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Diff for /imach/src/imach.c between versions 1.102 and 1.116

version 1.102, 2004/09/15 17:31:30	version 1.116, 2006/03/06 10:29:27
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	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	Revision 1.102 2004/09/15 17:31:30 brouard
Add the possibility to read data file including tab characters.	Add the possibility to read data file including tab characters.

Line 206	Line 261
#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 216	Line 278
/* #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 238	Line 300
#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 0.97c, September 2004, INED-EUROREVES ";	char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
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;
Line 261 int popbased=0;	Line 325 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 291 FILE *ficresvpl;	Line 356 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 optionfilext[10], optionfilefiname[FILENAMELENGTH], 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 313 long time_value;	Line 378 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 361 double *weight;	Line 429 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 368 double ftolhess; /* Tolerance for comput	Line 437 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 377 static int split( char path, char dirc	Line 446 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 385 static int split( char path, char dirc	Line 455 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 393 static int split( char path, char dirc	Line 464 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 410 static int split( char path, char dirc	Line 482 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 1261 double func( double *x)	Line 1334 double func( double *x)
*/	*/
/* 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 equal to probability to die before dh	die between last step unit time and current step unit time,
	which is also equal to probability to die before dh
minus probability to die before dh-stepm .	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
Line 1284 double func( double *x)	Line 1358 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 += out[s1][j];
	lli= survp;
	}

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

	else if (s2==-5) {
	for (j=1,survp=0. ; j<=2; j++)
	survp += out[s1][j];
	lli= 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 1580 void mlikeli(FILE *ficres,double p[], in	Line 1675 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 1848 void lubksb(double *a, int n, int indx	Line 1944 void lubksb(double *a, int n, int indx
}	}

/********** 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 1868 void freqsummary(char fileres[], int ia	Line 1964 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 1881 void freqsummary(char fileres[], int ia	Line 1977 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 1921 void freqsummary(char fileres[], int ia	Line 2017 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);*/
	fprintf(ficresp, "#Local time at start: %s", strstart);
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 2007 void freqsummary(char fileres[], int ia	Line 2103 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 2116 void concatwav(int wav[], int **dh, int	Line 2212 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 2134 void concatwav(int wav[], int **dh, int	Line 2230 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 2156 void concatwav(int wav[], int **dh, int	Line 2252 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 2170 void concatwav(int wav[], int **dh, int	Line 2272 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 2216 void concatwav(int wav[], int **dh, int	Line 2325 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 2263 void tricode(int Tvar, int *nbcode, in	Line 2372 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 2281 void tricode(int Tvar, int *nbcode, in	Line 2390 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 ij, int estepm,double delti[],double matcov,char strstart[] )

{	{
/* Health expectancies */	/* Health expectancies */
Line 2299 void evsij(char fileres[], double ***eij	Line 2408 void evsij(char fileres[], double ***eij
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,"# Local time at start: %s", strstart);
fprintf(ficreseij,"# Health expectancies\n");	fprintf(ficreseij,"# Health expectancies\n");
fprintf(ficreseij,"# Age");	fprintf(ficreseij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 2453 void evsij(char fileres[], double ***eij	Line 2563 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 2504 void varevsij(char optionfilefiname[], d	Line 2614 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);
	fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
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 2514 void varevsij(char optionfilefiname[], d	Line 2626 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);
	fprintf(ficresvij, "#Local time at start: %s", strstart);
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 the stable prevalence in health states i\n");
fprintf(ficresvij,"# Age");	fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 2751 void varevsij(char optionfilefiname[], d	Line 2864 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 2764 void varprevlim(char fileres[], double *	Line 2877 void varprevlim(char fileres[], double *
double gradg, trgradg;	double gradg, trgradg;
double age,agelim;	double age,agelim;
int theta;	int theta;
	fprintf(ficresvpl, "#Local time at start: %s", strstart);
fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");	fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
fprintf(ficresvpl,"# Age");	fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 2834 void varprevlim(char fileres[], double *	Line 2947 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 2879 void varprob(char optionfilefiname[], do	Line 2992 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);
	fprintf(ficresprob, "#Local time at start: %s", strstart);
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");
	fprintf(ficresprobcov, "#Local time at start: %s", strstart);
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");	fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcov,"# Age");
	fprintf(ficresprobcor, "#Local time at start: %s", strstart);
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");	fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcov,"# Age");

Line 3136 To be simple, these graphs help to under	Line 3251 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 3154 void printinghtml(char fileres[], char t	Line 3271 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,"\
Line 3164 void printinghtml(char fileres[], char t	Line 3284 void printinghtml(char fileres[], char t
- Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- 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): \	- Life expectancies by age and initial health status (estepm=%2d months) WRONG LINK (to be made): \
	<a href=\"%s\">%s</a> <br>\n</li>",
	estepm,subdirf2(fileres,"le"),subdirf2(fileres,"le"));
	fprintf(fichtm,"\
	- Health expectancies by age and initial health status with standard errors (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,"\
	- Variances and covariances of health expectancies by age and initial health status (estepm=%2d months) TO BE MADE: \
	<a href=\"%s\">%s</a> <br>\n</li>",
	estepm,subdirf2(fileres,"vch"),subdirf2(fileres,"vch"));


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

Line 3205 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3334 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 3218 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3347 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 (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",	- Life and health expectancies 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 stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
Line 3919 double gompertz(double x[])	Line 4048 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 3954 double gompertz(double x[])	Line 4083 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 3963 void printinghtmlmort(char fileres[], ch	Line 4092 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 4000 int main(int argc, char *argv[])	Line 4138 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 4021 int main(int argc, char *argv[])	Line 4162 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 4030 int main(int argc, char *argv[])	Line 4172 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 4096 int main(int argc, char *argv[])	Line 4240 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; /* Un peu sale */
	}
}	}
else{	else{
strcpy(pathtot,argv[1]);	strcpy(pathtot,argv[1]);
Line 4106 int main(int argc, char *argv[])	Line 4260 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);
strcpy(command,"mkdir ");	strcpy(command,"mkdir ");
strcat(command,optionfilefiname);	strcat(command,optionfilefiname);
Line 4276 int main(int argc, char *argv[])	Line 4434 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 4400 int main(int argc, char *argv[])	Line 4557 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))) {
for(j=0; line[j] != '\n';j++){ /* Untabifies line */	linei=linei+1;
if(line[j] == '\t')	for(j=strlen(line); j>=0;j--){ /* Untabifies line */
line[j] = ' ';	if(line[j] == '\t')
}	line[j] = ' ';
for (j=maxwav;j>=1;j--){	}
cutv(stra, strb,line,' '); s[j][i]=atoi(strb);	for(j=strlen(line)-1; (line[j]==' ')\|\|(line[j]==10)\|\|(line[j]==13);j--){
strcpy(line,stra);	;
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);	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 4450 int main(int argc, char *argv[])	Line 4681 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 4534 int main(int argc, char *argv[])	Line 4765 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 4568 int main(int argc, char *argv[])	Line 4798 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 4584 int main(int argc, char *argv[])	Line 4814 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 4742 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4971 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 4761 Interval (in months) between two waves:	Line 4990 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 4770 Interval (in months) between two waves:	Line 5000 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 4781 Interval (in months) between two waves:	Line 5011 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 4795 Interval (in months) between two waves:	Line 5029 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 4834 Interval (in months) between two waves:	Line 5068 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]));

	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,path); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,path); /* 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 5099 Interval (in months) between two waves:	Line 5368 Interval (in months) between two waves:
}	}
printf("Computing stable prevalence: result on file '%s' \n", filerespl);	printf("Computing stable prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);	fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
	fprintf(ficrespl, "#Local time at start: %s", strstart);
fprintf(ficrespl,"#Stable prevalence \n");	fprintf(ficrespl,"#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);
Line 5159 Interval (in months) between two waves:	Line 5429 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*/
	fprintf(ficrespij, "#Local time at start: %s", strstart);
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 5196 Interval (in months) between two waves:	Line 5466 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 5285 Interval (in months) between two waves:	Line 5555 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, 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);
}	}

	fprintf(ficrest, "#Local time at start: %s", strstart);
fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"#Total LEs with variances: 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 5367 Interval (in months) between two waves:	Line 5637 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 5379 Interval (in months) between two waves:	Line 5649 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 5398 Interval (in months) between two waves:	Line 5668 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 5416 Interval (in months) between two waves:	Line 5687 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 5433 Interval (in months) between two waves:	Line 5704 Interval (in months) between two waves:
/------ End -----------/	/------ End -----------/

chdir(path);	chdir(path);
strcpy(plotcmd,"\"");	/strcat(plotcmd,CHARSEPARATOR);/
strcat(plotcmd,pathimach);	sprintf(plotcmd,"gnuplot");
strcat(plotcmd,GNUPLOTPROGRAM);	#ifndef UNIX
strcat(plotcmd,"\"");	sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
strcat(plotcmd," ");	#endif
strcat(plotcmd,optionfilegnuplot);	if(!stat(plotcmd,&info)){
printf("Starting graphs with: %s",plotcmd);fflush(stdout);	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.1.102
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	Added in v.1.116