1]);	strcpy(pathtot,argv[1]);
Line 4097 int main(int argc, char *argv[])	Line 4433 int main(int argc, char *argv[])
printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/	printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
/* cutv(path,optionfile,pathtot,'\\');*/	/* cutv(path,optionfile,pathtot,'\\');*/

	/* Split argv[0], imach program to get pathimach */
	printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);	split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
	printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
/* strcpy(pathimach,argv[0]); */	/* strcpy(pathimach,argv[0]); */
	/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);	split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);	printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
chdir(path);	chdir(path); /* Can be a relative path */
	if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
	printf("Current directory %s!\n",pathcd);
strcpy(command,"mkdir ");	strcpy(command,"mkdir ");
strcat(command,optionfilefiname);	strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){	if((outcmd=system(command)) != 0){
Line 4267 int main(int argc, char *argv[])	Line 4609 int main(int argc, char *argv[])
}	}
fflush(ficlog);	fflush(ficlog);


p=param[1][1];	p=param[1][1];

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
Line 4368 int main(int argc, char *argv[])	Line 4709 int main(int argc, char *argv[])

/-------- data file ----------/	/-------- data file ----------/
if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem with datafile: %s\n", datafile);goto end;	printf("Problem while opening datafile: %s\n", datafile);goto end;
fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;	fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
}	}

n= lastobs;	n= lastobs;
Line 4391 int main(int argc, char *argv[])	Line 4732 int main(int argc, char *argv[])
ncodemax=ivector(1,8);	ncodemax=ivector(1,8);

i=1;	i=1;
while (fgets(line, MAXLINE, fic) != NULL) {	linei=0;
if ((i >= firstobs) && (i <=lastobs)) {	while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
	linei=linei+1;
for (j=maxwav;j>=1;j--){	for(j=strlen(line); j>=0;j--){ /* Untabifies line */
cutv(stra, strb,line,' '); s[j][i]=atoi(strb);	if(line[j] == '\t')
strcpy(line,stra);	line[j] = ' ';
cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);	}
cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);	for(j=strlen(line)-1; (line[j]==' ')\|\|(line[j]==10)\|\|(line[j]==13);j--){
	;
	};
	line[j+1]=0; /* Trims blanks at end of line */
	if(line[0]=='#'){
	fprintf(ficlog,"Comment line\n%s\n",line);
	printf("Comment line\n%s\n",line);
	continue;
	}

	for (j=maxwav;j>=1;j--){
	cutv(stra, strb,line,' ');
	errno=0;
	lval=strtol(strb,&endptr,10);
	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%d' at line number %d %s 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);
	exit(1);
}	}
	s[j][i]=lval;
cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);	strcpy(line,stra);
	cutv(stra, strb,line,' ');
cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);	}
	else if(iout=sscanf(strb,"%s.") != 0){
cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);	month=99;
for (j=ncovcol;j>=1;j--){	year=9999;
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);	}else{
}	printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
lstra=strlen(stra);	exit(1);
if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /	}
stratrunc = &(stra[lstra-9]);	anint[j][i]= (double) year;
num[i]=atol(stratrunc);	mint[j][i]= (double)month;
	strcpy(line,stra);
	} /* ENd Waves */

	cutv(stra, strb,line,' ');
	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
	}
	else if(iout=sscanf(strb,"%s.",dummy) != 0){
	month=99;
	year=9999;
	}else{
	printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
	exit(1);
	}
	andc[i]=(double) year;
	moisdc[i]=(double) month;
	strcpy(line,stra);

	cutv(stra, strb,line,' ');
	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
	}
	else if(iout=sscanf(strb,"%s.") != 0){
	month=99;
	year=9999;
	}else{
	printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
	exit(1);
	}
	annais[i]=(double)(year);
	moisnais[i]=(double)(month);
	strcpy(line,stra);

	cutv(stra, strb,line,' ');
	errno=0;
	lval=strtol(strb,&endptr,10);
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
	exit(1);
	}
	weight[i]=(double)(lval);
	strcpy(line,stra);

	for (j=ncovcol;j>=1;j--){
	cutv(stra, strb,line,' ');
	errno=0;
	lval=strtol(strb,&endptr,10);
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
	exit(1);
	}
	if(lval <-1 \|\| lval >1){
	printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);
	exit(1);
}	}
else	covar[j][i]=(double)(lval);
num[i]=atol(stra);	strcpy(line,stra);
	}
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){	lstra=strlen(stra);
printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
	if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /
i=i+1;	stratrunc = &(stra[lstra-9]);
}	num[i]=atol(stratrunc);
}	}
	else
	num[i]=atol(stra);
	/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
	printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/

	i=i+1;
	} /* End loop reading data */
	fclose(fic);
/* printf("ii=%d", ij);	/* printf("ii=%d", ij);
scanf("%d",i);*/	scanf("%d",i);*/
imx=i-1; /* Number of individuals */	imx=i-1; /* Number of individuals */
Line 4438 int main(int argc, char *argv[])	Line 4856 int main(int argc, char *argv[])
if (s[4][i]==9) s[4][i]=-1;	if (s[4][i]==9) s[4][i]=-1;
printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/	printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/

for (i=1; i<=imx; i++)	/* for (i=1; i<=imx; i++) */

/*if ((s[3][i]==3) \|\| (s[4][i]==3)) weight[i]=0.08;	/*if ((s[3][i]==3) \|\| (s[4][i]==3)) weight[i]=0.08;
else weight[i]=1;*/	else weight[i]=1;*/

/* Calculation of the number of parameter from char model*/	/* Calculation of the number of parameters from char model */
Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */	Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tprod=ivector(1,15);	Tprod=ivector(1,15);
Tvaraff=ivector(1,15);	Tvaraff=ivector(1,15);
Line 4522 int main(int argc, char *argv[])	Line 4940 int main(int argc, char *argv[])
printf("cptcovprod=%d ", cptcovprod);	printf("cptcovprod=%d ", cptcovprod);
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);	fprintf(ficlog,"cptcovprod=%d ", cptcovprod);

scanf("%d ",i);	scanf("%d ",i);*/
fclose(fic);*/

/* if(mle==1){*/	/* if(mle==1){*/
if (weightopt != 1) { /* Maximisation without weights*/	if (weightopt != 1) { /* Maximisation without weights*/
Line 4556 int main(int argc, char *argv[])	Line 4973 int main(int argc, char *argv[])
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);	agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
for(m=firstpass; (m<= lastpass); m++){	for(m=firstpass; (m<= lastpass); m++){
if(s[m][i] >0){	if(s[m][i] >0 \|\| s[m][i]==-2 \|\| s[m][i]==-4 \|\| s[m][i]==-5){
if (s[m][i] >= nlstate+1) {	if (s[m][i] >= nlstate+1) {
if(agedc[i]>0)	if(agedc[i]>0)
if((int)moisdc[i]!=99 && (int)andc[i]!=9999)	if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
Line 4572 int main(int argc, char *argv[])	Line 4989 int main(int argc, char *argv[])
}	}
}	}
else if(s[m][i] !=9){ /* Standard case, age in fractional	else if(s[m][i] !=9){ /* Standard case, age in fractional
years but with the precision of a	years but with the precision of a month */
month */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);	agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
if((int)mint[m][i]==99 \|\| (int)anint[m][i]==9999)	if((int)mint[m][i]==99 \|\| (int)anint[m][i]==9999)
agev[m][i]=1;	agev[m][i]=1;
Line 4715 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5131 Title=%s <br>Datafile=%s Firstpass=%d La
\n\	\n\
<hr size=\"2\" color=\"#EC5E5E\">\	<hr size=\"2\" color=\"#EC5E5E\">\
<ul><li><h4>Parameter files</h4>\n\	<ul><li><h4>Parameter files</h4>\n\
	- Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\	- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
- Log file of the run: <a href=\"%s\">%s</a><br>\n\	- Log file of the run: <a href=\"%s\">%s</a><br>\n\
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\	- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
- Date and time at start: %s</ul>\n",\	- Date and time at start: %s</ul>\n",\
fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\	fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
	optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\	fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);	filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
fflush(fichtm);	fflush(fichtm);
Line 4730 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5148 Title=%s <br>Datafile=%s Firstpass=%d La

/* Calculates basic frequencies. Computes observed prevalence at single age	/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */	and prints on file fileres'p'. */
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,strstart);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
fprintf(fichtm,"<br>Total number of observations=%d <br>\n\	fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 4749 Interval (in months) between two waves:	Line 5167 Interval (in months) between two waves:
p=param[1][1]; /* (((param +1)+1)+0) /	p=param[1][1]; /* (((param +1)+1)+0) /

globpr=0; /* To get the number ipmx of contributions and the sum of weights*/	globpr=0; /* To get the number ipmx of contributions and the sum of weights*/

if (mle==-3){	if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);	ximort=matrix(1,NDIM,1,NDIM);
cens=ivector(1,n);	cens=ivector(1,n);
Line 4758 Interval (in months) between two waves:	Line 5177 Interval (in months) between two waves:

for (i=1; i<=imx; i++){	for (i=1; i<=imx; i++){
dcwave[i]=-1;	dcwave[i]=-1;
for (j=1; j<=lastpass; j++)	for (m=firstpass; m<=lastpass; m++)
if (s[j][i]>nlstate) {	if (s[m][i]>nlstate) {
dcwave[i]=j;	dcwave[i]=m;
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/	/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
break;	break;
}	}
Line 4769 Interval (in months) between two waves:	Line 5188 Interval (in months) between two waves:
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
if (wav[i]>0){	if (wav[i]>0){
ageexmed[i]=agev[mw[1][i]][i];	ageexmed[i]=agev[mw[1][i]][i];
j=wav[i];agecens[i]=1.;	j=wav[i];
if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];	agecens[i]=1.;
cens[i]=1;
	if (ageexmed[i]> 1 && wav[i] > 0){
if (ageexmed[i]<1) cens[i]=-1;	agecens[i]=agev[mw[j][i]][i];
if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;	cens[i]= 1;
	}else if (ageexmed[i]< 1)
	cens[i]= -1;
	if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
	cens[i]=0 ;
}	}
else cens[i]=-1;	else cens[i]=-1;
}	}
Line 4783 Interval (in months) between two waves:	Line 5206 Interval (in months) between two waves:
for (j=1;j<=NDIM;j++)	for (j=1;j<=NDIM;j++)
ximort[i][j]=(i == j ? 1.0 : 0.0);	ximort[i][j]=(i == j ? 1.0 : 0.0);
}	}

p[1]=0.1; p[2]=0.1;	p[1]=0.0268; p[NDIM]=0.083;
/printf("%lf %lf", p[1], p[2]);/	/printf("%lf %lf", p[1], p[2]);/


printf("Powell\n"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
strcpy(filerespow,"pow-mort");	strcpy(filerespow,"pow-mort");
strcat(filerespow,fileres);	strcat(filerespow,fileres);
if((ficrespow=fopen(filerespow,"w"))==NULL) {	if((ficrespow=fopen(filerespow,"w"))==NULL) {
printf("Problem with resultfile: %s\n", filerespow);	printf("Problem with resultfile: %s\n", filerespow);
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);	fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
}	}
fprintf(ficrespow,"# Powell\n# iter -2*LL");	fprintf(ficrespow,"# Powell\n# iter -2*LL");
/* for (i=1;i<=nlstate;i++)	/* for (i=1;i<=nlstate;i++)
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");

powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);	powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
fclose(ficrespow);	fclose(ficrespow);

hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);	hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);

for(i=1; i <=NDIM; i++)	for(i=1; i <=NDIM; i++)
for(j=i+1;j<=NDIM;j++)	for(j=i+1;j<=NDIM;j++)
Line 4822 Interval (in months) between two waves:	Line 5245 Interval (in months) between two waves:
printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);	printf("iter=%d MLE=%f Eq=%lfexp(%lf(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
for (i=1;i<=NDIM;i++)	for (i=1;i<=NDIM;i++)
printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
	lsurv=vector(1,AGESUP);
	lpop=vector(1,AGESUP);
	tpop=vector(1,AGESUP);
	lsurv[agegomp]=100000;

	for (k=agegomp;k<=AGESUP;k++) {
	agemortsup=k;
	if (p[1]exp(p[2](k-agegomp))>1) break;
	}

	for (k=agegomp;k<agemortsup;k++)
	lsurv[k+1]=lsurv[k]-lsurv[k](p[1]exp(p[2]*(k-agegomp)));

	for (k=agegomp;k<agemortsup;k++){
	lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
	sumlpop=sumlpop+lpop[k];
	}

	tpop[agegomp]=sumlpop;
	for (k=agegomp;k<(agemortsup-3);k++){
	/* tpop[k+1]=2;*/
	tpop[k+1]=tpop[k]-lpop[k];
	}


	printf("\nAge lx qx dx Lx Tx e(x)\n");
	for (k=agegomp;k<(agemortsup-2);k++)
	printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]exp(p[2](k-agegomp)),(p[1]exp(p[2](k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);


	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);

printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \	printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov);	model,imx,p,matcov,agemortsup);

	free_vector(lsurv,1,AGESUP);
	free_vector(lpop,1,AGESUP);
	free_vector(tpop,1,AGESUP);
} /* Endof if mle==-3 */	} /* Endof if mle==-3 */

else{ /* For mle >=1 */	else{ /* For mle >=1 */

likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
Line 5055 Interval (in months) between two waves:	Line 5513 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,path); /* 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);

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
Line 5077 Interval (in months) between two waves:	Line 5535 Interval (in months) between two waves:
fclose(ficres);	fclose(ficres);


/--------------- Prevalence limit (stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/

strcpy(filerespl,"pl");	strcpy(filerespl,"pl");
strcat(filerespl,fileres);	strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;	printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;	fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
}	}
printf("Computing stable prevalence: result on file '%s' \n", filerespl);	printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);	fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficrespl,"#Stable prevalence \n");	pstamp(ficrespl);
	fprintf(ficrespl,"# Period (stable) prevalence \n");
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 5147 Interval (in months) between two waves:	Line 5606 Interval (in months) between two waves:
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

/* hstepm=1; aff par mois*/	/* 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 ");	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(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 5184 Interval (in months) between two waves:	Line 5643 Interval (in months) between two waves:
}	}
}	}

varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);	varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);

fclose(ficrespij);	fclose(ficrespij);

Line 5217 Interval (in months) between two waves:	Line 5676 Interval (in months) between two waves:
printf("Problem with total LE resultfile: %s\n", filerest);goto end;	printf("Problem with total LE resultfile: %s\n", filerest);goto end;
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;	fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
}	}
printf("Computing Total LEs with variances: file '%s' \n", filerest);	printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);	fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);


strcpy(filerese,"e");	strcpy(filerese,"e");
Line 5230 Interval (in months) between two waves:	Line 5689 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);

	strcpy(fileresstde,"stde");
	strcat(fileresstde,fileres);
	if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
	printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
	fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
	}
	printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
	fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);

	strcpy(filerescve,"cve");
	strcat(filerescve,fileres);
	if((ficrescveij=fopen(filerescve,"w"))==NULL) {
	printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
	fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
	}
	printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
	fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);

strcpy(fileresv,"v");	strcpy(fileresv,"v");
strcat(fileresv,fileres);	strcat(fileresv,fileres);
if((ficresvij=fopen(fileresv,"w"))==NULL) {	if((ficresvij=fopen(fileresv,"w"))==NULL) {
Line 5262 Interval (in months) between two waves:	Line 5739 Interval (in months) between two waves:
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");

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

fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 5273 Interval (in months) between two waves:	Line 5757 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;
evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);	evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
	cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
if(popbased==1){	if(popbased==1){
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
}	}

	pstamp(ficrest);
fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");

Line 5331 Interval (in months) between two waves:	Line 5816 Interval (in months) between two waves:
free_ivector(cod,1,n);	free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);	free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);	fclose(ficreseij);
	fclose(ficresstdeij);
	fclose(ficrescveij);
fclose(ficresvij);	fclose(ficresvij);
fclose(ficrest);	fclose(ficrest);
fclose(ficpar);	fclose(ficpar);

/------- Variance of stable prevalence------/	/------- Variance of period (stable) prevalence------/

strcpy(fileresvpl,"vpl");	strcpy(fileresvpl,"vpl");
strcat(fileresvpl,fileres);	strcat(fileresvpl,fileres);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {	if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);	printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);	exit(0);
}	}
printf("Computing Variance-covariance of 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++){
Line 5355 Interval (in months) between two waves:	Line 5842 Interval (in months) between two waves:

varpl=matrix(1,nlstate,(int) bage, (int) fage);	varpl=matrix(1,nlstate,(int) bage, (int) fage);
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);	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);
}	}
}	}
Line 5367 Interval (in months) between two waves:	Line 5854 Interval (in months) between two waves:
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 */
	free_matrix(prlim,1,nlstate,1,nlstate);
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);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);

free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
/free_vector(delti,1,npar);/	/free_vector(delti,1,npar);/
Line 5386 Interval (in months) between two waves:	Line 5873 Interval (in months) between two waves:
free_ivector(Tage,1,15);	free_ivector(Tage,1,15);
free_ivector(Tcode,1,100);	free_ivector(Tcode,1,100);

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

Line 5404 Interval (in months) between two waves:	Line 5892 Interval (in months) between two waves:
tm = *localtime(&end_time.tv_sec);	tm = *localtime(&end_time.tv_sec);
tmg = *gmtime(&end_time.tv_sec);	tmg = *gmtime(&end_time.tv_sec);
strcpy(strtend,asctime(&tm));	strcpy(strtend,asctime(&tm));
printf("Local time at start %s\nLocaltime 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(end_time.tv_sec -start_time.tv_sec,tmpout));

Line 5420 Interval (in months) between two waves:	Line 5908 Interval (in months) between two waves:
fclose(ficlog);	fclose(ficlog);
/------ End -----------/	/------ End -----------/

chdir(path);
strcpy(plotcmd,"\"");	printf("Before Current directory %s!\n",pathcd);
strcat(plotcmd,pathimach);	if(chdir(pathcd) != 0)
strcat(plotcmd,GNUPLOTPROGRAM);	printf("Can't move to directory %s!\n",path);
strcat(plotcmd,"\"");	if(getcwd(pathcd,MAXLINE) > 0)
strcat(plotcmd," ");	printf("Current directory %s!\n",pathcd);
strcat(plotcmd,optionfilegnuplot);	/strcat(plotcmd,CHARSEPARATOR);/
printf("Starting graphs with: %s",plotcmd);fflush(stdout);	sprintf(plotcmd,"gnuplot");
	#ifndef UNIX
	sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
	#endif
	if(!stat(plotcmd,&info)){
	printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
	if(!stat(getenv("GNUPLOTBIN"),&info)){
	printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
	}else
	strcpy(pplotcmd,plotcmd);
	#ifdef UNIX
	strcpy(plotcmd,GNUPLOTPROGRAM);
	if(!stat(plotcmd,&info)){
	printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
	}else
	strcpy(pplotcmd,plotcmd);
	#endif
	}else
	strcpy(pplotcmd,plotcmd);

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

if((outcmd=system(plotcmd)) != 0){	if((outcmd=system(plotcmd)) != 0){
printf(" Problem with gnuplot\n");	printf("\n Problem with gnuplot\n");
}	}
printf(" Wait...");	printf(" Wait...");
while (z[0] != 'q') {	while (z[0] != 'q') {

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

Removed from v.1.99
changed lines
	Added in v.1.120