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Diff for /imach/src/imach.c between versions 1.82 and 1.91

version 1.82, 2003/06/05 15:57:20	version 1.91, 2003/06/25 15:30:29
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.91 2003/06/25 15:30:29 brouard
	* imach.c (Repository): Duplicated warning errors corrected.
	(Repository): Elapsed time after each iteration is now output. It
	helps to forecast when convergence will be reached. Elapsed time
	is stamped in powell. We created a new html file for the graphs
	concerning matrix of covariance. It has extension -cov.htm.

	Revision 1.90 2003/06/24 12:34:15 brouard
	(Module): Some bugs corrected for windows. Also, when
	mle=-1 a template is output in file "or"mypar.txt with the design
	of the covariance matrix to be input.

	Revision 1.89 2003/06/24 12:30:52 brouard
	(Module): Some bugs corrected for windows. Also, when
	mle=-1 a template is output in file "or"mypar.txt with the design
	of the covariance matrix to be input.

	Revision 1.88 2003/06/23 17:54:56 brouard
	* imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.

	Revision 1.87 2003/06/18 12:26:01 brouard
	Version 0.96

	Revision 1.86 2003/06/17 20:04:08 brouard
	(Module): Change position of html and gnuplot routines and added
	routine fileappend.

	Revision 1.85 2003/06/17 13:12:43 brouard
	* imach.c (Repository): Check when date of death was earlier that
	current date of interview. It may happen when the death was just
	prior to the death. In this case, dh was negative and likelihood
	was wrong (infinity). We still send an "Error" but patch by
	assuming that the date of death was just one stepm after the
	interview.
	(Repository): Because some people have very long ID (first column)
	we changed int to long in num[] and we added a new lvector for
	memory allocation. But we also truncated to 8 characters (left
	truncation)
	(Repository): No more line truncation errors.

	Revision 1.84 2003/06/13 21:44:43 brouard
	* imach.c (Repository): Replace "freqsummary" at a correct
	place. It differs from routine "prevalence" which may be called
	many times. Probs is memory consuming and must be used with
	parcimony.
	Version 0.95a3 (should output exactly the same maximization than 0.8a2)

	Revision 1.83 2003/06/10 13:39:11 lievre
	* empty log message *

Revision 1.82 2003/06/05 15:57:20 brouard	Revision 1.82 2003/06/05 15:57:20 brouard
Add log in imach.c and fullversion number is now printed.	Add log in imach.c and fullversion number is now printed.

Line 65	Line 115
read parameterfile	read parameterfile
read datafile	read datafile
concatwav	concatwav
	freqsummary
if (mle >= 1)	if (mle >= 1)
mlikeli	mlikeli
print results files	print results files
Line 98	Line 149
#include <stdlib.h>	#include <stdlib.h>
#include <unistd.h>	#include <unistd.h>

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

#define MAXLINE 256	#define MAXLINE 256
#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 80	#define FILENAMELENGTH 132
/#define DEBUG/	/#define DEBUG/
#define windows	/#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 118	Line 173
#define YEARM 12. /* Number of months per year */	#define YEARM 12. /* Number of months per year */
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
#ifdef windows	#ifdef unix
#define DIRSEPARATOR '\\'
#define ODIRSEPARATOR '/'
#else
#define DIRSEPARATOR '/'	#define DIRSEPARATOR '/'
#define ODIRSEPARATOR '\\'	#define ODIRSEPARATOR '\\'
	#else
	#define DIRSEPARATOR '\\'
	#define ODIRSEPARATOR '/'
#endif	#endif

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

char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";	char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
int erreur; /* Error number */	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;
int npar=NPARMAX;	int npar=NPARMAX;
Line 143 int popbased=0;	Line 198 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 gipmx, gsw; /* Global variables on the number of contributions
	to the likelihood and the sum of weights (done by funcone)*/
int mle, weightopt;	int mle, weightopt;
int *mw; / mw[mi][i] is number of the mi wave for this individual */	int *mw; / mw[mi][i] is number of the mi wave for this individual */
int *dh; / dh[mi][i] is number of steps between mi,mi+1 for this individual */	int *dh; / dh[mi][i] is number of steps between mi,mi+1 for this individual */
Line 153 double oldm, newm, *savm; / Workin	Line 210 double oldm, newm, *savm; / Workin
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, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;
FILE ficlog, ficrespow;	FILE ficlog, ficrespow;
	int globpr; /* Global variable for printing or not */
	double fretone; /* Only one call to likelihood */
	long ipmx; /* Number of contributions */
	double sw; /* Sum of weights */
	char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
	FILE *ficresilk;
FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;	FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;
FILE *ficresprobmorprev;	FILE *ficresprobmorprev;
FILE fichtm; / Html File */	FILE fichtm, fichtmcov; /* Html File */
FILE *ficreseij;	FILE *ficreseij;
char filerese[FILENAMELENGTH];	char filerese[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
Line 165 char fileresvpl[FILENAMELENGTH];	Line 228 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];
	char tmpout[FILENAMELENGTH];
	char command[FILENAMELENGTH];
	int outcmd=0;

char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];	char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
	char lfileres[FILENAMELENGTH];
char filelog[FILENAMELENGTH]; /* Log file */	char filelog[FILENAMELENGTH]; /* Log file */
char filerest[FILENAMELENGTH];	char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];	char fileregp[FILENAMELENGTH];
char popfile[FILENAMELENGTH];	char popfile[FILENAMELENGTH];

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

	struct timeval start_time, end_time, curr_time, last_time, forecast_time;
	struct timezone tzp;
	extern int gettimeofday();
	struct tm tmg, tm, tmf, gmtime(), localtime();
	long time_value;
	extern long time();
	char strcurr[80], strfor[80];

#define NR_END 1	#define NR_END 1
#define FREE_ARG char*	#define FREE_ARG char*
Line 210 int estepm;	Line 285 int estepm;
/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/	/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/

int m,nb;	int m,nb;
int num, firstpass=0, lastpass=4,cod, ncodemax, Tage;	long *num;
	int firstpass=0, lastpass=4,cod, ncodemax, *Tage;
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
double pmmij, *probs;	double pmmij, *probs;
double dateintmean=0;	double dateintmean=0;
Line 250 static int split( char path, char dirc	Line 326 static int split( char path, char dirc
dirc[l1-l2] = 0; /* add zero */	dirc[l1-l2] = 0; /* add zero */
}	}
l1 = strlen( dirc ); /* length of directory */	l1 = strlen( dirc ); /* length of directory */
#ifdef windows	/*#ifdef windows
if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }	if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
#else	#else
if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }	if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
#endif	#endif
	*/
ss = strrchr( name, '.' ); /* find last / */	ss = strrchr( name, '.' ); /* find last / */
ss++;	ss++;
strcpy(ext,ss); /* save extension */	strcpy(ext,ss); /* save extension */
Line 268 static int split( char path, char dirc	Line 345 static int split( char path, char dirc

/******************************************/	/******************************************/

void replace(char s, chart)	void replace_back_to_slash(char s, chart)
{	{
int i;	int i;
int lg=20;	int lg=0;
i=0;	i=0;
lg=strlen(t);	lg=strlen(t);
for(i=0; i<= lg; i++) {	for(i=0; i<= lg; i++) {
Line 338 void free_vector(double*v, int nl, int n	Line 415 void free_vector(double*v, int nl, int n
}	}

/**********************ivector *****************************/	/**********************ivector *****************************/
char *cvector(long nl,long nh)	int *ivector(long nl,long nh)
{	{
char *v;	int *v;
v=(char ) malloc((size_t)((nh-nl+1+NR_END)sizeof(char)));	v=(int ) malloc((size_t)((nh-nl+1+NR_END)sizeof(int)));
if (!v) nrerror("allocation failure in cvector");	if (!v) nrerror("allocation failure in ivector");
return v-nl+NR_END;	return v-nl+NR_END;
}	}

/****************free ivector ************************/	/****************free ivector ************************/
void free_cvector(char *v, long nl, long nh)	void free_ivector(int *v, long nl, long nh)
{	{
free((FREE_ARG)(v+nl-NR_END));	free((FREE_ARG)(v+nl-NR_END));
}	}

/**********************ivector *****************************/	/**********************lvector *****************************/
int *ivector(long nl,long nh)	long *lvector(long nl,long nh)
{	{
int *v;	long *v;
v=(int ) malloc((size_t)((nh-nl+1+NR_END)sizeof(int)));	v=(long ) malloc((size_t)((nh-nl+1+NR_END)sizeof(long)));
if (!v) nrerror("allocation failure in ivector");	if (!v) nrerror("allocation failure in ivector");
return v-nl+NR_END;	return v-nl+NR_END;
}	}

/****************free ivector ************************/	/****************free lvector ************************/
void free_ivector(int *v, long nl, long nh)	void free_lvector(long *v, long nl, long nh)
{	{
free((FREE_ARG)(v+nl-NR_END));	free((FREE_ARG)(v+nl-NR_END));
}	}
Line 421 double **matrix(long nrl, long nrh, long	Line 498 double **matrix(long nrl, long nrh, long

for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;	for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;	return m;
/* print ((m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])	/* print ((m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
*/	*/
}	}

Line 651 void linmin(double p[], double xi[], int	Line 728 void linmin(double p[], double xi[], int
free_vector(pcom,1,n);	free_vector(pcom,1,n);
}	}

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

/************* powell **********************/	/************* powell **********************/
void powell(double p[], double *xi, int n, double ftol, int iter, double *fret,	void powell(double p[], double *xi, int n, double ftol, int iter, double *fret,
double (*func)(double []))	double (*func)(double []))
Line 661 void powell(double p[], double **xi, int	Line 751 void powell(double p[], double **xi, int
double del,t,pt,ptt,*xit;	double del,t,pt,ptt,*xit;
double fp,fptt;	double fp,fptt;
double *xits;	double *xits;
	int niterf, itmp;

pt=vector(1,n);	pt=vector(1,n);
ptt=vector(1,n);	ptt=vector(1,n);
xit=vector(1,n);	xit=vector(1,n);
Line 671 void powell(double p[], double **xi, int	Line 763 void powell(double p[], double **xi, int
fp=(*fret);	fp=(*fret);
ibig=0;	ibig=0;
del=0.0;	del=0.0;
printf("\nPowell iter=%d -2LL=%.12f",iter,*fret);	last_time=curr_time;
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f",iter,*fret);	(void) gettimeofday(&curr_time,&tzp);
fprintf(ficrespow,"%d %.12f",iter,fret);	printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
	fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tv_sec-start_time.tv_sec);
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);	fprintf(ficlog," %d %.12lf",i, p[i]);
Line 681 void powell(double p[], double **xi, int	Line 775 void powell(double p[], double **xi, int
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficrespow,"\n");	fprintf(ficrespow,"\n");fflush(ficrespow);
	if(*iter <=3){
	tm = *localtime(&curr_time.tv_sec);
	asctime_r(&tm,strcurr);
	forecast_time=curr_time;
	itmp = strlen(strcurr);
	if(strcurr[itmp-1]=='\n')
	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);
	fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
	for(niterf=10;niterf<=30;niterf+=10){
	forecast_time.tv_sec=curr_time.tv_sec+(niterf-iter)(curr_time.tv_sec-last_time.tv_sec);
	tmf = *localtime(&forecast_time.tv_sec);
	asctime_r(&tmf,strfor);
	/* strcpy(strfor,asctime(&tmf)); */
	itmp = strlen(strfor);
	if(strfor[itmp-1]=='\n')
	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);
	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);
	}
	}
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];	for (j=1;j<=n;j++) xit[j]=xi[j][i];
fptt=(*fret);	fptt=(*fret);
Line 1174 double func( double *x)	Line 1289 double func( double *x)
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
}else{ /* ml=4 no inter-extrapolation */	}else if (mle==4){ /* ml=4 no inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
Line 1196 double func( double *x)	Line 1311 double func( double *x)
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */

	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
	if( s2 > nlstate){
	lli=log(out[s1][s2] - savm[s1][s2]);
	}else{
	lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
	}
	ipmx +=1;
	sw += weight[i];
	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]); */
	} /* end of wave */
	} /* end of individual */
	}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
	for(mi=1; mi<= wav[i]-1; mi++){
	for (ii=1;ii<=nlstate+ndeath;ii++)
	for (j=1;j<=nlstate+ndeath;j++){
	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
	savm[ii][j]=(ii==j ? 1.0 : 0.0);
	}
	for(d=0; d<dh[mi][i]; d++){
	newm=savm;
	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
	for (kk=1; kk<=cptcovage;kk++) {
	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	}

	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
	savm=oldm;
	oldm=newm;
	} /* end mult */

	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
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 */
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
	/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]);/
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
} /* End of if */	} /* End of if */
Line 1209 double func( double *x)	Line 1362 double func( double *x)
return -l;	return -l;
}	}

	/************* log-likelihood ***********/
	double funcone( double *x)
	{
	/* Same as likeli but slower because of a lot of printf and if */
	int i, ii, j, k, mi, d, kk;
	double l, ll[NLSTATEMAX], cov[NCOVMAX];
	double **out;
	double lli; /* Individual log likelihood */
	double llt;
	int s1, s2;
	double bbh, survp;
	/extern weight /
	/* We are differentiating ll according to initial status */
	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
	/*for(i=1;i<imx;i++)
	printf(" %d\n",s[4][i]);
	*/
	cov[1]=1.;

	for(k=1; k<=nlstate; k++) ll[k]=0.;

	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
	for(mi=1; mi<= wav[i]-1; mi++){
	for (ii=1;ii<=nlstate+ndeath;ii++)
	for (j=1;j<=nlstate+ndeath;j++){
	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
	savm[ii][j]=(ii==j ? 1.0 : 0.0);
	}
	for(d=0; d<dh[mi][i]; d++){
	newm=savm;
	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
	for (kk=1; kk<=cptcovage;kk++) {
	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	}
	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
	savm=oldm;
	oldm=newm;
	} /* end mult */

	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
	bbh=(double)bh[mi][i]/(double)stepm;
	/* bias is positive if real duration
	* is higher than the multiple of stepm and negative otherwise.
	*/
	if( s2 > nlstate && (mle <5) ){ /* Jackson */
	lli=log(out[s1][s2] - savm[s1][s2]);
	} else if (mle==1){
	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
	} 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 */
	} else if(mle==3){ /* exponential inter-extrapolation */
	lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2])); / exponential inter-extrapolation */
	} else if (mle==4){ /* mle=4 no inter-extrapolation */
	lli=log(out[s1][s2]); /* Original formula */
	} else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
	lli=log(out[s1][s2]); /* Original formula */
	} /* End of if */
	ipmx +=1;
	sw += weight[i];
	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]); */
	if(globpr){
	fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
	%10.6f %10.6f %10.6f ", \
	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]);
	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
	llt +=ll[k]*gipmx/gsw;
	fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
	}
	fprintf(ficresilk," %10.6f\n", -llt);
	}
	} /* end of wave */
	} /* end of individual */
	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
	/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
	l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */
	if(globpr==0){ /* First time we count the contributions and weights */
	gipmx=ipmx;
	gsw=sw;
	}
	return -l;
	}

	char *subdirf(char fileres[])
	{
	/* Caution optionfilefiname is hidden */
	strcpy(tmpout,optionfilefiname);
	strcat(tmpout,"/"); /* Add to the right */
	strcat(tmpout,fileres);
	return tmpout;
	}

	char subdirf2(char fileres[], char preop)
	{

	strcpy(tmpout,optionfilefiname);
	strcat(tmpout,"/");
	strcat(tmpout,preop);
	strcat(tmpout,fileres);
	return tmpout;
	}
	char subdirf3(char fileres[], char preop, char *preop2)
	{

	strcpy(tmpout,optionfilefiname);
	strcat(tmpout,"/");
	strcat(tmpout,preop);
	strcat(tmpout,preop2);
	strcat(tmpout,fileres);
	return tmpout;
	}

	void likelione(FILE ficres,double p[], int npar, int nlstate, int globpri, long ipmx, double sw, double fretone, double (funcone)(double []))
	{
	/* This routine should help understanding what is done with
	the selection of individuals/waves and
	to check the exact contribution to the likelihood.
	Plotting could be done.
	*/
	int k;

	if(globpri !=0){ / Just counts and sums, no printings */
	strcpy(fileresilk,"ilk");
	strcat(fileresilk,fileres);
	if((ficresilk=fopen(fileresilk,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresilk);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
	}
	fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");
	fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
	/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */
	for(k=1; k<=nlstate; k++)
	fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);
	fprintf(ficresilk," -2gipw/gswweight*ll(total)\n");
	}

	fretone=(funcone)(p);
	if(*globpri !=0){
	fclose(ficresilk);
	fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
	fflush(fichtm);
	}
	return;
	}


/********* Maximum Likelihood Estimation *************/	/********* Maximum Likelihood Estimation *************/

Line 1217 void mlikeli(FILE *ficres,double p[], in	Line 1519 void mlikeli(FILE *ficres,double p[], in
int i,j, iter;	int i,j, iter;
double **xi;	double **xi;
double fret;	double fret;
	double fretone; /* Only one call to likelihood */
char filerespow[FILENAMELENGTH];	char filerespow[FILENAMELENGTH];
xi=matrix(1,npar,1,npar);	xi=matrix(1,npar,1,npar);
for (i=1;i<=npar;i++)	for (i=1;i<=npar;i++)
Line 1234 void mlikeli(FILE *ficres,double p[], in	Line 1537 void mlikeli(FILE *ficres,double p[], in
for(j=1;j<=nlstate+ndeath;j++)	for(j=1;j<=nlstate+ndeath;j++)
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
fprintf(ficrespow,"\n");	fprintf(ficrespow,"\n");

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

fclose(ficrespow);	fclose(ficrespow);
Line 1501 void lubksb(double *a, int n, int indx	Line 1805 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, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)	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)
{ /* 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 1555 void freqsummary(char fileres[], int ia	Line 1859 void freqsummary(char fileres[], int ia
if (bool==1){	if (bool==1){
for(m=firstpass; m<=lastpass; m++){	for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);	k2=anint[m][i]+(mint[m][i]/12.);
if ((k2>=dateprev1) && (k2<=dateprev2)) {	/if ((k2>=dateprev1) && (k2<=dateprev2)) {/
if(agev[m][i]==0) agev[m][i]=iagemax+1;	if(agev[m][i]==0) agev[m][i]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=iagemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];	if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
Line 1568 void freqsummary(char fileres[], int ia	Line 1872 void freqsummary(char fileres[], int ia
dateintsum=dateintsum+k2;	dateintsum=dateintsum+k2;
k2cpt++;	k2cpt++;
}	}
}	/}/
}	}
}	}
}	}

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);*/

if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
Line 1634 void freqsummary(char fileres[], int ia	Line 1938 void freqsummary(char fileres[], int ia
if( i <= iagemax){	if( i <= iagemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);	fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
probs[i][jk][j1]= pp[jk]/pos;	/probs[i][jk][j1]= pp[jk]/pos;/
/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/	/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/
}	}
else	else
Line 1667 void freqsummary(char fileres[], int ia	Line 1971 void freqsummary(char fileres[], int ia
}	}

/********** Prevalence ******************/	/********** Prevalence ******************/
void prevalence(double agemin, double agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)	void prevalence(double *probs, double agemin, double agemax, int s, double *agev, int nlstate, int imx, int Tvar, int *nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
{	{
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people	/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
in each health status at the date of interview (if between dateprev1 and dateprev2).	in each health status at the date of interview (if between dateprev1 and dateprev2).
Line 1785 void concatwav(int wav[], int **dh, int	Line 2089 void concatwav(int wav[], int **dh, int

wav[i]=mi;	wav[i]=mi;
if(mi==0){	if(mi==0){
	nbwarn++;
if(first==0){	if(first==0){
printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);	printf("Warning! None valid information for:%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:%d line=%d (skipped)\n",num[i],i);	fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
}	}
} /* end mi==0 */	} /* end mi==0 */
} /* End individuals */	} /* End individuals */
Line 1802 void concatwav(int wav[], int **dh, int	Line 2107 void concatwav(int wav[], int **dh, int
else{	else{
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
if (agedc[i] < 2*AGESUP) {	if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]12-agev[mw[mi][i]][i]12);	j= rint(agedc[i]12-agev[mw[mi][i]][i]12);
if(j==0) j=1; /* Survives at least one month after exam */	if(j==0) j=1; /* Survives at least one month after exam */
k=k+1;	else if(j<0){
if (j >= jmax) jmax=j;	nberr++;
if (j <= jmin) jmin=j;	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]);
sum=sum+j;	j=1; /* Temporary Dangerous patch */
/if (j<0) printf("j=%d num=%d \n",j,i);/	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("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,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]);
if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d 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);
	}
	k=k+1;
	if (j >= jmax) jmax=j;
	if (j <= jmin) jmin=j;
	sum=sum+j;
	/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);*/
}	}
}	}
else{	else{
Line 1821 void concatwav(int wav[], int **dh, int	Line 2133 void concatwav(int wav[], int **dh, int
else if (j <= jmin)jmin=j;	else if (j <= jmin)jmin=j;
/* 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)printf("Error! Negative delay (%d) between waves %d and %d of individual %d 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]);	if(j<0){
	nberr++;
	printf("Error! Negative delay (%d) 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) 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]);
	}
sum=sum+j;	sum=sum+j;
}	}
jk= j/stepm;	jk= j/stepm;
jl= j -jk*stepm;	jl= j -jk*stepm;
ju= j -(jk+1)*stepm;	ju= j -(jk+1)*stepm;
if(mle <=1){	if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
if(jl==0){	if(jl==0){
dh[mi][i]=jk;	dh[mi][i]=jk;
bh[mi][i]=0;	bh[mi][i]=0;
Line 1852 void concatwav(int wav[], int **dh, int	Line 2168 void concatwav(int wav[], int **dh, int
bh[mi][i]=ju; /* At least one step */	bh[mi][i]=ju; /* At least one step */
/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/	/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
}	}
}	} /* end if mle */
} /* end if mle */	}
} /* end wave */	} /* end wave */
}	}
jmean=sum/k;	jmean=sum/k;
Line 2154 void varevsij(char optionfilefiname[], d	Line 2470 void varevsij(char optionfilefiname[], d
fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);	fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
}	}
fprintf(ficresprobmorprev,"\n");	fprintf(ficresprobmorprev,"\n");
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {	fprintf(ficgp,"\n# Routine varevsij");
printf("Problem with gnuplot file: %s\n", optionfilegnuplot);	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(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
exit(0);	/* } */
}
else{
fprintf(ficgp,"\n# Routine varevsij");
}
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
printf("Problem with html file: %s\n", optionfilehtm);
fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
exit(0);
}
else{
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);
}
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);

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");
Line 2382 void varevsij(char optionfilefiname[], d	Line 2685 void varevsij(char optionfilefiname[], d
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /	/* fprintf(ficgp,"\n plot \"%s\" u 1:($3%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); /
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */	/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);	fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);	fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);	fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);	fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);	fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);	/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
*/	*/
fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);	/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
	fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,nlstate);	free_matrix(doldm,1,nlstate,1,nlstate);
Line 2399 void varevsij(char optionfilefiname[], d	Line 2703 void varevsij(char optionfilefiname[], d
free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficresprobmorprev);	fclose(ficresprobmorprev);
fclose(ficgp);	fflush(ficgp);
fclose(fichtm);	fflush(fichtm);
}	} /* 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)
Line 2557 void varprob(char optionfilefiname[], do	Line 2861 void varprob(char optionfilefiname[], do
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);	mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
varpij=ma3x(1,nlstate(nlstate+ndeath),1,nlstate(nlstate+ndeath),(int) bage, (int) fage);	varpij=ma3x(1,nlstate(nlstate+ndeath),1,nlstate(nlstate+ndeath),(int) bage, (int) fage);
first=1;	first=1;
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {	fprintf(ficgp,"\n# Routine varprob");
printf("Problem with gnuplot file: %s\n", optionfilegnuplot);	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);	fprintf(fichtm,"\n");
exit(0);
}	fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
else{	fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
fprintf(ficgp,"\n# Routine varprob");	file %s<br>\n",optionfilehtmcov);
}	fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {	and drawn. It helps understanding how is the covariance between two incidences.\
printf("Problem with html file: %s\n", optionfilehtm);	They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);	fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
exit(0);	It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
}	would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
else{	standard deviations wide on each axis. <br>\
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");	Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
fprintf(fichtm,"\n");	and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
	To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");

}

cov[1]=1;	cov[1]=1;
tj=cptcoveff;	tj=cptcoveff;
Line 2760 void varprob(char optionfilefiname[], do	Line 3059 void varprob(char optionfilefiname[], do
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);	fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);	:<a href=\"%s%d%1d%1d-%1d%1d.png\">\
fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);	%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);	subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
	subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
	fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
	fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
	fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
Line 2771 void varprob(char optionfilefiname[], do	Line 3074 void varprob(char optionfilefiname[], do
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));	mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
}else{	}else{
first=0;	first=0;
fprintf(fichtm," %d (%.3f),",(int) age, c12);	fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
Line 2780 void varprob(char optionfilefiname[], do	Line 3083 void varprob(char optionfilefiname[], do
}/* if first */	}/* if first */
} /* age mod 5 */	} /* age mod 5 */
} /* end loop age */	} /* end loop age */
fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);	fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
first=1;	first=1;
} /l12 /	} /l12 /
} /* k12 */	} /* k12 */
Line 2794 void varprob(char optionfilefiname[], do	Line 3097 void varprob(char optionfilefiname[], do
fclose(ficresprob);	fclose(ficresprob);
fclose(ficresprobcov);	fclose(ficresprobcov);
fclose(ficresprobcor);	fclose(ficresprobcor);
fclose(ficgp);	fflush(ficgp);
fclose(fichtm);	fflush(fichtmcov);
}	}


Line 2808 void printinghtml(char fileres[], char t	Line 3111 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;
/char optionfilehtm[FILENAMELENGTH];/	/char optionfilehtm[FILENAMELENGTH];/
if((fichtm=fopen(optionfilehtm,"a"))==NULL) {	/* if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
printf("Problem with %s \n",optionfilehtm), exit(0);	/* printf("Problem with %s \n",optionfilehtm), exit(0); */
fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);	/* fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
}	/* } */

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

Line 2837 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3143 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: pe%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: %s%d1.png<br> \
<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	<img src=\"%s%d1.png\">",stepm,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 before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
	<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Stable prevalence in each health state */	/* 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>- Stable prevalence in each health state : p%s%d%d.png<br> \
<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"%s%d%d.png\">",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): exp%s%d%d.png <br>	fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2): e%s%d.png<br>	health expectancies in states (1) and (2): %s%d.png<br>\
<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");


fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n	fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n	- Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
- Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n	- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
- Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n	- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n	- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n	- Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
- Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);	- Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
	rfileres,rfileres,\
	subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
	subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
	subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
	estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
	subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
	subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));

/* if(popforecast==1) fprintf(fichtm,"\n */	/* if(popforecast==1) fprintf(fichtm,"\n */
/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */	/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 2890 fprintf(fichtm," <ul><li><b>Graphs</b></	Line 3204 fprintf(fichtm," <ul><li><b>Graphs</b></
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed and period prevalence (with confident	fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
interval) in state (%d): v%s%d%d.png <br>	interval) in state (%d): %s%d%d.png <br>\
<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}	}
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");
fclose(fichtm);	fflush(fichtm);
}	}

/***************** Gnuplot file ************/	/***************** Gnuplot file ************/
void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){	void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){

	char dirfileres[132],optfileres[132];
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;	int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
int ng;	int ng;
if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
printf("Problem with file %s",optionfilegnuplot);	/* printf("Problem with file %s",optionfilegnuplot); */
fprintf(ficlog,"Problem with file %s",optionfilegnuplot);	/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
}	/* } */

/#ifdef windows /	/#ifdef windows /
fprintf(ficgp,"cd \"%s\" \n",pathc);	fprintf(ficgp,"cd \"%s\" \n",pathc);
/#endif /	/#endif /
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

	strcpy(dirfileres,optionfilefiname);
	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);	fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \n\
	set ylabel \"Probability\" \n\
	set ter png small\n\
	set size 0.65,0.65\n\
	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);	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);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
}	}
}	}
/2 eme/	/2 eme/

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);	fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);

for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l 0,");	fprintf(ficgp,"\" t\"\" w l 0,");
fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
Line 2974 m=pow(2,cptcoveff);	Line 3296 m=pow(2,cptcoveff);
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
k=2+nlstate(2cpt-2);	k=2+nlstate(2cpt-2);
fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);	fprintf(ficgp,"set ter png small\n\
	set size 0.65,0.65\n\
	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 2985 m=pow(2,cptcoveff);	Line 3309 m=pow(2,cptcoveff);

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

}	}
}	}
Line 2995 m=pow(2,cptcoveff);	Line 3319 m=pow(2,cptcoveff);
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=3;	k=3;
fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
	set ter png small\nset size 0.65,0.65\n\
	unset log y\n\
	plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);

for (i=1; i<= nlstate ; i ++)	for (i=1; i< nlstate ; i ++)
fprintf(ficgp,"+$%d",k+i+1);	fprintf(ficgp,"+$%d",k+i+1);
fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);	fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);

l=3+(nlstate+ndeath)*cpt;	l=3+(nlstate+ndeath)*cpt;
fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);	fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
for (i=1; i< nlstate ; i ++) {	for (i=1; i< nlstate ; i ++) {
l=3+(nlstate+ndeath)*cpt;	l=3+(nlstate+ndeath)*cpt;
fprintf(ficgp,"+$%d",l+i+1);	fprintf(ficgp,"+$%d",l+i+1);
Line 3027 m=pow(2,cptcoveff);	Line 3354 m=pow(2,cptcoveff);

for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/	for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
for(jk=1; jk <=m; jk++) {	for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
if (ng==2)	if (ng==2)
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
else	else
Line 3074 m=pow(2,cptcoveff);	Line 3401 m=pow(2,cptcoveff);
} /* end k2 */	} /* end k2 */
} /* end jk */	} /* end jk */
} /* end ng */	} /* end ng */
fclose(ficgp);	fflush(ficgp);
} /* end gnuplot */	} /* end gnuplot */


Line 3137 prevforecast(char fileres[], double anpr	Line 3464 prevforecast(char fileres[], double anpr
char fileresf[FILENAMELENGTH];	char fileresf[FILENAMELENGTH];

agelim=AGESUP;	agelim=AGESUP;
prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);

strcpy(fileresf,"f");	strcpy(fileresf,"f");
strcat(fileresf,fileres);	strcat(fileresf,fileres);
Line 3260 populforecast(char fileres[], double anp	Line 3587 populforecast(char fileres[], double anp
agelim=AGESUP;	agelim=AGESUP;
calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;	calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;

prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);


strcpy(filerespop,"pop");	strcpy(filerespop,"pop");
Line 3402 populforecast(char fileres[], double anp	Line 3729 populforecast(char fileres[], double anp
free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficrespop);	fclose(ficrespop);
	} /* End of popforecast */

	int fileappend(FILE fichier, char optionfich)
	{
	if((fichier=fopen(optionfich,"a"))==NULL) {
	printf("Problem with file: %s\n", optionfich);
	fprintf(ficlog,"Problem with file: %s\n", optionfich);
	return (0);
	}
	fflush(fichier);
	return (1);
}	}
	void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
	{

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

	printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
	fprintf(ficparo,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
	for(i=1; i <=nlstate; i++){
	jj=0;
	for(j=1; j <=nlstate+ndeath; j++){
	if(j==i) continue;
	jj++;
	/ca[0]= k+'a'-1;ca[1]='\0';/
	printf("%1d%1d",i,j);
	fprintf(ficparo,"%1d%1d",i,j);
	for(k=1; k<=ncovmodel;k++){
	/* printf(" %lf",param[i][j][k]); */
	/* fprintf(ficparo," %lf",param[i][j][k]); */
	printf(" 0.");
	fprintf(ficparo," 0.");
	}
	printf("\n");
	fprintf(ficparo,"\n");
	}
	}
	printf("# Scales (for hessian or gradient estimation)\n");
	fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
	npar= (nlstate+ndeath-1)nlstatencovmodel; /* Number of parameters*/
	for(i=1; i <=nlstate; i++){
	jj=0;
	for(j=1; j <=nlstate+ndeath; j++){
	if(j==i) continue;
	jj++;
	fprintf(ficparo,"%1d%1d",i,j);
	printf("%1d%1d",i,j);
	fflush(stdout);
	for(k=1; k<=ncovmodel;k++){
	/* printf(" %le",delti3[i][j][k]); */
	/* fprintf(ficparo," %le",delti3[i][j][k]); */
	printf(" 0.");
	fprintf(ficparo," 0.");
	}
	numlinepar++;
	printf("\n");
	fprintf(ficparo,"\n");
	}
	}
	printf("# Covariance matrix\n");
	/* # 121 Var(a12)\n\ */
	/* # 122 Cov(b12,a12) Var(b12)\n\ */
	/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
	/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
	/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
	/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
	/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
	/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
	fflush(stdout);
	fprintf(ficparo,"# Covariance matrix\n");
	/* # 121 Var(a12)\n\ */
	/* # 122 Cov(b12,a12) Var(b12)\n\ */
	/* # ...\n\ */
	/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */

	for(itimes=1;itimes<=2;itimes++){
	jj=0;
	for(i=1; i <=nlstate; i++){
	for(j=1; j <=nlstate+ndeath; j++){
	if(j==i) continue;
	for(k=1; k<=ncovmodel;k++){
	jj++;
	ca[0]= k+'a'-1;ca[1]='\0';
	if(itimes==1){
	printf("#%1d%1d%d",i,j,k);
	fprintf(ficparo,"#%1d%1d%d",i,j,k);
	}else{
	printf("%1d%1d%d",i,j,k);
	fprintf(ficparo,"%1d%1d%d",i,j,k);
	/* printf(" %.5le",matcov[i][j]); */
	}
	ll=0;
	for(li=1;li <=nlstate; li++){
	for(lj=1;lj <=nlstate+ndeath; lj++){
	if(lj==li) continue;
	for(lk=1;lk<=ncovmodel;lk++){
	ll++;
	if(ll<=jj){
	cb[0]= lk +'a'-1;cb[1]='\0';
	if(ll<jj){
	if(itimes==1){
	printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
	fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
	}else{
	printf(" 0.");
	fprintf(ficparo," 0.");
	}
	}else{
	if(itimes==1){
	printf(" Var(%s%1d%1d)",ca,i,j);
	fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
	}else{
	printf(" 0.");
	fprintf(ficparo," 0.");
	}
	}
	}
	} /* end lk */
	} /* end lj */
	} /* end li */
	printf("\n");
	fprintf(ficparo,"\n");
	numlinepar++;
	} /* end k*/
	} /end j /
	} /* end i */
	}

	} /* end of prwizard */


/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
Line 3412 int main(int argc, char *argv[])	Line 3870 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 jj, imk;
	int numlinepar=0; /* Current linenumber of parameter file */
	/* FILE fichtm; //* Html File */
	/* FILE ficgp;/ /Gnuplot File /
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 3423 int main(int argc, char *argv[])	Line 3885 int main(int argc, char *argv[])
double ***mobaverage;	double ***mobaverage;
int *indx;	int *indx;
char line[MAXLINE], linepar[MAXLINE];	char line[MAXLINE], linepar[MAXLINE];
char path[80],pathc[80],pathcd[80],pathtot[80],model[80];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
	char pathr[MAXLINE];
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 3455 int main(int argc, char *argv[])	Line 3918 int main(int argc, char *argv[])


char z[1]="c", occ;	char z[1]="c", occ;
#include <sys/time.h>
#include <time.h>
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 *stratrunc;
	int lstra;

	long total_usecs;

/* long total_usecs;	/* gettimeofday(&start_time, (struct timezone)0); / /* at first time */
struct timeval start_time, end_time;	(void) gettimeofday(&start_time,&tzp);
	curr_time=start_time;
gettimeofday(&start_time, (struct timezone)0); / /* at first time */	tm = *localtime(&start_time.tv_sec);
	tmg = *gmtime(&start_time.tv_sec);
	strcpy(strstart,asctime(&tm));

	/* printf("Localtime (at start)=%s",strstart); */
	/* tp.tv_sec = tp.tv_sec +86400; */
	/* tm = localtime(&start_time.tv_sec); /
	/* tmg.tm_year=tmg.tm_year +dsigndyear; /
	/* tmg.tm_mon=tmg.tm_mon +dsigndmonth; /
	/* tmg.tm_hour=tmg.tm_hour + 1; */
	/* tp.tv_sec = mktime(&tmg); */
	/* strt=asctime(&tmg); */
	/* printf("Time(after) =%s",strstart); */
	/* (void) time (&time_value);
	* printf("time=%d,t-=%d\n",time_value,time_value-86400);
	* tm = *localtime(&time_value);
	* strstart=asctime(&tm);
	* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
	*/

	nberr=0; /* Number of errors and warnings */
	nbwarn=0;
getcwd(pathcd, size);	getcwd(pathcd, size);

printf("\n%s\n%s",version,fullversion);	printf("\n%s\n%s",version,fullversion);
Line 3473 int main(int argc, char *argv[])	Line 3961 int main(int argc, char *argv[])
else{	else{
strcpy(pathtot,argv[1]);	strcpy(pathtot,argv[1]);
}	}
/if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");/	/if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");/
/*cygwin_split_path(pathtot,path,optionfile);	/*cygwin_split_path(pathtot,path,optionfile);
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(pathtot,path,optionfile,optionfilext,optionfilefiname);	split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);	printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
chdir(path);	chdir(path);
replace(pathc,path);	strcpy(command,"mkdir ");
	strcat(command,optionfilefiname);
	if((outcmd=system(command)) != 0){
	printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
	/* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
	/* fclose(ficlog); */
	/* exit(1); */
	}
	/* if((imk=mkdir(optionfilefiname))<0){ */
	/* perror("mkdir"); */
	/* } */

/-------- arguments in the command line --------/	/-------- arguments in the command line --------/

Line 3493 int main(int argc, char *argv[])	Line 3991 int main(int argc, char *argv[])
goto end;	goto end;
}	}
fprintf(ficlog,"Log filename:%s\n",filelog);	fprintf(ficlog,"Log filename:%s\n",filelog);
fprintf(ficlog,"\n%s",version);	fprintf(ficlog,"\n%s\n%s",version,fullversion);
fprintf(ficlog,"\nEnter the parameter file name: ");	fprintf(ficlog,"\nEnter the parameter file name: ");
fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);	fprintf(ficlog,"pathtot=%s\n\
	path=%s \n\
	optionfile=%s\n\
	optionfilext=%s\n\
	optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);

	printf("Localtime (at start):%s",strstart);
	fprintf(ficlog,"Localtime (at start): %s",strstart);
fflush(ficlog);	fflush(ficlog);
	/* (void) gettimeofday(&curr_time,&tzp); */
	/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */

/* */	/* */
strcpy(fileres,"r");	strcpy(fileres,"r");
Line 3508 int main(int argc, char *argv[])	Line 4015 int main(int argc, char *argv[])
if((ficpar=fopen(optionfile,"r"))==NULL) {	if((ficpar=fopen(optionfile,"r"))==NULL) {
printf("Problem with optionfile %s\n",optionfile);	printf("Problem with optionfile %s\n",optionfile);
fprintf(ficlog,"Problem with optionfile %s\n",optionfile);	fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
	fflush(ficlog);
goto end;	goto end;
}	}



strcpy(filereso,"o");	strcpy(filereso,"o");
strcat(filereso,fileres);	strcat(filereso,fileres);
if((ficparo=fopen(filereso,"w"))==NULL) {	if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
printf("Problem with Output resultfile: %s\n", filereso);	printf("Problem with Output resultfile: %s\n", filereso);
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);	fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
	fflush(ficlog);
goto end;	goto end;
}	}

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
	numlinepar=0;
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);	fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
	numlinepar++;
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
	fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
	fflush(ficlog);
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);


covar=matrix(0,NCOVMAX,1,n);	covar=matrix(0,NCOVMAX,1,n);
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement/
Line 3546 int main(int argc, char *argv[])	Line 4065 int main(int argc, char *argv[])

ncovmodel=2+cptcovn; /Number of variables = cptcovn + intercept + age /	ncovmodel=2+cptcovn; /Number of variables = cptcovn + intercept + age /
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */	nvar=ncovmodel-1; /* Suppressing age as a basic covariate */

	if(mle==-1){ /* Print a wizard for help writing covariance matrix */
	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
	printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
	fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
	fclose (ficparo);
	fclose (ficlog);
	exit(0);
	}
/* Read guess parameters */	/* Read guess parameters */
/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
for(i=1; i <=nlstate; i++)	for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){	j=0;
	for(jj=1; jj <=nlstate+ndeath; jj++){
	if(jj==i) continue;
	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
	if ((i1 != i) && (j1 != j)){
	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
	exit(1);
	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
if(mle==1)	if(mle==1)
printf("%1d%1d",i,j);	printf("%1d%1d",i,j);
Line 3576 int main(int argc, char *argv[])	Line 4112 int main(int argc, char *argv[])
fprintf(ficparo," %lf",param[i][j][k]);	fprintf(ficparo," %lf",param[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
	numlinepar++;
if(mle==1)	if(mle==1)
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
	}
	fflush(ficlog);

npar= (nlstate+ndeath-1)nlstatencovmodel; /* Number of parameters*/	npar= (nlstate+ndeath-1)nlstatencovmodel; /* Number of parameters*/

p=param[1][1];	p=param[1][1];
Line 3590 int main(int argc, char *argv[])	Line 4129 int main(int argc, char *argv[])
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

Line 3600 int main(int argc, char *argv[])	Line 4141 int main(int argc, char *argv[])
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){	for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
	if ((i1-i)*(j1-j)!=0){
	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
	exit(1);
	}
printf("%1d%1d",i,j);	printf("%1d%1d",i,j);
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
	fprintf(ficlog,"%1d%1d",i1,j1);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar,"%le",&delti3[i][j][k]);	fscanf(ficpar,"%le",&delti3[i][j][k]);
printf(" %le",delti3[i][j][k]);	printf(" %le",delti3[i][j][k]);
fprintf(ficparo," %le",delti3[i][j][k]);	fprintf(ficparo," %le",delti3[i][j][k]);
	fprintf(ficlog," %le",delti3[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
	numlinepar++;
printf("\n");	printf("\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
	fprintf(ficlog,"\n");
}	}
}	}
	fflush(ficlog);

delti=delti3[1][1];	delti=delti3[1][1];


Line 3621 int main(int argc, char *argv[])	Line 4172 int main(int argc, char *argv[])
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

Line 3637 int main(int argc, char *argv[])	Line 4190 int main(int argc, char *argv[])
fscanf(ficpar," %le",&matcov[i][j]);	fscanf(ficpar," %le",&matcov[i][j]);
if(mle==1){	if(mle==1){
printf(" %.5le",matcov[i][j]);	printf(" %.5le",matcov[i][j]);
fprintf(ficlog," %.5le",matcov[i][j]);
}	}
else	fprintf(ficlog," %.5le",matcov[i][j]);
fprintf(ficlog," %.5le",matcov[i][j]);
fprintf(ficparo," %.5le",matcov[i][j]);	fprintf(ficparo," %.5le",matcov[i][j]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
	numlinepar++;
if(mle==1)	if(mle==1)
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
Line 3657 int main(int argc, char *argv[])	Line 4209 int main(int argc, char *argv[])
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");

	fflush(ficlog);

/-------- Rewriting paramater file ----------/	/-------- Rewriting paramater file ----------/
strcpy(rfileres,"r"); /* "Rparameterfile */	strcpy(rfileres,"r"); /* "Rparameterfile */
Line 3678 int main(int argc, char *argv[])	Line 4231 int main(int argc, char *argv[])
n= lastobs;	n= lastobs;
severity = vector(1,maxwav);	severity = vector(1,maxwav);
outcome=imatrix(1,maxwav+1,1,n);	outcome=imatrix(1,maxwav+1,1,n);
num=ivector(1,n);	num=lvector(1,n);
moisnais=vector(1,n);	moisnais=vector(1,n);
annais=vector(1,n);	annais=vector(1,n);
moisdc=vector(1,n);	moisdc=vector(1,n);
Line 3714 int main(int argc, char *argv[])	Line 4267 int main(int argc, char *argv[])
for (j=ncovcol;j>=1;j--){	for (j=ncovcol;j>=1;j--){
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
}	}
num[i]=atol(stra);	lstra=strlen(stra);
	if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /
	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)){	/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
printf("%d %.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;}*/	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;	i=i+1;
}	}
Line 3733 int main(int argc, char *argv[])	Line 4292 int main(int argc, char *argv[])
}*/	}*/
/* for (i=1; i<=imx; i++){	/* for (i=1; i<=imx; i++){
if (s[4][i]==9) s[4][i]=-1;	if (s[4][i]==9) s[4][i]=-1;
printf("%d %.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++)

Line 3836 int main(int argc, char *argv[])	Line 4395 int main(int argc, char *argv[])
s[m][i]=-1;	s[m][i]=-1;
}	}
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){	if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);	nberr++;
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);	printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
s[m][i]=-1;	s[m][i]=-1;
}	}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){	if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);	nberr++;
fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);	printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
s[m][i]=-1;	fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
	s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
}	}
}	}
}	}
Line 3859 int main(int argc, char *argv[])	Line 4420 int main(int argc, char *argv[])
/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/	/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/
else {	else {
if ((int)andc[i]!=9999){	if ((int)andc[i]!=9999){
printf("Warning negative age at death: %d line:%d\n",num[i],i);	nbwarn++;
fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);	printf("Warning negative age at death: %ld line:%d\n",num[i],i);
	fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
agev[m][i]=-1;	agev[m][i]=-1;
}	}
}	}
Line 3895 int main(int argc, char *argv[])	Line 4457 int main(int argc, char *argv[])
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=firstpass; (m<=lastpass); m++){	for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
	nberr++;
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
goto end;	goto end;
Line 3904 int main(int argc, char *argv[])	Line 4467 int main(int argc, char *argv[])

/*for (i=1; i<=imx; i++){	/*for (i=1; i<=imx; i++){
for (m=firstpass; (m<lastpass); m++){	for (m=firstpass; (m<lastpass); m++){
printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);	printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
}	}

}*/	}*/
Line 3963 int main(int argc, char *argv[])	Line 4526 int main(int argc, char *argv[])
}	}
scanf("%d",i);*/	scanf("%d",i);*/

	/------------ gnuplot -------------/
	strcpy(optionfilegnuplot,optionfilefiname);
	strcat(optionfilegnuplot,".gp");
	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
	printf("Problem with file %s",optionfilegnuplot);
	}
	else{
	fprintf(ficgp,"\n# %s\n", version);
	fprintf(ficgp,"# %s\n", optionfilegnuplot);
	fprintf(ficgp,"set missing 'NaNq'\n");
	}
	/* fclose(ficgp);*/
	/--------- index.htm --------/

	strcpy(optionfilehtm,optionfilefiname); /* Main html file */
	strcat(optionfilehtm,".htm");
	if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
	printf("Problem with %s \n",optionfilehtm), exit(0);
	}

	strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
	strcat(optionfilehtmcov,"-cov.htm");
	if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
	printf("Problem with %s \n",optionfilehtmcov), exit(0);
	}
	else{
	fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
	fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
	}

	fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
	\n\
	<hr size=\"2\" color=\"#EC5E5E\">\
	<ul><li><h4>Parameter files</h4>\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\
	- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
	- Date and time at start: %s</ul>\n",\
	fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
	fileres,fileres,\
	filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
	fflush(fichtm);

	strcpy(pathr,path);
	strcat(pathr,optionfilefiname);
	chdir(optionfilefiname); /* Move to directory named optionfile */
	strcpy(lfileres,fileres);
	strcat(lfileres,"/");
	strcat(lfileres,optionfilefiname);

/* 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);

pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	fprintf(fichtm,"\n");
	fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
	Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
	imx,agemin,agemax,jmin,jmax,jmean);
	pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
Line 3977 int main(int argc, char *argv[])	Line 4600 int main(int argc, char *argv[])
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */	so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
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*/
	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
	printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
	for (k=1; k<=npar;k++)
	printf(" %d %8.5f",k,p[k]);
	printf("\n");
	globpr=1; /* to print the contributions */
	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
	printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
	for (k=1; k<=npar;k++)
	printf(" %d %8.5f",k,p[k]);
	printf("\n");
if(mle>=1){ /* Could be 1 or 2 */	if(mle>=1){ /* Could be 1 or 2 */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}	}
Line 4008 int main(int argc, char *argv[])	Line 4643 int main(int argc, char *argv[])
}	}
}	}
}	}
if(mle==1){	if(mle!=0){
/* Computing hessian and covariance matrix */	/* Computing hessian and covariance matrix */
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, p, npar, delti, ftolhess, func);
Line 4139 int main(int argc, char *argv[])	Line 4774 int main(int argc, char *argv[])
fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);	fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);	fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);

probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	/* 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);/

/------------ gnuplot -------------/
strcpy(optionfilegnuplot,optionfilefiname);
strcat(optionfilegnuplot,".gp");
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);
}
else{
fprintf(ficgp,"\n# %s\n", version);
fprintf(ficgp,"# %s\n", optionfilegnuplot);
fprintf(ficgp,"set missing 'NaNq'\n");
}
fclose(ficgp);
printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
/--------- index.htm --------/

strcpy(optionfilehtm,optionfile);	replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
strcat(optionfilehtm,".htm");	printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);
}

fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n	model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
\n	jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
Total number of observations=%d <br>\n
Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
<hr size=\"2\" color=\"#EC5E5E\">
<ul><li><h4>Parameter files</h4>\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
- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
fclose(fichtm);

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);

/------------ free_vector -------------/	/------------ free_vector -------------/
chdir(path);	/* chdir(path); */

free_ivector(wav,1,imx);	free_ivector(wav,1,imx);
free_imatrix(dh,1,lastpass-firstpass+1,1,imx);	free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
free_imatrix(bh,1,lastpass-firstpass+1,1,imx);	free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);	free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
free_ivector(num,1,n);	free_lvector(num,1,n);
free_vector(agedc,1,n);	free_vector(agedc,1,n);
/free_matrix(covar,0,NCOVMAX,1,n);/	/free_matrix(covar,0,NCOVMAX,1,n);/
/free_matrix(covar,1,NCOVMAX,1,n);/	/free_matrix(covar,1,NCOVMAX,1,n);/
Line 4304 Interval (in months) between two waves:	Line 4910 Interval (in months) between two waves:

fclose(ficrespij);	fclose(ficrespij);

	probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);

/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
/if((stepm == 1) && (strcmp(model,".")==0)){/	/if((stepm == 1) && (strcmp(model,".")==0)){/
Line 4351 Interval (in months) between two waves:	Line 4958 Interval (in months) between two waves:
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);

/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */	/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\	/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
*/	*/
Line 4495 ageminpar, agemax, s[lastpass][imx], age	Line 5102 ageminpar, agemax, s[lastpass][imx], age
free_ivector(Tage,1,15);	free_ivector(Tage,1,15);
free_ivector(Tcode,1,100);	free_ivector(Tcode,1,100);

/* fclose(fichtm);*/	fflush(fichtm);
/* fclose(ficgp);/ / ALready done */	fflush(ficgp);


if(erreur >0){	if((nberr >0) \|\| (nbwarn>0)){
printf("End of Imach with error or warning %d\n",erreur);	printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);	fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
}else{	}else{
printf("End of Imach\n");	printf("End of Imach\n");
fprintf(ficlog,"End of Imach\n");	fprintf(ficlog,"End of Imach\n");
}	}
printf("See log file on %s\n",filelog);	printf("See log file on %s\n",filelog);
fclose(ficlog);
/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */	/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */
	(void) gettimeofday(&end_time,&tzp);
/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/	tm = *localtime(&end_time.tv_sec);
/printf("Total time was %d uSec.\n", total_usecs);/	tmg = *gmtime(&end_time.tv_sec);
	strcpy(strtend,asctime(&tm));
	printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
	fprintf(ficlog,"Localtime 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 was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
	fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
	fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
	/* printf("Total time was %d uSec.\n", total_usecs);*/
	/* if(fileappend(fichtm,optionfilehtm)){ */
	fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
	fclose(fichtm);
	fclose(fichtmcov);
	fclose(ficgp);
	fclose(ficlog);
/------ End -----------/	/------ End -----------/

end:	chdir(path);
#ifdef windows
/* chdir(pathcd);*/
#endif
/system("wgnuplot graph.plt");/
/system("../gp37mgw/wgnuplot graph.plt");/
/system("cd ../gp37mgw");/
/* system("..\\gp37mgw\\wgnuplot graph.plt");*/
strcpy(plotcmd,GNUPLOTPROGRAM);	strcpy(plotcmd,GNUPLOTPROGRAM);
strcat(plotcmd," ");	strcat(plotcmd," ");
strcat(plotcmd,optionfilegnuplot);	strcat(plotcmd,optionfilegnuplot);
printf("Starting graphs with: %s",plotcmd);fflush(stdout);	printf("Starting graphs with: %s",plotcmd);fflush(stdout);
system(plotcmd);	if((outcmd=system(plotcmd)) != 0){
	printf(" Problem with gnuplot\n");
	}
printf(" Wait...");	printf(" Wait...");

/#ifdef windows/
while (z[0] != 'q') {	while (z[0] != 'q') {
/* chdir(path); */	/* chdir(path); */
printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");	printf("\nType e to edit output files, g to graph again and q for exiting: ");
scanf("%s",z);	scanf("%s",z);
if (z[0] == 'c') system("./imach");	/* if (z[0] == 'c') system("./imach"); */
else if (z[0] == 'e') system(optionfilehtm);	if (z[0] == 'e') system(optionfilehtm);
else if (z[0] == 'g') system(plotcmd);	else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);	else if (z[0] == 'q') exit(0);
}	}
/#endif /	end:
	while (z[0] != 'q') {
	printf("\nType q for exiting: ");
	scanf("%s",z);
	}
}	}

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